![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 13 months ago
#9513 closed defect (fixed)
Nucleotide restore state is None
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted: Platform: Linux-4.18.0-500.el8.x86_64-x86_64-with-glibc2.28 ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description
The error occurs upon attempting to load a session file previously written by ChimeraX 1.6.1. Limited local debugging suggests that it is associated with loading "NucleotideState" data. The issue manifested after upgrading from ChimeraX 1.3. We can provide a session file with which we can reliably reproduce the issue, but not via e-mail, on account of file size. In addition to a bug fix, we hope you can provide advice and / or assistance with recovering the seemingly-corrupted session files.
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs format
> session
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06, shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576, pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at level
8, step 1, values float32
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 734, in restore
obj = sm.restore_snapshot(self, data)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/nucleotides/_data.py", line 472, in restore_snapshot
if data['version'] != 1:
TypeError: 'NoneType' object is not subscriptable
Log from Mon Jul 31 16:31:22 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06, shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at level 3,
step 1, values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at level 3,
step 1, values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576, pixel
1.06, shown at level 3, step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at level 3,
step 1, values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at level 3, step
1, values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at level 3,
step 1, values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at level
3, step 1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at level 3,
step 1, values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at level
3, step 1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at level 3,
step 1, values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at level
3, step 1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at level 3,
step 1, values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at level
3, step 1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at level 3,
step 1, values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at level
3, step 1, values float32
Log from Mon Jul 31 14:44:45 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06, shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576, pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at level
8, step 1, values float32
Log from Thu Jul 20 18:51:54 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06, shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576, pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at level
8, step 1, values float32
Log from Wed Jul 19 18:31:44 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06, shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576, pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at level
8, step 1, values float32
Log from Tue Jul 18 13:01:32 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06, shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576, pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at level
8, step 1, values float32
Log from Tue Jul 18 11:01:24 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06, shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576, pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at level
8, step 1, values float32
Log from Thu Jun 15 17:34:19 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06, shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576, pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at level
8, step 1, values float32
Log from Thu Jun 15 13:56:32 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06, shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576, pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at level
8, step 1, values float32
Log from Mon Jun 12 17:35:46 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06, shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576, pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at level
6, step 1, values float32
Log from Mon Jun 12 15:39:44 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06, shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576, pixel
1.06, shown at level 3, step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Log from Tue May 23 15:01:38 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06, shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576, pixel
1.06, shown at level 4, step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Log from Mon May 22 15:00:55 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06, shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576, pixel
1.06, shown at level 4, step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Log from Mon May 22 11:11:24 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06, shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576, pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at level 4,
step 1, values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step 1,
values float32
Log from Tue May 16 16:53:33 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open gtpys/helix/gtpys_helix.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06, shown
at level 0.000164, step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at level 4,
step 1, values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at level 4,
step 1, values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576, pixel
1.06, shown at level 4, step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at level 4,
step 1, values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at level 4, step
1, values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at level 4,
step 1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at level 4,
step 1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at level 4,
step 1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at level 4,
step 1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at level 4,
step 1, values float32
Log from Tue May 16 16:15:28 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open gtpys/helix/argb_helix.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06, shown
at step 4, values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576, pixel
1.06, shown at step 1, values float32
Opened arg_j152.mrc as #20.1, grid size 380,380,380, pixel 1.05, shown at step
1, values float32
Opened arg-apo.mrc as #21.1, grid size 360,360,360, pixel 1.08, shown at step
1, values float32
Opened POST_j93ct15_pplocal_g0_n.mrc as #15.1, grid size 576,576,576, pixel
1.06, shown at step 1, values float32
Opened PREC_job225_ct14_pplocal_g0_n.mrc as #10.1, grid size 576,576,576,
pixel 1.06, shown at step 1, values float32
opened ChimeraX session
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_startup_gtpys.cxc
> close all
> open /data/EmilyRundlet/ChimeraX_70S/Maps/4ybb_50Score_3A.mrc
Opened 4ybb_50Score_3A.mrc as #1, grid size 576,576,576, pixel 1.06, shown at
level 0.000164, step 4, values float32
> rename #1 id #100
> open /data/EmilyRundlet/ChimeraX_70S/Models/prec_7n1p_50S.pdb
Chain information for prec_7n1p_50S.pdb #1
---
Chain | Description
3 | No description available
5 | No description available
P | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #101
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_post.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/post_50S.pdb name
> post5
Chain information for post5 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #15.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/post_30S.pdb name
> post3
Chain information for post3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
y | No description available
> rename #1 id #15.3
> open
> /data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/POST_j93ct15_pplocal_g0_n.mrc
> name post
Opened post as #1, grid size 576,576,576, pixel 1.06, shown at level 1.16,
step 4, values float32
> rename #1 id #15.1
> rename #15 post
> matchmaker #15.5 to #101 matrix Nucleic bring #15.1#15.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with post5, chain 3 (#15.5),
sequence alignment score = 11580.3
RMSD between 2766 pruned atom pairs is 0.341 angstroms; (across all 2904
pairs: 2.745)
> fitmap #15.1 inMap #100
Fit map post in map 4ybb_50Score_3A.mrc using 29937 points
correlation = 0.7033, correlation about mean = 0.6059, overlap = 7.619e+04
steps = 48, shift = 0.0376, angle = 0.0465 degrees
Position of post (#15.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates:
Matrix rotation and translation
0.99999983 0.00051499 -0.00026539 -0.07015622
-0.00051501 0.99999986 -0.00009768 0.21094928
0.00026534 0.00009781 0.99999996 -0.12735627
Axis 0.16636276 -0.45165257 -0.87654628
Axis point 413.67366807 137.87803145 0.00000000
Rotation angle (degrees) 0.03366312
Shift along axis 0.00468650
> fitmap #15.5 inMap #15.1
Fit molecule post5 (#15.5) to map post (#15.1) using 90903 atoms
average map value = 15.29, steps = 40
shifted from previous position = 0.0173
rotated from previous position = 0.0481 degrees
atoms outside contour = 27101, contour level = 1.1571
Position of post5 (#15.5) relative to post (#15.1) coordinates:
Matrix rotation and translation
1.00000000 0.00007488 -0.00001293 -0.00984527
-0.00007488 1.00000000 0.00003964 0.01927617
0.00001293 -0.00003964 1.00000000 0.00608995
Axis -0.46249937 -0.15083335 -0.87369539
Axis point 250.02744189 154.19286933 0.00000000
Rotation angle (degrees) 0.00491036
Shift along axis -0.00367482
> fitmap #15.3 inMap #15.1
Fit molecule post3 (#15.3) to map post (#15.1) using 55643 atoms
average map value = 11.56, steps = 40
shifted from previous position = 0.0883
rotated from previous position = 0.0476 degrees
atoms outside contour = 13831, contour level = 1.1571
Position of post3 (#15.3) relative to post (#15.1) coordinates:
Matrix rotation and translation
1.00000000 -0.00005318 -0.00004310 0.02635100
0.00005318 1.00000000 -0.00000125 -0.02050708
0.00004310 0.00000124 1.00000000 -0.01832489
Axis 0.01818364 -0.62958007 0.77672279
Axis point 395.65049914 495.82230346 0.00000000
Rotation angle (degrees) 0.00392252
Shift along axis -0.00084336
executed 70S_open_post.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_prec.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/prec_50S.pdb name
> prec5
Chain information for prec5 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #10.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/prec_30S.pdb name
> prec3
Chain information for prec3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
y | No description available
> rename #1 id #10.3
> open
> /data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/PREC*local*.mrc
> name prec
Opened prec as #1, grid size 576,576,576, pixel 1.06, shown at level 0.719,
step 4, values float32
> rename #1 id #10.1
> rename #10 prec
> matchmaker #10.5 to #101 matrix Nucleic bring #10.1#10.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with prec5, chain 3 (#10.5),
sequence alignment score = 11585.2
RMSD between 2904 pruned atom pairs is 0.000 angstroms; (across all 2904
pairs: 0.000)
> fitmap #10.1 inMap #100
Fit map prec in map 4ybb_50Score_3A.mrc using 29930 points
correlation = 0.705, correlation about mean = 0.6153, overlap = 7.403e+04
steps = 100, shift = 0.0276, angle = 0.0213 degrees
Position of prec (#10.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates:
Matrix rotation and translation
0.99999993 0.00023597 -0.00028739 0.01666834
-0.00023597 0.99999997 0.00000377 0.08653163
0.00028739 -0.00000370 0.99999996 -0.10871255
Axis -0.01003658 -0.77282074 -0.63454501
Axis point 373.98904576 -0.00000000 57.97612114
Rotation angle (degrees) 0.02130699
Shift along axis 0.00194228
> fitmap #10.5 inMap #10.1
Fit molecule prec5 (#10.5) to map prec (#10.1) using 93196 atoms
average map value = 15.31, steps = 40
shifted from previous position = 0.0241
rotated from previous position = 0.0378 degrees
atoms outside contour = 32220, contour level = 0.71858
Position of prec5 (#10.5) relative to prec (#10.1) coordinates:
Matrix rotation and translation
0.99999996 0.00028462 -0.00008450 -0.07054285
-0.00028461 0.99999995 0.00015462 0.06036830
0.00008454 -0.00015460 0.99999998 0.02731692
Axis -0.46188152 -0.25249170 -0.85024314
Axis point 206.84210925 257.43360450 0.00000000
Rotation angle (degrees) 0.01917937
Shift along axis -0.00588608
> fitmap #10.3 inMap #10.1
Fit molecule prec3 (#10.3) to map prec (#10.1) using 56259 atoms
average map value = 11.39, steps = 48
shifted from previous position = 0.0796
rotated from previous position = 0.0392 degrees
atoms outside contour = 16720, contour level = 0.71858
Position of prec3 (#10.3) relative to prec (#10.1) coordinates:
Matrix rotation and translation
0.99999994 0.00035395 -0.00002496 -0.09187678
-0.00035394 0.99999993 0.00014842 0.08455945
0.00002502 -0.00014841 0.99999999 0.04385687
Axis -0.38587760 -0.06497510 -0.92025905
Axis point 236.94211808 270.96015369 0.00000000
Rotation angle (degrees) 0.02203670
Shift along axis -0.01040075
executed 70S_open_prec.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_fa.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/fa_50S.pdb name
> i2fa5
Chain information for i2fa5 #1
---
Chain | Description
3 | No description available
5 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
K | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #14.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/fa_30S.pdb name
> i2fa3
Chain information for i2fa3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
x | No description available
y | No description available
> rename #1 id #14.3
> open
> /data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/FA*local*.mrc
Opened FA_j118_localres_filt_g0_n.mrc as #1, grid size 576,576,576, pixel
1.06, shown at level 0.555, step 4, values float32
> rename #1 id #14.1
> matchmaker #14.5 to #101 matrix Nucleic bring #14.1#14.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with i2fa5, chain 3 (#14.5),
sequence alignment score = 11567.9
RMSD between 2675 pruned atom pairs is 0.458 angstroms; (across all 2903
pairs: 3.500)
> rename #14 fa
> fitmap #14.1 inMap #100
Fit map FA_j118_localres_filt_g0_n.mrc in map 4ybb_50Score_3A.mrc using 29876
points
correlation = 0.7652, correlation about mean = 0.6917, overlap = 8.026e+04
steps = 124, shift = 0.0674, angle = 0.0469 degrees
Position of FA_j118_localres_filt_g0_n.mrc (#14.1) relative to
4ybb_50Score_3A.mrc (#100) coordinates:
Matrix rotation and translation
0.99999951 0.00082837 -0.00054821 -0.07721517
-0.00082823 0.99999963 0.00024790 0.22483688
0.00054841 -0.00024745 0.99999982 -0.11895947
Axis -0.24193109 -0.53558675 -0.80908354
Axis point 267.87230737 94.97670830 0.00000000
Rotation angle (degrees) 0.05865666
Shift along axis -0.00549075
> fitmap #14.5 inMap #14.1
Fit molecule i2fa5 (#14.5) to map FA_j118_localres_filt_g0_n.mrc (#14.1) using
94455 atoms
average map value = 14.71, steps = 44
shifted from previous position = 0.0492
rotated from previous position = 0.0489 degrees
atoms outside contour = 26009, contour level = 0.5555
Position of i2fa5 (#14.5) relative to FA_j118_localres_filt_g0_n.mrc (#14.1)
coordinates:
Matrix rotation and translation
0.99999999 0.00013549 0.00005439 -0.05910674
-0.00013549 0.99999999 -0.00008462 0.07061428
-0.00005440 0.00008461 0.99999999 -0.01606966
Axis 0.50141948 0.32233497 -0.80291884
Axis point 506.79859217 458.57499403 0.00000000
Rotation angle (degrees) 0.00966859
Shift along axis 0.00602682
> fitmap #14.3 inMap #14.1
Fit molecule i2fa3 (#14.3) to map FA_j118_localres_filt_g0_n.mrc (#14.1) using
60702 atoms
average map value = 7.538, steps = 40
shifted from previous position = 0.104
rotated from previous position = 0.0489 degrees
atoms outside contour = 11367, contour level = 0.5555
Position of i2fa3 (#14.3) relative to FA_j118_localres_filt_g0_n.mrc (#14.1)
coordinates:
Matrix rotation and translation
0.99999996 0.00022144 0.00016174 -0.14067075
-0.00022141 0.99999996 -0.00017040 0.12305826
-0.00016178 0.00017037 0.99999997 -0.00200513
Axis 0.52777238 0.50104898 -0.68586167
Axis point 581.05763080 608.65192133 0.00000000
Rotation angle (degrees) 0.01849719
Shift along axis -0.01120868
executed 70S_open_fa.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_spc.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/spc_50S.pdb name
> i1spc5
Chain information for i1spc5 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #13.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/spc_30S.pdb name
> i1spc3
Chain information for i1spc3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
x | No description available
y | No description available
> rename #1 id #13.3
> open
> /data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/INT1_spc*local*.mrc
> name i1spc
Opened i1spc as #1, grid size 576,576,576, pixel 1.06, shown at level 0.527,
step 4, values float32
> rename #1 id #13.1
> rename #13 i1spc
> matchmaker #13.5 to #101 matrix Nucleic bring #13.1#13.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with i1spc5, chain 3 (#13.5),
sequence alignment score = 11576.1
RMSD between 2613 pruned atom pairs is 0.440 angstroms; (across all 2904
pairs: 4.190)
> fitmap #13.1 inMap #100
Fit map i1spc in map 4ybb_50Score_3A.mrc using 29799 points
correlation = 0.7329, correlation about mean = 0.6398, overlap = 7.208e+04
steps = 104, shift = 0.0985, angle = 0.0628 degrees
Position of i1spc (#13.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates:
Matrix rotation and translation
0.99999127 -0.00305790 -0.00284733 1.91534327
0.00305942 0.99999518 0.00052889 -1.13631859
0.00284570 -0.00053760 0.99999581 -1.01117770
Axis -0.12659581 -0.67578369 0.72614730
Axis point 418.51647841 616.51914515 0.00000000
Rotation angle (degrees) 0.24134036
Shift along axis -0.20883282
> fitmap #13.5 inMap #13.1
Fit molecule i1spc5 (#13.5) to map i1spc (#13.1) using 93017 atoms
average map value = 14.57, steps = 48
shifted from previous position = 0.0733
rotated from previous position = 0.0651 degrees
atoms outside contour = 27434, contour level = 0.52653
Position of i1spc5 (#13.5) relative to i1spc (#13.1) coordinates:
Matrix rotation and translation
1.00000000 -0.00000053 -0.00005875 0.01737643
0.00000053 1.00000000 -0.00002655 0.00255801
0.00005875 0.00002655 1.00000000 -0.03456253
Axis 0.41177423 -0.91124934 0.00816220
Axis point 588.98331322 0.00000000 263.93669119
Rotation angle (degrees) 0.00369369
Shift along axis 0.00454208
> fitmap #13.3 inMap #13.1
Fit molecule i1spc3 (#13.3) to map i1spc (#13.1) using 61103 atoms
average map value = 9.699, steps = 60
shifted from previous position = 0.162
rotated from previous position = 0.0627 degrees
atoms outside contour = 14669, contour level = 0.52653
Position of i1spc3 (#13.3) relative to i1spc (#13.1) coordinates:
Matrix rotation and translation
0.99999999 0.00006855 -0.00007419 -0.00808096
-0.00006856 1.00000000 -0.00003421 0.02476248
0.00007419 0.00003421 1.00000000 -0.04490669
Axis 0.32075098 -0.69563238 -0.64281755
Axis point 526.89840240 0.00000000 -148.08272269
Rotation angle (degrees) 0.00611054
Shift along axis 0.00904925
executed 70S_open_spc.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_h1.cxc
> open
> /data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/apo_H1*local*.mrc
> name hy1
Opened hy1 as #1, grid size 576,576,576, pixel 1.06, shown at level 0.822,
step 4, values float32
> rename #1 id #12.1
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/h1_50S.pdb name
> hy15
Chain information for hy15 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #12.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/h1_30S.pdb name
> hy13
Chain information for hy13 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
y | No description available
> rename #1 id #12.3
> matchmaker #12.5 to #101 matrix Nucleic bring #12.1#12.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with hy15, chain 3 (#12.5),
sequence alignment score = 11572.3
RMSD between 2683 pruned atom pairs is 0.437 angstroms; (across all 2902
pairs: 4.227)
> fitmap #12.1 inMap #100
Fit map hy1 in map 4ybb_50Score_3A.mrc using 29865 points
correlation = 0.7182, correlation about mean = 0.6351, overlap = 7.48e+04
steps = 80, shift = 0.0539, angle = 0.0362 degrees
Position of hy1 (#12.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates:
Matrix rotation and translation
0.99999993 0.00033939 -0.00014651 -0.03967194
-0.00033939 0.99999994 0.00003379 0.08904027
0.00014652 -0.00003374 0.99999999 -0.04209798
Axis -0.09096206 -0.39471037 -0.91429187
Axis point 270.42268136 115.08181596 0.00000000
Rotation angle (degrees) 0.02126851
Shift along axis 0.00695336
> fitmap #12.5 inMap #12.1
Fit molecule hy15 (#12.5) to map hy1 (#12.1) using 91053 atoms
average map value = 15.92, steps = 40
shifted from previous position = 0.0355
rotated from previous position = 0.0365 degrees
atoms outside contour = 31662, contour level = 0.82202
Position of hy15 (#12.5) relative to hy1 (#12.1) coordinates:
Matrix rotation and translation
1.00000000 0.00001739 -0.00003452 0.00191493
-0.00001738 1.00000000 0.00005119 -0.00075625
0.00003452 -0.00005119 1.00000000 0.00373129
Axis -0.79805293 -0.53818813 -0.27104440
Axis point 0.00000000 61.60073087 37.19705100
Rotation angle (degrees) 0.00367501
Shift along axis -0.00213255
> fitmap #12.3 inMap #12.1
Fit molecule hy13 (#12.3) to map hy1 (#12.1) using 55765 atoms
average map value = 9.817, steps = 44
shifted from previous position = 0.0694
rotated from previous position = 0.0332 degrees
atoms outside contour = 14540, contour level = 0.82202
Position of hy13 (#12.3) relative to hy1 (#12.1) coordinates:
Matrix rotation and translation
1.00000000 -0.00000897 0.00000895 -0.00690250
0.00000897 0.99999999 0.00011154 -0.02727097
-0.00000895 -0.00011154 0.99999999 0.03999319
Axis -0.99361126 0.07969592 0.07990759
Axis point 0.00000000 352.90975575 250.15609103
Rotation angle (degrees) 0.00643159
Shift along axis 0.00788078
executed 70S_open_h1.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_ys.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1a_50S.pdb name
> ys-H1a5
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1a_50S.pdb
---
warnings | Ignored bad PDB record found on line 4
LINK ZN ZN Le0201 SG CY 04
Ignored bad PDB record found on line 5
LINK ZN ZN Le0201 SG CY 03
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 01
Ignored bad PDB record found on line 7
LINK ZN ZN Le0201 SG CY 01
Ignored bad PDB record found on line 8
LINK ZN ZN Lj0101 ND1 HI 03
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue ASP (2432820)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-H1a5 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #30.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1a_30S.pdb name
> ys-H1a3
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1a_30S.pdb
---
warnings | Ignored bad PDB record found on line 4
LINK ZN ZN Le0201 SG CY 04
Ignored bad PDB record found on line 5
LINK ZN ZN Le0201 SG CY 03
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 01
Ignored bad PDB record found on line 7
LINK ZN ZN Le0201 SG CY 01
Ignored bad PDB record found on line 8
LINK ZN ZN Lj0101 ND1 HI 03
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue ASP (2432820)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-H1a3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
x | No description available
y | No description available
> rename #1 id #30.3
> open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/ys-H1a*.mrc name ys-H1a
Opened ys-H1a as #1, grid size 512,512,512, pixel 0.826, shown at level 3.13,
step 2, values float32
> rename #1 id #30.1
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1b_50S.pdb name
> ys-H1b5
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1b_50S.pdb
---
warnings | Ignored bad PDB record found on line 5
LINK ZN ZN Le0201 SG CY 04
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 03
Ignored bad PDB record found on line 7
LINK ZN ZN Le0201 SG CY 01
Ignored bad PDB record found on line 8
LINK ZN ZN Le0201 SG CY 01
Ignored bad PDB record found on line 9
LINK ZN ZN Lj0101 ND1 HI 03
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue LYS (2432823)
Cannot find LINK/SSBOND residue THR (2432824)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-H1b5 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #31.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1b_30S.pdb name
> ys-H1b3
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1b_30S.pdb
---
warnings | Ignored bad PDB record found on line 5
LINK ZN ZN Le0201 SG CY 04
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 03
Ignored bad PDB record found on line 7
LINK ZN ZN Le0201 SG CY 01
Ignored bad PDB record found on line 8
LINK ZN ZN Le0201 SG CY 01
Ignored bad PDB record found on line 9
LINK ZN ZN Lj0101 ND1 HI 03
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue LYS (2432823)
Cannot find LINK/SSBOND residue THR (2432824)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-H1b3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
x | No description available
y | No description available
> rename #1 id #31.3
> open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/ys-H1b*.mrc name ys-H1b
Opened ys-H1b as #1, grid size 512,512,512, pixel 0.826, shown at level 3.16,
step 2, values float32
> rename #1 id #31.1
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1c_50S.pdb name
> ys-H1c5
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1c_50S.pdb
---
warnings | Ignored bad PDB record found on line 2
LINK ZN ZN Lj0101 ND1 HI 03
Ignored bad PDB record found on line 3
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 4
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 5
LINK ZN ZN Lj0101 SG CY 02
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 04
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-H1c5 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #32.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1c_30S.pdb name
> ys-H1c3
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1c_30S.pdb
---
warnings | Ignored bad PDB record found on line 2
LINK ZN ZN Lj0101 ND1 HI 03
Ignored bad PDB record found on line 3
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 4
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 5
LINK ZN ZN Lj0101 SG CY 02
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 04
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-H1c3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
x | No description available
y | No description available
> rename #1 id #32.3
> open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/ys-H1c*.mrc name ys-H1c
Opened ys-H1c as #1, grid size 512,512,512, pixel 0.826, shown at level 3.11,
step 2, values float32
> rename #1 id #32.1
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1a_50S.pdb name
> ys-I1a5
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1a_50S.pdb
---
warnings | Ignored bad PDB record found on line 2
LINK ZN ZN Lj0101 ND1 HI 03
Ignored bad PDB record found on line 3
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 4
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 5
LINK ZN ZN Lj0101 SG CY 02
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 04
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-I1a5 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #33.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1a_30S.pdb name
> ys-I1a3
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1a_30S.pdb
---
warnings | Ignored bad PDB record found on line 2
LINK ZN ZN Lj0101 ND1 HI 03
Ignored bad PDB record found on line 3
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 4
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 5
LINK ZN ZN Lj0101 SG CY 02
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 04
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-I1a3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
x | No description available
y | No description available
> rename #1 id #33.3
> open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/ys-I1a*.mrc name ys-I1a
Opened ys-I1a as #1, grid size 512,512,512, pixel 0.826, shown at level 3.09,
step 2, values float32
> rename #1 id #33.1
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1b_50S.pdb name
> ys-I1b5
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1b_50S.pdb
---
warnings | Ignored bad PDB record found on line 2
LINK ZN ZN Lj0101 ND1 HI 03
Ignored bad PDB record found on line 3
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 4
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 5
LINK ZN ZN Lj0101 SG CY 02
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 04
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-I1b5 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #34.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1b_30S.pdb name
> ys-I1b3
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1b_30S.pdb
---
warnings | Ignored bad PDB record found on line 2
LINK ZN ZN Lj0101 ND1 HI 03
Ignored bad PDB record found on line 3
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 4
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 5
LINK ZN ZN Lj0101 SG CY 02
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 04
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-I1b3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
x | No description available
y | No description available
> rename #1 id #34.3
> open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/ys-I1b*.mrc name ys-I1b
Opened ys-I1b as #1, grid size 512,512,512, pixel 0.826, shown at level 3.09,
step 2, values float32
> rename #1 id #34.1
> matchmaker #30.5 to #101 matrix Nucleic bring #30.1#30.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with ys-H1a5, chain 3 (#30.5),
sequence alignment score = 11576.1
RMSD between 2631 pruned atom pairs is 0.435 angstroms; (across all 2904
pairs: 4.260)
> matchmaker #31.5 to #101 matrix Nucleic bring #31.1#31.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with ys-H1b5, chain 3 (#31.5),
sequence alignment score = 11576.1
RMSD between 2629 pruned atom pairs is 0.438 angstroms; (across all 2904
pairs: 4.264)
> matchmaker #32.5 to #101 matrix Nucleic bring #32.1#32.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with ys-H1c5, chain 3 (#32.5),
sequence alignment score = 11576.1
RMSD between 2600 pruned atom pairs is 0.428 angstroms; (across all 2904
pairs: 4.256)
> matchmaker #33.5 to #101 matrix Nucleic bring #33.1#33.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with ys-I1a5, chain 3 (#33.5),
sequence alignment score = 11576.1
RMSD between 2595 pruned atom pairs is 0.428 angstroms; (across all 2904
pairs: 4.252)
> matchmaker #34.5 to #101 matrix Nucleic bring #34.1#34.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with ys-I1b5, chain 3 (#34.5),
sequence alignment score = 11576.1
RMSD between 2617 pruned atom pairs is 0.432 angstroms; (across all 2904
pairs: 4.229)
> fitmap #30.1 inMap #100
Fit map ys-H1a in map 4ybb_50Score_3A.mrc using 167516 points
correlation = 0.7712, correlation about mean = 0.5068, overlap = 5.636e+05
steps = 116, shift = 0.0431, angle = 0.06 degrees
Position of ys-H1a (#30.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates:
Matrix rotation and translation
-0.16096874 0.07054784 0.98443490 117.93148350
-0.09736653 -0.99371151 0.05529186 532.16401993
0.98214501 -0.08695075 0.16682549 84.98416227
Axis -0.64633407 0.01040498 -0.76298362
Axis point 42.26680055 265.56440366 0.00000000
Rotation angle (degrees) 173.68249450
Shift along axis -135.52750571
> fitmap #30.5 inMap #30.1
Fit molecule ys-H1a5 (#30.5) to map ys-H1a (#30.1) using 92994 atoms
average map value = 7.904, steps = 44
shifted from previous position = 0.0158
rotated from previous position = 0.0583 degrees
atoms outside contour = 20674, contour level = 3.1252
Position of ys-H1a5 (#30.5) relative to ys-H1a (#30.1) coordinates:
Matrix rotation and translation
1.00000000 0.00007896 0.00002842 -0.01618923
-0.00007896 1.00000000 0.00000766 0.01408032
-0.00002842 -0.00000766 1.00000000 0.00064511
Axis -0.09088428 0.33726732 -0.93701163
Axis point 154.32943537 198.57692600 0.00000000
Rotation angle (degrees) 0.00482813
Shift along axis 0.00561570
> fitmap #30.3 inMap #30.1
Fit molecule ys-H1a3 (#30.3) to map ys-H1a (#30.1) using 60930 atoms
average map value = 5.423, steps = 44
shifted from previous position = 0.107
rotated from previous position = 0.0638 degrees
atoms outside contour = 21357, contour level = 3.1252
Position of ys-H1a3 (#30.3) relative to ys-H1a (#30.1) coordinates:
Matrix rotation and translation
1.00000000 -0.00007009 0.00004160 -0.00010326
0.00007009 1.00000000 -0.00003531 -0.00429301
-0.00004159 0.00003531 1.00000000 -0.00573932
Axis 0.39752790 0.46828522 0.78910108
Axis point 17.28659253 35.84690625 0.00000000
Rotation angle (degrees) 0.00508928
Shift along axis -0.00658030
> fitmap #31.1 inMap #100
Fit map ys-H1b in map 4ybb_50Score_3A.mrc using 167746 points
correlation = 0.7557, correlation about mean = 0.4732, overlap = 4.809e+05
steps = 104, shift = 0.0913, angle = 0.169 degrees
Position of ys-H1b (#31.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates:
Matrix rotation and translation
-0.16402794 0.07279267 0.98376626 117.06968879
-0.09958269 -0.99340097 0.05690170 531.99178964
0.98141639 -0.08863262 0.17019441 84.62198725
Axis -0.64507570 0.01041575 -0.76404768
Axis point 42.56283115 265.45365415 0.00000000
Rotation angle (degrees) 173.52301718
Shift along axis -134.63295191
> fitmap #31.5 inMap #31.1
Fit molecule ys-H1b5 (#31.5) to map ys-H1b (#31.1) using 92994 atoms
average map value = 6.419, steps = 48
shifted from previous position = 0.0121
rotated from previous position = 0.0631 degrees
atoms outside contour = 25942, contour level = 3.1558
Position of ys-H1b5 (#31.5) relative to ys-H1b (#31.1) coordinates:
Matrix rotation and translation
0.99999984 0.00056889 -0.00006451 -0.12124833
-0.00056878 0.99999829 0.00175780 -0.12851585
0.00006551 -0.00175777 0.99999845 0.36559707
Axis -0.95083394 -0.03516616 -0.30769816
Axis point 0.00000000 209.20515420 73.16839244
Rotation angle (degrees) 0.10592152
Shift along axis 0.00731289
> fitmap #31.3 inMap #31.1
Fit molecule ys-H1b3 (#31.3) to map ys-H1b (#31.1) using 60958 atoms
average map value = 4.602, steps = 44
shifted from previous position = 0.0971
rotated from previous position = 0.114 degrees
atoms outside contour = 25030, contour level = 3.1558
Position of ys-H1b3 (#31.3) relative to ys-H1b (#31.1) coordinates:
Matrix rotation and translation
0.99999972 -0.00035593 0.00066202 -0.06165935
0.00035492 0.99999877 0.00152816 -0.29466909
-0.00066256 -0.00152792 0.99999861 0.44538378
Axis -0.89731715 0.38891986 0.20871819
Axis point 0.00000000 286.71155040 201.62993409
Rotation angle (degrees) 0.09756906
Shift along axis 0.03368503
> fitmap #32.1 inMap #100
Fit map ys-H1c in map 4ybb_50Score_3A.mrc using 167598 points
correlation = 0.7687, correlation about mean = 0.5028, overlap = 5.462e+05
steps = 64, shift = 0.174, angle = 0.0444 degrees
Position of ys-H1c (#32.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates:
Matrix rotation and translation
-0.16402649 0.07085424 0.98390802 117.46660733
-0.09904792 -0.99355948 0.05503707 532.18633927
0.98147074 -0.08842650 0.16998804 84.56695102
Axis -0.64511751 0.01095977 -0.76400477
Axis point 42.50698240 265.58065026 0.00000000
Rotation angle (degrees) 173.61597695
Shift along axis -134.55667780
> fitmap #32.5 inMap #32.1
Fit molecule ys-H1c5 (#32.5) to map ys-H1c (#32.1) using 92992 atoms
average map value = 7.486, steps = 36
shifted from previous position = 0.0219
rotated from previous position = 0.0647 degrees
atoms outside contour = 22168, contour level = 3.1136
Position of ys-H1c5 (#32.5) relative to ys-H1c (#32.1) coordinates:
Matrix rotation and translation
0.99999983 -0.00057175 0.00006040 0.12367865
0.00057186 0.99999823 -0.00179030 0.13731617
-0.00005938 0.00179034 0.99999840 -0.36604473
Axis 0.95211000 0.03184871 0.30409245
Axis point 0.00000000 206.36170644 76.30401858
Rotation angle (degrees) 0.10773729
Shift along axis 0.01081758
> fitmap #32.3 inMap #32.1
Fit molecule ys-H1c3 (#32.3) to map ys-H1c (#32.1) using 60097 atoms
average map value = 5.192, steps = 48
shifted from previous position = 0.133
rotated from previous position = 0.0654 degrees
atoms outside contour = 21804, contour level = 3.1136
Position of ys-H1c3 (#32.3) relative to ys-H1c (#32.1) coordinates:
Matrix rotation and translation
0.99999975 0.00002916 -0.00070103 0.13056968
-0.00003034 0.99999858 -0.00168673 0.26834816
0.00070098 0.00168675 0.99999833 -0.48614194
Axis 0.92330390 -0.38372472 -0.01628638
Axis point 0.00000000 288.12835311 164.65187972
Rotation angle (degrees) 0.10467114
Shift along axis 0.02550116
> fitmap #33.1 inMap #100
Fit map ys-I1a in map 4ybb_50Score_3A.mrc using 167703 points
correlation = 0.7667, correlation about mean = 0.498, overlap = 5.302e+05
steps = 104, shift = 0.0538, angle = 0.0755 degrees
Position of ys-I1a (#33.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates:
Matrix rotation and translation
-0.16092884 0.07096607 0.98441136 117.88246252
-0.09669854 -0.99374659 0.05583104 532.06291528
0.98221754 -0.08620632 0.16678480 84.75523562
Axis -0.64635360 0.00998316 -0.76297271
Axis point 42.30362323 265.49282475 0.00000000
Rotation angle (degrees) 173.69183881
Shift along axis -135.54801612
> fitmap #33.5 inMap #33.1
Fit molecule ys-I1a5 (#33.5) to map ys-I1a (#33.1) using 92992 atoms
average map value = 7.334, steps = 36
shifted from previous position = 0.0203
rotated from previous position = 0.0746 degrees
atoms outside contour = 22072, contour level = 3.0948
Position of ys-I1a5 (#33.5) relative to ys-I1a (#33.1) coordinates:
Matrix rotation and translation
1.00000000 0.00006785 0.00002158 -0.01571402
-0.00006785 1.00000000 0.00000247 0.01394877
-0.00002158 -0.00000247 1.00000000 0.00028445
Axis -0.03462129 0.30294566 -0.95237875
Axis point 185.47857319 229.29962927 0.00000000
Rotation angle (degrees) 0.00408210
Shift along axis 0.00449885
> fitmap #33.3 inMap #33.1
Fit molecule ys-I1a3 (#33.3) to map ys-I1a (#33.1) using 61025 atoms
average map value = 5.134, steps = 60
shifted from previous position = 0.135
rotated from previous position = 0.08 degrees
atoms outside contour = 22330, contour level = 3.0948
Position of ys-I1a3 (#33.3) relative to ys-I1a (#33.1) coordinates:
Matrix rotation and translation
0.99999998 -0.00017787 0.00003522 0.02444707
0.00017787 0.99999998 -0.00002049 -0.02796573
-0.00003522 0.00002050 1.00000000 0.00287850
Axis 0.11232351 0.19300468 0.97474747
Axis point 157.40269238 137.32963987 0.00000000
Rotation angle (degrees) 0.01045538
Shift along axis 0.00015427
> fitmap #34.1 inMap #100
Fit map ys-I1b in map 4ybb_50Score_3A.mrc using 167622 points
correlation = 0.7694, correlation about mean = 0.5021, overlap = 5.244e+05
steps = 48, shift = 0.0515, angle = 0.0695 degrees
Position of ys-I1b (#34.1) relative to 4ybb_50Score_3A.mrc (#100) coordinates:
Matrix rotation and translation
-0.15974764 0.06847542 0.98478008 118.03715648
-0.09853124 -0.99371554 0.05311334 533.28558991
0.98222822 -0.08854688 0.16549068 85.54764208
Axis -0.64682093 0.01165178 -0.76255290
Axis point 41.99640823 266.19892413 0.00000000
Rotation angle (degrees) 173.71321980
Shift along axis -135.36977768
> fitmap #34.5 inMap #34.1
Fit molecule ys-I1b5 (#34.5) to map ys-I1b (#34.1) using 92992 atoms
average map value = 7.158, steps = 44
shifted from previous position = 0.014
rotated from previous position = 0.0687 degrees
atoms outside contour = 22660, contour level = 3.0873
Position of ys-I1b5 (#34.5) relative to ys-I1b (#34.1) coordinates:
Matrix rotation and translation
1.00000000 -0.00003647 0.00000880 0.00851051
0.00003647 1.00000000 0.00003193 -0.01982466
-0.00000880 -0.00003193 1.00000000 0.00942241
Axis -0.64817747 0.17854187 0.74026263
Axis point 533.41299576 196.36486997 0.00000000
Rotation angle (degrees) 0.00282273
Shift along axis -0.00208080
> fitmap #34.3 inMap #34.1
Fit molecule ys-I1b3 (#34.3) to map ys-I1b (#34.1) using 61064 atoms
average map value = 4.951, steps = 48
shifted from previous position = 0.125
rotated from previous position = 0.0753 degrees
atoms outside contour = 23372, contour level = 3.0873
Position of ys-I1b3 (#34.3) relative to ys-I1b (#34.1) coordinates:
Matrix rotation and translation
0.99999999 -0.00013951 0.00000938 0.01771739
0.00013951 0.99999999 -0.00004705 -0.01825677
-0.00000937 0.00004706 1.00000000 -0.00740427
Axis 0.31895163 0.06356485 0.94563702
Axis point 129.73074307 132.73108386 0.00000000
Rotation angle (degrees) 0.00845277
Shift along axis -0.00251125
> rename #30 ys-H1a
> rename #31 ys-H1b
> rename #32 ys-H1c
> rename #33 ys-I1a
> rename #34 ys-I1b
executed 70S_open_ys.cxc
executed 70S_startup_gtpys.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/helix/gtpys_helix.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_assign.cxc
> name atomods #*.3,5,7
> name emmaps #*.1
> name lsu #*.5
> name ssu #*.3
> name rna /y,v,w,3,6,5
> name r23s /3
> name r16s /6
> name r5s /5
> name pt /y
> name dt /v
> name efg /x
> name pep /p
> name mrna /w
> name GSP :GSP
> name GDP :GDP
> name GTP :GTP
> name ntide :GTP|:GDP|:GSP
> name spc :SCM
> name fua :FUA
> name par :PAR
> name argb :LIG | #20.7/b
> name drugs argb|par|fua|spc
> name D1 /x:start-293
> name D2 /x:294-410
> name D3 /x:411-489
> name D4 /x:490-612
> name D5 /x:613-end
> name sw1 /x:38-65
> name sw2 /x:89-108
> name pl /x:18-25
> name nkxd /x:142-146
> name kirby #20.7
> name mg /x:MG
> name trna /y,v
> name anticodon /y,v:34-36
> name antiplus /y,v:32-38
> name cca /y,v:74-76
> name astem /y,v:1-7,66-73
> name darm /y,v:8-25
> name aarm /y,v:26-43
> name varm /y,v:44-48
> name tarm /y,v:49-65
> name head #*.3/A/C/S/M/G/N/I/J/6:927-1390
> name arg-head #20.3/A/C/S/M/G/N/I/J/6:927-1390
> name post-head #15.3/A/C/S/M/G/N/I/J/6:927-1390
> name fa-head #14.3/A/C/S/M/G/N/I/J/6:927-1390
> name body #*.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name arg-body #20.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name post-body #15.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name fa-body #14.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name h8 /6:144-178
> name h14 /6:339-350
> name h18 /6:511-540
> name h23 /6:674-716
> name h24 /6:769-810
> name h27 /6:894-905
> name h28 /6:921-937,1379-1400
> name h29 /6:938-943,1337-1346
> name h30 /6:945-955,1225-1235
> name h31 /6:956-975
> name h32 /6:984-990,1215-1221
> name h34 /6:1045-1065,1188-1211
> name h35 /6:1066-1073,1102-1110
> name h36 /6:1074-1083
> name h44 /6:1401-1502
> name h45 /6:1506-1529
> name aploop /6:956-959
> name term16S /6:1503-end
> name aphelix /6:1228-1230
> name us3 #*.3/C
> name us5 #*.3/E
> name us7 #*.3/G
> name us9 #*.3/I
> name us11 #*.3/K
> name us12 #*.3/L
> name us13 #*.3/M
> name us14 #*.3/N
> name us15 #*.3/O
> name us9-130 #*.3/I:130
> name l1stalk /3:2097-2191
> name srl /3:2652-2668
> name H68 /3:1832-1906
> name H69 /3:1907-1924
> name H95 /3:2647-2673
> name ul2 #*.5/B
> name ul5 #*.5/E
> name ul14 #*.5/N
> name ul19 #*.5/S
> name ul31 #*.5/e
executed 70S_assign.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_display.cxc
> alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6;
> alias nucribthin cartoon style nucleic xsect oval width 1.2 thick 1.2;
> alias cylinders cartoon style protein modeh tube rad 2 sides 24;
> alias licorice car style protein modeh default arrows f xsect oval width 1
> thick 1;
> dssp
> windowsize 1000 1000
> set bgColor white
> lighting full
> set silhouettes true
> set silhouetteWidth 1.7
> set silhouettes true
> set silhouetteDepthJump 0.02
> cartoon style width 2.5
> size atomRadius 2
Changed 1614330 atom radii
> nucleotides fill
> size ions atomRadius 1.6
Changed 31 atom radii
> size stickRadius 0.1
Changed 1744812 bond radii
> style stick ringFill thin
Changed 1614330 atom styles, 122200 residue ring styles
> show ribbons
> hide H
> hide :HOH
> hide target a
> show nucleic target a
> show drugs target a
> style drugs ball
Changed 106 atom styles
> nucrib
> graphics selection color black
> volume emmaps style surface step 1 level 4
> surface dust emmaps size 3
> volume surfaceSmoothing true
> cartoon tether trna shape cone opacity 1
> dssp
executed 70S_display.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colors.cxc
> color name efg-t 100,0,0,50
Color 'efg-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
> color name sw1-t 100,92,0,50
Color 'sw1-t' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
> color name sw2-t 68,81,0,50
Color 'sw2-t' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
> color name pl-t 23,59,0,50
Color 'pl-t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
> color name d1-t 100,18,4,50
Color 'd1-t' is 50% transparent: rgba(100%, 18%, 4%, 50%) hex: #ff2e0a80
> color name d2-t 100,40,4,50
Color 'd2-t' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
> color name d3-t 100,27,36,50
Color 'd3-t' is 50% transparent: rgba(100%, 27%, 36%, 50%) hex: #ff455c80
> color name d4-t 80,0,23,50
Color 'd4-t' is 50% transparent: rgba(80%, 0%, 23%, 50%) hex: #cc003b80
> color name d5-t 100,60,4,50
Color 'd5-t' is 50% transparent: rgba(100%, 60%, 4%, 50%) hex: #ff990a80
> color name fa-t 100,90,4,50
Color 'fa-t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
> color name gtp-t 45,53,60,50
Color 'gtp-t' is 50% transparent: rgba(45%, 53%, 60%, 50%) hex: #73879980
> color name mg-t 1,39,16,50
Color 'mg-t' is 50% transparent: rgba(1%, 39%, 16%, 50%) hex: #03632980
> color name spc-t 100,0,0,50
Color 'spc-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
> color name argb-t 50,0,50,50
Color 'argb-t' is 50% transparent: rgba(50%, 0%, 50%, 50%) hex: #80008080
> color name g-1t 98,42,30,50
Color 'g-1t' is 50% transparent: rgba(98%, 42%, 30%, 50%) hex: #fa6b4d80
> color name g-2t 95,35,25,50
Color 'g-2t' is 50% transparent: rgba(95%, 35%, 25%, 50%) hex: #f2594080
> color name g-3t 92,28,20,50
Color 'g-3t' is 50% transparent: rgba(92%, 28%, 20%, 50%) hex: #eb473380
> color name g-4t 89,21,15,50
Color 'g-4t' is 50% transparent: rgba(89%, 21%, 15%, 50%) hex: #e3362680
> color name g-5t 86,14,10,50
Color 'g-5t' is 50% transparent: rgba(86%, 14%, 10%, 50%) hex: #db241a80
> color name g-6t 83,7,5,50
Color 'g-6t' is 50% transparent: rgba(83%, 7%, 5%, 50%) hex: #d4120d80
> color name g-7t 80,0,0,50
Color 'g-7t' is 50% transparent: rgba(80%, 0%, 0%, 50%) hex: #cc000080
> color name p-t 40,60,2,50
Color 'p-t' is 50% transparent: rgba(40%, 60%, 2%, 50%) hex: #66990580
> color name p-1t 4,34,1,50
Color 'p-1t' is 50% transparent: rgba(4%, 34%, 1%, 50%) hex: #0a570380
> color name p-2t 12,39,1,50
Color 'p-2t' is 50% transparent: rgba(12%, 39%, 1%, 50%) hex: #1f630380
> color name p-3t 20,44,1,50
Color 'p-3t' is 50% transparent: rgba(20%, 44%, 1%, 50%) hex: #33700380
> color name p-4t 28,49,1,50
Color 'p-4t' is 50% transparent: rgba(28%, 49%, 1%, 50%) hex: #477d0380
> color name p-5t 36,54,2,50
Color 'p-5t' is 50% transparent: rgba(36%, 54%, 2%, 50%) hex: #5c8a0580
> color name p-6t 44,59,2,50
Color 'p-6t' is 50% transparent: rgba(44%, 59%, 2%, 50%) hex: #70960580
> color name p-7t 52,64,2,50
Color 'p-7t' is 50% transparent: rgba(52%, 64%, 2%, 50%) hex: #85a30580
> color name p-8t 60,69,2,50
Color 'p-8t' is 50% transparent: rgba(60%, 69%, 2%, 50%) hex: #99b00580
> color name p-9t 68,74,3,50
Color 'p-9t' is 50% transparent: rgba(68%, 74%, 3%, 50%) hex: #adbd0880
> color name p-10t 76,79,3,50
Color 'p-10t' is 50% transparent: rgba(76%, 79%, 3%, 50%) hex: #c2c90880
> color name p-11t 84,84,3,50
Color 'p-11t' is 50% transparent: rgba(84%, 84%, 3%, 50%) hex: #d6d60880
> color name d-t 100,75,4,50
Color 'd-t' is 50% transparent: rgba(100%, 75%, 4%, 50%) hex: #ffbf0a80
> color name d-1t 100,100,4,50
Color 'd-1t' is 50% transparent: rgba(100%, 100%, 4%, 50%) hex: #ffff0a80
> color name d-2t 100,93,4,50
Color 'd-2t' is 50% transparent: rgba(100%, 93%, 4%, 50%) hex: #ffed0a80
> color name d-3t 100,86,4,50
Color 'd-3t' is 50% transparent: rgba(100%, 86%, 4%, 50%) hex: #ffdb0a80
> color name d-4t 100,79,4,50
Color 'd-4t' is 50% transparent: rgba(100%, 79%, 4%, 50%) hex: #ffc90a80
> color name d-5t 100,72,4,50
Color 'd-5t' is 50% transparent: rgba(100%, 72%, 4%, 50%) hex: #ffb80a80
> color name d-6t 100,65,4,50
Color 'd-6t' is 50% transparent: rgba(100%, 65%, 4%, 50%) hex: #ffa60a80
> color name d-7t 100,58,4,50
Color 'd-7t' is 50% transparent: rgba(100%, 58%, 4%, 50%) hex: #ff940a80
> color name d-8t 100,51,4,50
Color 'd-8t' is 50% transparent: rgba(100%, 51%, 4%, 50%) hex: #ff820a80
> color name d-9t 100,44,4,50
Color 'd-9t' is 50% transparent: rgba(100%, 44%, 4%, 50%) hex: #ff700a80
> color name d-10t 100,37,4,50
Color 'd-10t' is 50% transparent: rgba(100%, 37%, 4%, 50%) hex: #ff5e0a80
> color name d-11t 100,30,4,50
Color 'd-11t' is 50% transparent: rgba(100%, 30%, 4%, 50%) hex: #ff4d0a80
> color name m-t 95,43,62,50
Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
> color name m-1t 100,80,90,50
Color 'm-1t' is 50% transparent: rgba(100%, 80%, 90%, 50%) hex: #ffcce680
> color name m-2t 98,76,87,50
Color 'm-2t' is 50% transparent: rgba(98%, 76%, 87%, 50%) hex: #fac2de80
> color name m-3t 96,72,84,50
Color 'm-3t' is 50% transparent: rgba(96%, 72%, 84%, 50%) hex: #f5b8d680
> color name m-4t 94,68,81,50
Color 'm-4t' is 50% transparent: rgba(94%, 68%, 81%, 50%) hex: #f0adcf80
> color name m-5t 92,64,78,50
Color 'm-5t' is 50% transparent: rgba(92%, 64%, 78%, 50%) hex: #eba3c780
> color name m-6t 90,60,75,50
Color 'm-6t' is 50% transparent: rgba(90%, 60%, 75%, 50%) hex: #e699bf80
> color name m-7t 88,56,72,50
Color 'm-7t' is 50% transparent: rgba(88%, 56%, 72%, 50%) hex: #e08fb880
> color name m-8t 86,52,69,50
Color 'm-8t' is 50% transparent: rgba(86%, 52%, 69%, 50%) hex: #db85b080
> color name m-9t 84,48,66,50
Color 'm-9t' is 50% transparent: rgba(84%, 48%, 66%, 50%) hex: #d67aa880
> color name m-10t 82,44,63,50
Color 'm-10t' is 50% transparent: rgba(82%, 44%, 63%, 50%) hex: #d170a180
> color name m-11t 80,40,60,50
Color 'm-11t' is 50% transparent: rgba(80%, 40%, 60%, 50%) hex: #cc669980
> color name head-t 71,51,66,50
Color 'head-t' is 50% transparent: rgba(71%, 51%, 66%, 50%) hex: #b582a880
> color name head-c 89,89,100,100
Color 'head-c' is opaque: rgb(89%, 89%, 100%) hex: #e3e3ff
> color name headfa-t 80,79,100,50
Color 'headfa-t' is 50% transparent: rgba(80%, 79%, 100%, 50%) hex: #ccc9ff80
> color name headblue-t 59,78,94,50
Color 'headblue-t' is 50% transparent: rgba(59%, 78%, 94%, 50%) hex: #96c7f080
> color name headh1-t 41,64,100,50
Color 'headh1-t' is 50% transparent: rgba(41%, 64%, 100%, 50%) hex: #69a3ff80
> color name headh2-t 50,70,100,50
Color 'headh2-t' is 50% transparent: rgba(50%, 70%, 100%, 50%) hex: #80b3ff80
> color name headgray-t 60,60,60,50
Color 'headgray-t' is 50% transparent: rgba(60%, 60%, 60%, 50%) hex: #99999980
> color name darkhead-s 58,34,52,100
Color 'darkhead-s' is opaque: rgb(58%, 34%, 52%) hex: #945785
> color name bodywhite-t 90,90,90,50
Color 'bodywhite-t' is 50% transparent: rgba(90%, 90%, 90%, 50%) hex:
#e6e6e680
> color name rps-t 75,88,93,50
Color 'rps-t' is 50% transparent: rgba(75%, 88%, 93%, 50%) hex: #bfe0ed80
> color name ssu-t 57,71,75,50
Color 'ssu-t' is 50% transparent: rgba(57%, 71%, 75%, 50%) hex: #91b5bf80
> color name h18-t 31,59,68,50
Color 'h18-t' is 50% transparent: rgba(31%, 59%, 68%, 50%) hex: #4f96ad80
> color name h23-t 18,36,100,50
Color 'h23-t' is 50% transparent: rgba(18%, 36%, 100%, 50%) hex: #2e5cff80
> color name h23-c 18,36,100,100
Color 'h23-c' is opaque: rgb(18%, 36%, 100%) hex: #2e5cff
> color name h24-t 50,70,90,50
Color 'h24-t' is 50% transparent: rgba(50%, 70%, 90%, 50%) hex: #80b3e680
> color name h24-c 50,70,90,100
Color 'h24-c' is opaque: rgb(50%, 70%, 90%) hex: #80b3e6
> color name h28-t 0,24,57,50
Color 'h28-t' is 50% transparent: rgba(0%, 24%, 57%, 50%) hex: #003d9180
> color name h28-c 0,24,57,100
Color 'h28-c' is opaque: rgb(0%, 24%, 57%) hex: #003d91
> color name h29-t 80,69,92,50
Color 'h29-t' is 50% transparent: rgba(80%, 69%, 92%, 50%) hex: #ccb0eb80
> color name h29-c 80,69,92,100
Color 'h29-c' is opaque: rgb(80%, 69%, 92%) hex: #ccb0eb
> color name h30-t 40,40,59,50
Color 'h30-t' is 50% transparent: rgba(40%, 40%, 59%, 50%) hex: #66669680
> color name h31-t 45,18,59,50
Color 'h31-t' is 50% transparent: rgba(45%, 18%, 59%, 50%) hex: #732e9680
> color name h31-c 45,18,59,100
Color 'h31-c' is opaque: rgb(45%, 18%, 59%) hex: #732e96
> color name h34-t 59,18,59,50
Color 'h34-t' is 50% transparent: rgba(59%, 18%, 59%, 50%) hex: #962e9680
> color name h34-c 59,18,59,100
Color 'h34-c' is opaque: rgb(59%, 18%, 59%) hex: #962e96
> color name h35-t 50,22,45,50
Color 'h35-t' is 50% transparent: rgba(50%, 22%, 45%, 50%) hex: #80387380
> color name h44-t 27,50,80,50
Color 'h44-t' is 50% transparent: rgba(27%, 50%, 80%, 50%) hex: #4580cc80
> color name aploop-t 27,0,50,50
Color 'aploop-t' is 50% transparent: rgba(27%, 0%, 50%, 50%) hex: #45008080
> color name term16-t 40,64,64,50
Color 'term16-t' is 50% transparent: rgba(40%, 64%, 64%, 50%) hex: #66a3a380
> color name uS3-t 64,41,82,50
Color 'uS3-t' is 50% transparent: rgba(64%, 41%, 82%, 50%) hex: #a369d180
> color name uS5-t 0,50,45,50
Color 'uS5-t' is 50% transparent: rgba(0%, 50%, 45%, 50%) hex: #00807380
> color name gray-t 70,70,70,50
Color 'gray-t' is 50% transparent: rgba(70%, 70%, 70%, 50%) hex: #b3b3b380
> color name hx68-t 50,50,50,50
Color 'hx68-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name hx69-t 30,30,30,50
Color 'hx69-t' is 50% transparent: rgba(30%, 30%, 30%, 50%) hex: #4d4d4d80
> color name srl-t 50,50,50,50
Color 'srl-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name lightgrayt 83,83,83,50
Color 'lightgrayt' is 50% transparent: rgba(83%, 83%, 83%, 50%) hex: #d4d4d480
> color name silvert 75,75,75,50
Color 'silvert' is 50% transparent: rgba(75%, 75%, 75%, 50%) hex: #bfbfbf80
> color name grayt 50,50,50,50
Color 'grayt' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name lightcyant 88,100,100,50
Color 'lightcyant' is 50% transparent: rgba(88%, 100%, 100%, 50%) hex:
#e0ffff80
> color name yellowt 100,90,0,50
Color 'yellowt' is 50% transparent: rgba(100%, 90%, 0%, 50%) hex: #ffe60080
> color name deeppinkt 100,8,58,50
Color 'deeppinkt' is 50% transparent: rgba(100%, 8%, 58%, 50%) hex: #ff149480
> color name oranget 100,65,0,50
Color 'oranget' is 50% transparent: rgba(100%, 65%, 0%, 50%) hex: #ffa60080
> color name yellowgreent 60,80,20,50
Color 'yellowgreent' is 50% transparent: rgba(60%, 80%, 20%, 50%) hex:
#99cc3380
> color name darkmagentat 54,0,54,50
Color 'darkmagentat' is 50% transparent: rgba(54%, 0%, 54%, 50%) hex:
#8a008a80
> color name orchidt 86,44,84,50
Color 'orchidt' is 50% transparent: rgba(86%, 44%, 84%, 50%) hex: #db70d680
> color name paleturquoiset 69,93,93,50
Color 'paleturquoiset' is 50% transparent: rgba(69%, 93%, 93%, 50%) hex:
#b0eded80
> color name pinkt 100,75,80,50
Color 'pinkt' is 50% transparent: rgba(100%, 75%, 80%, 50%) hex: #ffbfcc80
> color name darkgreent 0,39,0,50
Color 'darkgreent' is 50% transparent: rgba(0%, 39%, 0%, 50%) hex: #00630080
> color name limegreent 20,80,20,50
Color 'limegreent' is 50% transparent: rgba(20%, 80%, 20%, 50%) hex: #33cc3380
> color name turquoiset 25,88,82,50
Color 'turquoiset' is 50% transparent: rgba(25%, 88%, 82%, 50%) hex: #40e0d180
> color name tealt 0,50,50,50
Color 'tealt' is 50% transparent: rgba(0%, 50%, 50%, 50%) hex: #00808080
> color name darkoranget 100,50,0,50
Color 'darkoranget' is 50% transparent: rgba(100%, 50%, 0%, 50%) hex:
#ff800080
> color name lightyellowt 100,100,50,50
Color 'lightyellowt' is 50% transparent: rgba(100%, 100%, 50%, 50%) hex:
#ffff8080
> color name goldt 100,75,0,50
Color 'goldt' is 50% transparent: rgba(100%, 75%, 0%, 50%) hex: #ffbf0080
> color name plumt 87,63,87,50
Color 'plumt' is 50% transparent: rgba(87%, 63%, 87%, 50%) hex: #dea1de80
> color name ssubluet 68,86,90,50
Color 'ssubluet' is 50% transparent: rgba(68%, 86%, 90%, 50%) hex: #addbe680
> color name p-prect 10,41,0,50
Color 'p-prect' is 50% transparent: rgba(10%, 41%, 0%, 50%) hex: #1a690080
> color name p-h2t 23,59,0,50
Color 'p-h2t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
> color name p-h1t 40,73,0,50
Color 'p-h1t' is 50% transparent: rgba(40%, 73%, 0%, 50%) hex: #66ba0080
> color name p-h1c 40,73,0,100
Color 'p-h1c' is opaque: rgb(40%, 73%, 0%) hex: #66ba00
> color name p-spct 68,81,0,50
Color 'p-spct' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
> color name p-spcc 68,81,0,100
Color 'p-spcc' is opaque: rgb(68%, 81%, 0%) hex: #adcf00
> color name p-fat 82,92,0,50
Color 'p-fat' is 50% transparent: rgba(82%, 92%, 0%, 50%) hex: #d1eb0080
> color name p-postt 100,92,0,50
Color 'p-postt' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
> color name d-t 100,80,4,50
Color 'd-t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
> color name d-prect 95,100,50,50
Color 'd-prect' is 50% transparent: rgba(95%, 100%, 50%, 50%) hex: #f2ff8080
> color name d-h2t 100,90,4,50
Color 'd-h2t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
> color name d-h1t 100,80,4,50
Color 'd-h1t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
> color name d-spct 100,70,4,50
Color 'd-spct' is 50% transparent: rgba(100%, 70%, 4%, 50%) hex: #ffb30a80
> color name d-fat 100,55,4,50
Color 'd-fat' is 50% transparent: rgba(100%, 55%, 4%, 50%) hex: #ff8c0a80
> color name d-fac 100,55,4,100
Color 'd-fac' is opaque: rgb(100%, 55%, 4%) hex: #ff8c0a
> color name d-postt 100,40,4,50
Color 'd-postt' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
> color name m-t 95,43,62,50
Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
> color name m-prect 100,85,95,50
Color 'm-prect' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex: #ffd9f280
> color name m-h2t 100,85,95,50
Color 'm-h2t' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex: #ffd9f280
> color name m-h1t 100,75,95,50
Color 'm-h1t' is 50% transparent: rgba(100%, 75%, 95%, 50%) hex: #ffbff280
> color name m-spct 89,63,75,50
Color 'm-spct' is 50% transparent: rgba(89%, 63%, 75%, 50%) hex: #e3a1bf80
> color name m-fat 95,51,75,50
Color 'm-fat' is 50% transparent: rgba(95%, 51%, 75%, 50%) hex: #f282bf80
> color name m-fac 95,51,75,100
Color 'm-fac' is opaque: rgb(95%, 51%, 75%) hex: #f282bf
> color name m-postt 95,43,62,50
Color 'm-postt' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
executed 70S_colors.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colorstandard.cxc
> color 100,100,100,50
> color lsu silvert
> color /3 lightgrayt
> color /5 lightgrayt
> color ssu ssu-t
> color head head-t
> color efg efg-t
> color dt d-t
> color pt p-t
> color pep p-t
> color mrna m-t
executed 70S_colorstandard.cxc
> windowsize 1000 1000
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_helices.cxc
> color h18 h18-t
> color h23 h23-t
> color h24 h24-t
> color h28 h28-t
> color h29 h29-t
> color h30 h30-t
> color h31 h31-t
> color h34 h34-t
> color h35 h35-t
> color h36 h36-t
> color h44 h44-t
executed 70S_color_helices.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_helices.cxc
> color h18 h18-t
> color h23 h23-t
> color h24 h24-t
> color h28 h28-t
> color h29 h29-t
> color h30 h30-t
> color h31 h31-t
> color h34 h34-t
> color h35 h35-t
> color h36 h36-t
> color h44 h44-t
executed 70S_color_helices.cxc
> color h30|h36|h35 head-t
> color zone #12.1 near #12.3,5 distance 5
> color zone #13.1 near #13.3,5 distance 5
> color zone #14.1 near #14.3,5 distance 5
> color zone #30.1 near #30.3,5 distance 5
> color zone #31.1 near #31.3,5 distance 5
> color zone #32.1 near #32.3,5 distance 5
> color zone #33.1 near #33.3,5 distance 5
> color zone #34.1 near #34.3,5 distance 5
> color h30|h36|h35 head-c
> color h28 h28-c
> color h29 h29-c
> color h34 h34-c
> color h23 h23-c
> color h24 h24-c
> color h31 h31-c
> hide #!100
> hide #101 models
> cartoon style nucleic xsection oval width 1.3 thickness 1.3
> transparency #*.3 0 target abc
executed gtpys_helix.cxc
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/helix/gtpys_helix.cxs
——— End of log from Tue May 16 16:15:28 2023 ———
opened ChimeraX session
> hide models
> show #13.3,5 models
> ui mousemode right pivot
> color h69 hx69-t
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color H69 hx69-t
> ui tool show "Side View"
> view name dc1
> view name dc2
[Repeated 1 time(s)]
> show #13.1 models
> view name dc3
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
——— End of log from Tue May 16 16:53:33 2023 ———
opened ChimeraX session
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_assign.cxc
> name atomods #*.3,5,7
> name emmaps #*.1
> name lsu #*.5
> name ssu #*.3
> name rna /y,v,w,3,6,5
> name r23s /3
> name r16s /6
> name r5s /5
> name pt /y
> name dt /v
> name efg /x
> name pep /p
> name mrna /w
> name GSP :GSP
> name GDP :GDP
> name GTP :GTP
> name ntide :GTP|:GDP|:GSP
> name spc :SCM
> name fua :FUA
> name par :PAR
> name argb :LIG | #20.7/b
> name drugs argb|par|fua|spc
> name D1 /x:start-293
> name D2 /x:294-410
> name D3 /x:411-489
> name D4 /x:490-612
> name D5 /x:613-end
> name sw1 /x:38-65
> name sw2 /x:89-108
> name pl /x:18-25
> name nkxd /x:142-146
> name kirby #20.7
> name mg /x:MG
> name trna /y,v
> name anticodon /y,v:34-36
> name antiplus /y,v:32-38
> name cca /y,v:74-76
> name astem /y,v:1-7,66-73
> name darm /y,v:8-25
> name aarm /y,v:26-43
> name varm /y,v:44-48
> name tarm /y,v:49-65
> name head #*.3/A/C/S/M/G/N/I/J/6:927-1390
> name arg-head #20.3/A/C/S/M/G/N/I/J/6:927-1390
> name post-head #15.3/A/C/S/M/G/N/I/J/6:927-1390
> name fa-head #14.3/A/C/S/M/G/N/I/J/6:927-1390
> name body #*.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name arg-body #20.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name post-body #15.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name fa-body #14.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name h8 /6:144-178
> name h14 /6:339-350
> name h18 /6:511-540
> name h23 /6:674-716
> name h24 /6:769-810
> name h27 /6:894-905
> name h28 /6:921-937,1379-1400
> name h29 /6:938-943,1337-1346
> name h30 /6:945-955,1225-1235
> name h31 /6:956-975
> name h32 /6:984-990,1215-1221
> name h34 /6:1045-1065,1188-1211
> name h35 /6:1066-1073,1102-1110
> name h36 /6:1074-1083
> name h44 /6:1401-1502
> name h45 /6:1506-1529
> name aploop /6:956-959
> name term16S /6:1503-end
> name aphelix /6:1228-1230
> name us3 #*.3/C
> name us5 #*.3/E
> name us7 #*.3/G
> name us9 #*.3/I
> name us11 #*.3/K
> name us12 #*.3/L
> name us13 #*.3/M
> name us14 #*.3/N
> name us15 #*.3/O
> name us9-130 #*.3/I:130
> name l1stalk /3:2097-2191
> name srl /3:2652-2668
> name H68 /3:1832-1906
> name H69 /3:1907-1924
> name H95 /3:2647-2673
> name ul2 #*.5/B
> name ul5 #*.5/E
> name ul14 #*.5/N
> name ul19 #*.5/S
> name ul31 #*.5/e
executed 70S_assign.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_display.cxc
> alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6;
> alias nucribthin cartoon style nucleic xsect oval width 1.2 thick 1.2;
> alias cylinders cartoon style protein modeh tube rad 2 sides 24;
> alias licorice car style protein modeh default arrows f xsect oval width 1
> thick 1;
> dssp
> windowsize 1000 1000
> set bgColor white
> lighting full
> set silhouettes true
> set silhouetteWidth 1.7
> set silhouettes true
> set silhouetteDepthJump 0.02
> cartoon style width 2.5
> size atomRadius 2
Changed 1614330 atom radii
> nucleotides fill
> size ions atomRadius 1.6
Changed 31 atom radii
> size stickRadius 0.1
Changed 1744812 bond radii
> style stick ringFill thin
Changed 1614330 atom styles, 122200 residue ring styles
> show ribbons
> hide H
> hide :HOH
> hide target a
> show nucleic target a
> show drugs target a
> style drugs ball
Changed 106 atom styles
> nucrib
> graphics selection color black
> volume emmaps style surface step 1 level 4
> surface dust emmaps size 3
> volume surfaceSmoothing true
> cartoon tether trna shape cone opacity 1
> dssp
executed 70S_display.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colors.cxc
> color name efg-t 100,0,0,50
Color 'efg-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
> color name sw1-t 100,92,0,50
Color 'sw1-t' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
> color name sw2-t 68,81,0,50
Color 'sw2-t' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
> color name pl-t 23,59,0,50
Color 'pl-t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
> color name d1-t 100,18,4,50
Color 'd1-t' is 50% transparent: rgba(100%, 18%, 4%, 50%) hex: #ff2e0a80
> color name d2-t 100,40,4,50
Color 'd2-t' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
> color name d3-t 100,27,36,50
Color 'd3-t' is 50% transparent: rgba(100%, 27%, 36%, 50%) hex: #ff455c80
> color name d4-t 80,0,23,50
Color 'd4-t' is 50% transparent: rgba(80%, 0%, 23%, 50%) hex: #cc003b80
> color name d5-t 100,60,4,50
Color 'd5-t' is 50% transparent: rgba(100%, 60%, 4%, 50%) hex: #ff990a80
> color name fa-t 100,90,4,50
Color 'fa-t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
> color name gtp-t 45,53,60,50
Color 'gtp-t' is 50% transparent: rgba(45%, 53%, 60%, 50%) hex: #73879980
> color name mg-t 1,39,16,50
Color 'mg-t' is 50% transparent: rgba(1%, 39%, 16%, 50%) hex: #03632980
> color name spc-t 100,0,0,50
Color 'spc-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
> color name argb-t 50,0,50,50
Color 'argb-t' is 50% transparent: rgba(50%, 0%, 50%, 50%) hex: #80008080
> color name g-1t 98,42,30,50
Color 'g-1t' is 50% transparent: rgba(98%, 42%, 30%, 50%) hex: #fa6b4d80
> color name g-2t 95,35,25,50
Color 'g-2t' is 50% transparent: rgba(95%, 35%, 25%, 50%) hex: #f2594080
> color name g-3t 92,28,20,50
Color 'g-3t' is 50% transparent: rgba(92%, 28%, 20%, 50%) hex: #eb473380
> color name g-4t 89,21,15,50
Color 'g-4t' is 50% transparent: rgba(89%, 21%, 15%, 50%) hex: #e3362680
> color name g-5t 86,14,10,50
Color 'g-5t' is 50% transparent: rgba(86%, 14%, 10%, 50%) hex: #db241a80
> color name g-6t 83,7,5,50
Color 'g-6t' is 50% transparent: rgba(83%, 7%, 5%, 50%) hex: #d4120d80
> color name g-7t 80,0,0,50
Color 'g-7t' is 50% transparent: rgba(80%, 0%, 0%, 50%) hex: #cc000080
> color name p-t 40,60,2,50
Color 'p-t' is 50% transparent: rgba(40%, 60%, 2%, 50%) hex: #66990580
> color name p-c 40,60,2,100
Color 'p-c' is opaque: rgb(40%, 60%, 2%) hex: #669905
> color name p-1t 4,34,1,50
Color 'p-1t' is 50% transparent: rgba(4%, 34%, 1%, 50%) hex: #0a570380
> color name p-2t 12,39,1,50
Color 'p-2t' is 50% transparent: rgba(12%, 39%, 1%, 50%) hex: #1f630380
> color name p-3t 20,44,1,50
Color 'p-3t' is 50% transparent: rgba(20%, 44%, 1%, 50%) hex: #33700380
> color name p-4t 28,49,1,50
Color 'p-4t' is 50% transparent: rgba(28%, 49%, 1%, 50%) hex: #477d0380
> color name p-5t 36,54,2,50
Color 'p-5t' is 50% transparent: rgba(36%, 54%, 2%, 50%) hex: #5c8a0580
> color name p-6t 44,59,2,50
Color 'p-6t' is 50% transparent: rgba(44%, 59%, 2%, 50%) hex: #70960580
> color name p-7t 52,64,2,50
Color 'p-7t' is 50% transparent: rgba(52%, 64%, 2%, 50%) hex: #85a30580
> color name p-8t 60,69,2,50
Color 'p-8t' is 50% transparent: rgba(60%, 69%, 2%, 50%) hex: #99b00580
> color name p-9t 68,74,3,50
Color 'p-9t' is 50% transparent: rgba(68%, 74%, 3%, 50%) hex: #adbd0880
> color name p-10t 76,79,3,50
Color 'p-10t' is 50% transparent: rgba(76%, 79%, 3%, 50%) hex: #c2c90880
> color name p-11t 84,84,3,50
Color 'p-11t' is 50% transparent: rgba(84%, 84%, 3%, 50%) hex: #d6d60880
> color name d-t 100,75,4,50
Color 'd-t' is 50% transparent: rgba(100%, 75%, 4%, 50%) hex: #ffbf0a80
> color name d-c 100,75,4,100
Color 'd-c' is opaque: rgb(100%, 75%, 4%) hex: #ffbf0a
> color name d-1t 100,100,4,50
Color 'd-1t' is 50% transparent: rgba(100%, 100%, 4%, 50%) hex: #ffff0a80
> color name d-2t 100,93,4,50
Color 'd-2t' is 50% transparent: rgba(100%, 93%, 4%, 50%) hex: #ffed0a80
> color name d-3t 100,86,4,50
Color 'd-3t' is 50% transparent: rgba(100%, 86%, 4%, 50%) hex: #ffdb0a80
> color name d-4t 100,79,4,50
Color 'd-4t' is 50% transparent: rgba(100%, 79%, 4%, 50%) hex: #ffc90a80
> color name d-5t 100,72,4,50
Color 'd-5t' is 50% transparent: rgba(100%, 72%, 4%, 50%) hex: #ffb80a80
> color name d-6t 100,65,4,50
Color 'd-6t' is 50% transparent: rgba(100%, 65%, 4%, 50%) hex: #ffa60a80
> color name d-7t 100,58,4,50
Color 'd-7t' is 50% transparent: rgba(100%, 58%, 4%, 50%) hex: #ff940a80
> color name d-8t 100,51,4,50
Color 'd-8t' is 50% transparent: rgba(100%, 51%, 4%, 50%) hex: #ff820a80
> color name d-9t 100,44,4,50
Color 'd-9t' is 50% transparent: rgba(100%, 44%, 4%, 50%) hex: #ff700a80
> color name d-10t 100,37,4,50
Color 'd-10t' is 50% transparent: rgba(100%, 37%, 4%, 50%) hex: #ff5e0a80
> color name d-11t 100,30,4,50
Color 'd-11t' is 50% transparent: rgba(100%, 30%, 4%, 50%) hex: #ff4d0a80
> color name m-t 95,43,62,50
Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
> color name m-c 95,43,62,100
Color 'm-c' is opaque: rgb(95%, 43%, 62%) hex: #f26e9e
> color name m-1t 100,80,90,50
Color 'm-1t' is 50% transparent: rgba(100%, 80%, 90%, 50%) hex: #ffcce680
> color name m-2t 98,76,87,50
Color 'm-2t' is 50% transparent: rgba(98%, 76%, 87%, 50%) hex: #fac2de80
> color name m-3t 96,72,84,50
Color 'm-3t' is 50% transparent: rgba(96%, 72%, 84%, 50%) hex: #f5b8d680
> color name m-4t 94,68,81,50
Color 'm-4t' is 50% transparent: rgba(94%, 68%, 81%, 50%) hex: #f0adcf80
> color name m-5t 92,64,78,50
Color 'm-5t' is 50% transparent: rgba(92%, 64%, 78%, 50%) hex: #eba3c780
> color name m-6t 90,60,75,50
Color 'm-6t' is 50% transparent: rgba(90%, 60%, 75%, 50%) hex: #e699bf80
> color name m-7t 88,56,72,50
Color 'm-7t' is 50% transparent: rgba(88%, 56%, 72%, 50%) hex: #e08fb880
> color name m-8t 86,52,69,50
Color 'm-8t' is 50% transparent: rgba(86%, 52%, 69%, 50%) hex: #db85b080
> color name m-9t 84,48,66,50
Color 'm-9t' is 50% transparent: rgba(84%, 48%, 66%, 50%) hex: #d67aa880
> color name m-10t 82,44,63,50
Color 'm-10t' is 50% transparent: rgba(82%, 44%, 63%, 50%) hex: #d170a180
> color name m-11t 80,40,60,50
Color 'm-11t' is 50% transparent: rgba(80%, 40%, 60%, 50%) hex: #cc669980
> color name head-t 71,51,66,50
Color 'head-t' is 50% transparent: rgba(71%, 51%, 66%, 50%) hex: #b582a880
> color name head-c 89,89,100,100
Color 'head-c' is opaque: rgb(89%, 89%, 100%) hex: #e3e3ff
> color name headfa-t 80,79,100,50
Color 'headfa-t' is 50% transparent: rgba(80%, 79%, 100%, 50%) hex: #ccc9ff80
> color name headblue-t 59,78,94,50
Color 'headblue-t' is 50% transparent: rgba(59%, 78%, 94%, 50%) hex: #96c7f080
> color name headh1-t 41,64,100,50
Color 'headh1-t' is 50% transparent: rgba(41%, 64%, 100%, 50%) hex: #69a3ff80
> color name headh2-t 50,70,100,50
Color 'headh2-t' is 50% transparent: rgba(50%, 70%, 100%, 50%) hex: #80b3ff80
> color name headgray-t 60,60,60,50
Color 'headgray-t' is 50% transparent: rgba(60%, 60%, 60%, 50%) hex: #99999980
> color name darkhead-s 58,34,52,100
Color 'darkhead-s' is opaque: rgb(58%, 34%, 52%) hex: #945785
> color name bodywhite-t 90,90,90,50
Color 'bodywhite-t' is 50% transparent: rgba(90%, 90%, 90%, 50%) hex:
#e6e6e680
> color name rps-t 75,88,93,50
Color 'rps-t' is 50% transparent: rgba(75%, 88%, 93%, 50%) hex: #bfe0ed80
> color name ssu-t 57,71,75,50
Color 'ssu-t' is 50% transparent: rgba(57%, 71%, 75%, 50%) hex: #91b5bf80
> color name h18-t 31,59,68,50
Color 'h18-t' is 50% transparent: rgba(31%, 59%, 68%, 50%) hex: #4f96ad80
> color name h18-c 31,59,68,100
Color 'h18-c' is opaque: rgb(31%, 59%, 68%) hex: #4f96ad
> color name h23-t 18,36,100,50
Color 'h23-t' is 50% transparent: rgba(18%, 36%, 100%, 50%) hex: #2e5cff80
> color name h23-c 18,36,100,100
Color 'h23-c' is opaque: rgb(18%, 36%, 100%) hex: #2e5cff
> color name h24-t 50,70,90,50
Color 'h24-t' is 50% transparent: rgba(50%, 70%, 90%, 50%) hex: #80b3e680
> color name h24-c 50,70,90,100
Color 'h24-c' is opaque: rgb(50%, 70%, 90%) hex: #80b3e6
> color name h28-t 0,24,57,50
Color 'h28-t' is 50% transparent: rgba(0%, 24%, 57%, 50%) hex: #003d9180
> color name h28-c 0,24,57,100
Color 'h28-c' is opaque: rgb(0%, 24%, 57%) hex: #003d91
> color name h29-t 80,69,92,50
Color 'h29-t' is 50% transparent: rgba(80%, 69%, 92%, 50%) hex: #ccb0eb80
> color name h29-c 80,69,92,100
Color 'h29-c' is opaque: rgb(80%, 69%, 92%) hex: #ccb0eb
> color name h30-t 40,40,59,50
Color 'h30-t' is 50% transparent: rgba(40%, 40%, 59%, 50%) hex: #66669680
> color name h30-c 40,40,59,100
Color 'h30-c' is opaque: rgb(40%, 40%, 59%) hex: #666696
> color name h31-t 45,18,59,50
Color 'h31-t' is 50% transparent: rgba(45%, 18%, 59%, 50%) hex: #732e9680
> color name h31-c 45,18,59,100
Color 'h31-c' is opaque: rgb(45%, 18%, 59%) hex: #732e96
> color name h34-t 59,18,59,50
Color 'h34-t' is 50% transparent: rgba(59%, 18%, 59%, 50%) hex: #962e9680
> color name h34-c 59,18,59,100
Color 'h34-c' is opaque: rgb(59%, 18%, 59%) hex: #962e96
> color name h35-t 50,22,45,50
Color 'h35-t' is 50% transparent: rgba(50%, 22%, 45%, 50%) hex: #80387380
> color name h35-c 50,22,45,100
Color 'h35-c' is opaque: rgb(50%, 22%, 45%) hex: #803873
> color name h44-t 27,50,80,50
Color 'h44-t' is 50% transparent: rgba(27%, 50%, 80%, 50%) hex: #4580cc80
> color name h44-c 27,50,80,100
Color 'h44-c' is opaque: rgb(27%, 50%, 80%) hex: #4580cc
> color name aploop-t 27,0,50,50
Color 'aploop-t' is 50% transparent: rgba(27%, 0%, 50%, 50%) hex: #45008080
> color name term16-t 40,64,64,50
Color 'term16-t' is 50% transparent: rgba(40%, 64%, 64%, 50%) hex: #66a3a380
> color name uS3-t 64,41,82,50
Color 'uS3-t' is 50% transparent: rgba(64%, 41%, 82%, 50%) hex: #a369d180
> color name uS5-t 0,50,45,50
Color 'uS5-t' is 50% transparent: rgba(0%, 50%, 45%, 50%) hex: #00807380
> color name gray-t 70,70,70,50
Color 'gray-t' is 50% transparent: rgba(70%, 70%, 70%, 50%) hex: #b3b3b380
> color name hx68-t 50,50,50,50
Color 'hx68-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name hx68-c 50,50,50,100
Color 'hx68-c' is opaque: gray(50%) hex: #808080
> color name hx69-t 40,40,40,50
Color 'hx69-t' is 50% transparent: rgba(40%, 40%, 40%, 50%) hex: #66666680
> color name hx69-c 40,40,40,100
Color 'hx69-c' is opaque: gray(40%) hex: #666666
> color name srl-t 50,50,50,50
Color 'srl-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name srl-t 50,50,50,100
Color 'srl-t' is opaque: gray(50%) hex: #808080
> color name lightgrayt 83,83,83,50
Color 'lightgrayt' is 50% transparent: rgba(83%, 83%, 83%, 50%) hex: #d4d4d480
> color name silvert 75,75,75,50
Color 'silvert' is 50% transparent: rgba(75%, 75%, 75%, 50%) hex: #bfbfbf80
> color name grayt 50,50,50,50
Color 'grayt' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name lightcyant 88,100,100,50
Color 'lightcyant' is 50% transparent: rgba(88%, 100%, 100%, 50%) hex:
#e0ffff80
> color name yellowt 100,90,0,50
Color 'yellowt' is 50% transparent: rgba(100%, 90%, 0%, 50%) hex: #ffe60080
> color name deeppinkt 100,8,58,50
Color 'deeppinkt' is 50% transparent: rgba(100%, 8%, 58%, 50%) hex: #ff149480
> color name oranget 100,65,0,50
Color 'oranget' is 50% transparent: rgba(100%, 65%, 0%, 50%) hex: #ffa60080
> color name yellowgreent 60,80,20,50
Color 'yellowgreent' is 50% transparent: rgba(60%, 80%, 20%, 50%) hex:
#99cc3380
> color name darkmagentat 54,0,54,50
Color 'darkmagentat' is 50% transparent: rgba(54%, 0%, 54%, 50%) hex:
#8a008a80
> color name orchidt 86,44,84,50
Color 'orchidt' is 50% transparent: rgba(86%, 44%, 84%, 50%) hex: #db70d680
> color name paleturquoiset 69,93,93,50
Color 'paleturquoiset' is 50% transparent: rgba(69%, 93%, 93%, 50%) hex:
#b0eded80
> color name pinkt 100,75,80,50
Color 'pinkt' is 50% transparent: rgba(100%, 75%, 80%, 50%) hex: #ffbfcc80
> color name darkgreent 0,39,0,50
Color 'darkgreent' is 50% transparent: rgba(0%, 39%, 0%, 50%) hex: #00630080
> color name limegreent 20,80,20,50
Color 'limegreent' is 50% transparent: rgba(20%, 80%, 20%, 50%) hex: #33cc3380
> color name turquoiset 25,88,82,50
Color 'turquoiset' is 50% transparent: rgba(25%, 88%, 82%, 50%) hex: #40e0d180
> color name tealt 0,50,50,50
Color 'tealt' is 50% transparent: rgba(0%, 50%, 50%, 50%) hex: #00808080
> color name darkoranget 100,50,0,50
Color 'darkoranget' is 50% transparent: rgba(100%, 50%, 0%, 50%) hex:
#ff800080
> color name lightyellowt 100,100,50,50
Color 'lightyellowt' is 50% transparent: rgba(100%, 100%, 50%, 50%) hex:
#ffff8080
> color name goldt 100,75,0,50
Color 'goldt' is 50% transparent: rgba(100%, 75%, 0%, 50%) hex: #ffbf0080
> color name plumt 87,63,87,50
Color 'plumt' is 50% transparent: rgba(87%, 63%, 87%, 50%) hex: #dea1de80
> color name ssubluet 68,86,90,50
Color 'ssubluet' is 50% transparent: rgba(68%, 86%, 90%, 50%) hex: #addbe680
> color name p-prect 10,41,0,50
Color 'p-prect' is 50% transparent: rgba(10%, 41%, 0%, 50%) hex: #1a690080
> color name p-h2t 23,59,0,50
Color 'p-h2t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
> color name p-h1t 40,73,0,50
Color 'p-h1t' is 50% transparent: rgba(40%, 73%, 0%, 50%) hex: #66ba0080
> color name p-h1c 40,73,0,100
Color 'p-h1c' is opaque: rgb(40%, 73%, 0%) hex: #66ba00
> color name p-spct 68,81,0,50
Color 'p-spct' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
> color name p-spcc 68,81,0,100
Color 'p-spcc' is opaque: rgb(68%, 81%, 0%) hex: #adcf00
> color name p-fat 82,92,0,50
Color 'p-fat' is 50% transparent: rgba(82%, 92%, 0%, 50%) hex: #d1eb0080
> color name p-postt 100,92,0,50
Color 'p-postt' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
> color name d-t 100,80,4,50
Color 'd-t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
> color name d-prect 95,100,50,50
Color 'd-prect' is 50% transparent: rgba(95%, 100%, 50%, 50%) hex: #f2ff8080
> color name d-h2t 100,90,4,50
Color 'd-h2t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
> color name d-h1t 100,80,4,50
Color 'd-h1t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
> color name d-spct 100,70,4,50
Color 'd-spct' is 50% transparent: rgba(100%, 70%, 4%, 50%) hex: #ffb30a80
> color name d-fat 100,55,4,50
Color 'd-fat' is 50% transparent: rgba(100%, 55%, 4%, 50%) hex: #ff8c0a80
> color name d-fac 100,55,4,100
Color 'd-fac' is opaque: rgb(100%, 55%, 4%) hex: #ff8c0a
> color name d-postt 100,40,4,50
Color 'd-postt' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
> color name m-t 95,43,62,50
Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
> color name m-prect 100,85,95,50
Color 'm-prect' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex: #ffd9f280
> color name m-h2t 100,85,95,50
Color 'm-h2t' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex: #ffd9f280
> color name m-h1t 100,75,95,50
Color 'm-h1t' is 50% transparent: rgba(100%, 75%, 95%, 50%) hex: #ffbff280
> color name m-spct 89,63,75,50
Color 'm-spct' is 50% transparent: rgba(89%, 63%, 75%, 50%) hex: #e3a1bf80
> color name m-fat 95,51,75,50
Color 'm-fat' is 50% transparent: rgba(95%, 51%, 75%, 50%) hex: #f282bf80
> color name m-fac 95,51,75,100
Color 'm-fac' is opaque: rgb(95%, 51%, 75%) hex: #f282bf
> color name m-postt 95,43,62,50
Color 'm-postt' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
executed 70S_colors.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colorstandard.cxc
> color 100,100,100,50
> color lsu silvert
> color /3 lightgrayt
> color /5 lightgrayt
> color ssu ssu-t
> color head head-t
> color efg efg-t
> color dt d-t
> color pt p-t
> color pep p-t
> color mrna m-t
executed 70S_colorstandard.cxc
> windowsize 1000 1000
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_helices.cxc
> color h18 h18-t
> color h23 h23-t
> color h24 h24-t
> color h28 h28-t
> color h29 h29-t
> color h30 h30-t
> color h31 h31-t
> color h34 h34-t
> color h35 h35-t
> color h36 h36-t
> color h44 h44-t
> color H69 hx69-t
executed 70S_color_helices.cxc
> color h30|h36|h35 head-t
> view dc3
> surface cap true
> color zone #12.1 near #12.3,5 distance 5
> color zone #13.1 near #13.3,5 distance 5
> color zone #14.1 near #14.3,5 distance 5
> color zone #30.1 near #30.3,5 distance 5
> color zone #31.1 near #31.3,5 distance 5
> color zone #32.1 near #32.3,5 distance 5
> color zone #33.1 near #33.3,5 distance 5
> color zone #34.1 near #34.3,5 distance 5
> color h30|h36|h35 head-c
> color h28 h28-c
> color h29 h29-c
> color h34 h34-c
> color h23 h23-c
> color h24 h24-c
> color h31 h31-c
> hide #!100
> hide #101 models
> cartoon style nucleic xsection oval width 1.3 thickness 1.3
> transparency #*.3 0 target abc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_helices-s.cxc
> color h18 h18-c
> color h23 h23-c
> color h24 h24-c
[had to delete some of the log to fit within ticket length limits]
> name H79 #*.5/3:2200-2223
> name H80 #*.5/3:2246-2258
> name H81 #*.5/3:2259-2281
> name H82 #*.5/3:2284-2285|#*.5/3:2383-2384
> name H83 #*.5/3:2288-2295|#*.5/3:2337-2344
> name H84 #*.5/3:2296-2322
> name H85 #*.5/3:2323-2332
> name H86 #*.5/3:2347-2370
> name H87 #*.5/3:2372-2381
> name H88 #*.5/3:2395-2421
> name H89 #*.5/3:2453-2498
> name H90 #*.5/3:2507-2517|#*.5/3:2567-2582
> name H91 #*.5/3:2520-2545
> name H92 #*.5/3:2547-2561
> name H93 #*.5/3:2588-2606
> name H94 #*.5/3:2630-2643|#*.5/3:2771-2788
> name H95 #*.5/3:2646-2674
> name H96 #*.5/3:2675-2732
> name H97 #*.5/3:2735-2769
> name H98 #*.5/3:2791-2805
> name H99 #*.5/3:2811-2814|#*.5/3:2886-2889
> name H100 #*.5/3:2815-2831
executed 70S_assign.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_display.cxc
> alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6;
> alias nucribthin cartoon style nucleic xsect oval width 1.2 thick 1.2;
> alias cylinders cartoon style protein modeh tube rad 2 sides 24;
> alias licorice car style protein modeh default arrows f xsect oval width 1
> thick 1;
> dssp
> windowsize 1000 1000
> set bgColor white
> lighting full
> set silhouettes true
> set silhouetteWidth 1.7
> set silhouettes true
> set silhouetteDepthJump 0.02
> cartoon style width 2.5
> size atomRadius 2
Changed 1614330 atom radii
> nucleotides fill
> size ions atomRadius 1.6
Changed 31 atom radii
> size stickRadius 0.1
Changed 1744812 bond radii
> style stick ringFill thin
Changed 1614330 atom styles, 122200 residue ring styles
> show ribbons
> hide H
> hide :HOH
> hide target a
> show nucleic target a
> show drugs target a
> style drugs ball
Changed 106 atom styles
> graphics selection color black
> cartoon style protein xsection round width 2 thickness 0.6
> cartoon style modeHelix wrap
> cartoon style sides 24
> cartoon style strand xsection oval arrows false
> cartoon suppressBackboneDisplay true
> alias thinbois style ball;size ballscale 0.09; size stickradius 0.13;
> alias thickbois style stick;size stickradius 0.4;style stick ringFill thick;
> volume emmaps style surface step 1 level 4
> surface dust emmaps size 3
> volume surfaceSmoothing true
> cartoon tether trna shape cone opacity 1
> dssp
> thickbois
Changed 1614330 atom styles
Changed 1744812 bond radii
Changed 1614330 atom styles, 122200 residue ring styles
executed 70S_display.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colors.cxc
> color name efg-t 100,0,0,50
Color 'efg-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
> color name sw1-t 100,92,0,50
Color 'sw1-t' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
> color name sw2-t 68,81,0,50
Color 'sw2-t' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
> color name pl-t 23,59,0,50
Color 'pl-t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
> color name d1-t 100,18,4,50
Color 'd1-t' is 50% transparent: rgba(100%, 18%, 4%, 50%) hex: #ff2e0a80
> color name d2-t 100,40,4,50
Color 'd2-t' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
> color name d3-t 100,27,36,50
Color 'd3-t' is 50% transparent: rgba(100%, 27%, 36%, 50%) hex: #ff455c80
> color name d4-t 80,0,23,50
Color 'd4-t' is 50% transparent: rgba(80%, 0%, 23%, 50%) hex: #cc003b80
> color name d5-t 100,60,4,50
Color 'd5-t' is 50% transparent: rgba(100%, 60%, 4%, 50%) hex: #ff990a80
> color name fa-t 100,90,4,50
Color 'fa-t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
> color name gtp-t 45,53,60,50
Color 'gtp-t' is 50% transparent: rgba(45%, 53%, 60%, 50%) hex: #73879980
> color name mg-t 1,39,16,50
Color 'mg-t' is 50% transparent: rgba(1%, 39%, 16%, 50%) hex: #03632980
> color name spc-t 100,0,0,50
Color 'spc-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
> color name argb-t 50,0,50,50
Color 'argb-t' is 50% transparent: rgba(50%, 0%, 50%, 50%) hex: #80008080
> color name g-1t 98,42,30,50
Color 'g-1t' is 50% transparent: rgba(98%, 42%, 30%, 50%) hex: #fa6b4d80
> color name g-2t 95,35,25,50
Color 'g-2t' is 50% transparent: rgba(95%, 35%, 25%, 50%) hex: #f2594080
> color name g-3t 92,28,20,50
Color 'g-3t' is 50% transparent: rgba(92%, 28%, 20%, 50%) hex: #eb473380
> color name g-4t 89,21,15,50
Color 'g-4t' is 50% transparent: rgba(89%, 21%, 15%, 50%) hex: #e3362680
> color name g-5t 86,14,10,50
Color 'g-5t' is 50% transparent: rgba(86%, 14%, 10%, 50%) hex: #db241a80
> color name g-6t 83,7,5,50
Color 'g-6t' is 50% transparent: rgba(83%, 7%, 5%, 50%) hex: #d4120d80
> color name g-7t 80,0,0,50
Color 'g-7t' is 50% transparent: rgba(80%, 0%, 0%, 50%) hex: #cc000080
> color name p-t 44,59,2,50
Color 'p-t' is 50% transparent: rgba(44%, 59%, 2%, 50%) hex: #70960580
> color name p-c 44,59,2,100
Color 'p-c' is opaque: rgb(44%, 59%, 2%) hex: #709605
> color name p-1t 4,34,1,50
Color 'p-1t' is 50% transparent: rgba(4%, 34%, 1%, 50%) hex: #0a570380
> color name p-2t 12,39,1,50
Color 'p-2t' is 50% transparent: rgba(12%, 39%, 1%, 50%) hex: #1f630380
> color name p-3t 20,44,1,50
Color 'p-3t' is 50% transparent: rgba(20%, 44%, 1%, 50%) hex: #33700380
> color name p-4t 28,49,1,50
Color 'p-4t' is 50% transparent: rgba(28%, 49%, 1%, 50%) hex: #477d0380
> color name p-5t 36,54,2,50
Color 'p-5t' is 50% transparent: rgba(36%, 54%, 2%, 50%) hex: #5c8a0580
> color name p-6t 44,59,2,50
Color 'p-6t' is 50% transparent: rgba(44%, 59%, 2%, 50%) hex: #70960580
> color name p-7t 52,64,2,50
Color 'p-7t' is 50% transparent: rgba(52%, 64%, 2%, 50%) hex: #85a30580
> color name p-8t 60,69,2,50
Color 'p-8t' is 50% transparent: rgba(60%, 69%, 2%, 50%) hex: #99b00580
> color name p-9t 68,74,3,50
Color 'p-9t' is 50% transparent: rgba(68%, 74%, 3%, 50%) hex: #adbd0880
> color name p-10t 76,79,3,50
Color 'p-10t' is 50% transparent: rgba(76%, 79%, 3%, 50%) hex: #c2c90880
> color name p-11t 84,84,3,50
Color 'p-11t' is 50% transparent: rgba(84%, 84%, 3%, 50%) hex: #d6d60880
> color name d-t 100,65,4,50
Color 'd-t' is 50% transparent: rgba(100%, 65%, 4%, 50%) hex: #ffa60a80
> color name d-c 100,65,4,100
Color 'd-c' is opaque: rgb(100%, 65%, 4%) hex: #ffa60a
> color name d-1t 100,100,4,50
Color 'd-1t' is 50% transparent: rgba(100%, 100%, 4%, 50%) hex: #ffff0a80
> color name d-2t 100,93,4,50
Color 'd-2t' is 50% transparent: rgba(100%, 93%, 4%, 50%) hex: #ffed0a80
> color name d-3t 100,86,4,50
Color 'd-3t' is 50% transparent: rgba(100%, 86%, 4%, 50%) hex: #ffdb0a80
> color name d-4t 100,79,4,50
Color 'd-4t' is 50% transparent: rgba(100%, 79%, 4%, 50%) hex: #ffc90a80
> color name d-5t 100,72,4,50
Color 'd-5t' is 50% transparent: rgba(100%, 72%, 4%, 50%) hex: #ffb80a80
> color name d-6t 100,65,4,50
Color 'd-6t' is 50% transparent: rgba(100%, 65%, 4%, 50%) hex: #ffa60a80
> color name d-7t 100,58,4,50
Color 'd-7t' is 50% transparent: rgba(100%, 58%, 4%, 50%) hex: #ff940a80
> color name d-8t 100,51,4,50
Color 'd-8t' is 50% transparent: rgba(100%, 51%, 4%, 50%) hex: #ff820a80
> color name d-9t 100,44,4,50
Color 'd-9t' is 50% transparent: rgba(100%, 44%, 4%, 50%) hex: #ff700a80
> color name d-10t 100,37,4,50
Color 'd-10t' is 50% transparent: rgba(100%, 37%, 4%, 50%) hex: #ff5e0a80
> color name d-11t 100,30,4,50
Color 'd-11t' is 50% transparent: rgba(100%, 30%, 4%, 50%) hex: #ff4d0a80
> color name m-t 95,43,62,50
Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
> color name m-c 95,43,62,100
Color 'm-c' is opaque: rgb(95%, 43%, 62%) hex: #f26e9e
> color name m-1t 100,80,90,50
Color 'm-1t' is 50% transparent: rgba(100%, 80%, 90%, 50%) hex: #ffcce680
> color name m-2t 98,76,87,50
Color 'm-2t' is 50% transparent: rgba(98%, 76%, 87%, 50%) hex: #fac2de80
> color name m-3t 96,72,84,50
Color 'm-3t' is 50% transparent: rgba(96%, 72%, 84%, 50%) hex: #f5b8d680
> color name m-4t 94,68,81,50
Color 'm-4t' is 50% transparent: rgba(94%, 68%, 81%, 50%) hex: #f0adcf80
> color name m-5t 92,64,78,50
Color 'm-5t' is 50% transparent: rgba(92%, 64%, 78%, 50%) hex: #eba3c780
> color name m-6t 90,60,75,50
Color 'm-6t' is 50% transparent: rgba(90%, 60%, 75%, 50%) hex: #e699bf80
> color name m-7t 88,56,72,50
Color 'm-7t' is 50% transparent: rgba(88%, 56%, 72%, 50%) hex: #e08fb880
> color name m-8t 86,52,69,50
Color 'm-8t' is 50% transparent: rgba(86%, 52%, 69%, 50%) hex: #db85b080
> color name m-9t 84,48,66,50
Color 'm-9t' is 50% transparent: rgba(84%, 48%, 66%, 50%) hex: #d67aa880
> color name m-10t 82,44,63,50
Color 'm-10t' is 50% transparent: rgba(82%, 44%, 63%, 50%) hex: #d170a180
> color name m-11t 80,40,60,50
Color 'm-11t' is 50% transparent: rgba(80%, 40%, 60%, 50%) hex: #cc669980
> color name head-t 82,74,84,50
Color 'head-t' is 50% transparent: rgba(82%, 74%, 84%, 50%) hex: #d1bdd680
> color name head-c 82,74,84,100
Color 'head-c' is opaque: rgb(82%, 74%, 84%) hex: #d1bdd6
> color name headfa-t 54,41,54,50
Color 'headfa-t' is 50% transparent: rgba(54%, 41%, 54%, 50%) hex: #8a698a80
> color name headblue-t 59,78,94,50
Color 'headblue-t' is 50% transparent: rgba(59%, 78%, 94%, 50%) hex: #96c7f080
> color name headh1-t 41,64,100,50
Color 'headh1-t' is 50% transparent: rgba(41%, 64%, 100%, 50%) hex: #69a3ff80
> color name headh2-t 50,70,100,50
Color 'headh2-t' is 50% transparent: rgba(50%, 70%, 100%, 50%) hex: #80b3ff80
> color name headgray-t 60,60,60,50
Color 'headgray-t' is 50% transparent: rgba(60%, 60%, 60%, 50%) hex: #99999980
> color name darkhead-s 54,41,54,100
Color 'darkhead-s' is opaque: rgb(54%, 41%, 54%) hex: #8a698a
> color name bodywhite-t 90,90,90,50
Color 'bodywhite-t' is 50% transparent: rgba(90%, 90%, 90%, 50%) hex:
#e6e6e680
> color name rps-t 75,88,93,50
Color 'rps-t' is 50% transparent: rgba(75%, 88%, 93%, 50%) hex: #bfe0ed80
> color name ssu-t 69,79,82,50
Color 'ssu-t' is 50% transparent: rgba(69%, 79%, 82%, 50%) hex: #b0c9d180
> color name ssu-c 69,79,82,100
Color 'ssu-c' is opaque: rgb(69%, 79%, 82%) hex: #b0c9d1
> color name h16-t 79,85,89,50
Color 'h16-t' is 50% transparent: rgba(79%, 85%, 89%, 50%) hex: #c9d9e380
> color name h16-c 79,85,89,100
Color 'h16-c' is opaque: rgb(79%, 85%, 89%) hex: #c9d9e3
> color name h18-t 31,59,68,50
Color 'h18-t' is 50% transparent: rgba(31%, 59%, 68%, 50%) hex: #4f96ad80
> color name h18-dt 6,47,62,50
Color 'h18-dt' is 50% transparent: rgba(6%, 47%, 62%, 50%) hex: #0f789e80
> color name h18-dc 6,47,62,100
Color 'h18-dc' is opaque: rgb(6%, 47%, 62%) hex: #0f789e
> color name h18-c 31,59,68,100
Color 'h18-c' is opaque: rgb(31%, 59%, 68%) hex: #4f96ad
> color name h23-t 40,61,80,50
Color 'h23-t' is 50% transparent: rgba(40%, 61%, 80%, 50%) hex: #669ccc80
> color name h23-c 40,61,80,100
Color 'h23-c' is opaque: rgb(40%, 61%, 80%) hex: #669ccc
> color name h24-t 50,70,90,50
Color 'h24-t' is 50% transparent: rgba(50%, 70%, 90%, 50%) hex: #80b3e680
> color name h24-c 50,70,90,100
Color 'h24-c' is opaque: rgb(50%, 70%, 90%) hex: #80b3e6
> color name h28-t 21,27,56,50
Color 'h28-t' is 50% transparent: rgba(21%, 27%, 56%, 50%) hex: #36458f80
> color name h28-c 21,27,56,100
Color 'h28-c' is opaque: rgb(21%, 27%, 56%) hex: #36458f
> color name h29-t 80,69,92,50
Color 'h29-t' is 50% transparent: rgba(80%, 69%, 92%, 50%) hex: #ccb0eb80
> color name h29-c 80,69,92,100
Color 'h29-c' is opaque: rgb(80%, 69%, 92%) hex: #ccb0eb
> color name h30-t 40,40,59,50
Color 'h30-t' is 50% transparent: rgba(40%, 40%, 59%, 50%) hex: #66669680
> color name h30-c 40,40,59,100
Color 'h30-c' is opaque: rgb(40%, 40%, 59%) hex: #666696
> color name h31-t 45,35,55,50
Color 'h31-t' is 50% transparent: rgba(45%, 35%, 55%, 50%) hex: #73598c80
> color name h31-c 45,35,55,100
Color 'h31-c' is opaque: rgb(45%, 35%, 55%) hex: #73598c
> color name h32-t 75,62,79,50
Color 'h32-t' is 50% transparent: rgba(75%, 62%, 79%, 50%) hex: #bf9ec980
> color name h32-c 75,62,79,100
Color 'h32-c' is opaque: rgb(75%, 62%, 79%) hex: #bf9ec9
> color name h33-t 88,82,90,50
Color 'h33-t' is 50% transparent: rgba(88%, 82%, 90%, 50%) hex: #e0d1e680
> color name h33-c 88,82,90,100
Color 'h33-c' is opaque: rgb(88%, 82%, 90%) hex: #e0d1e6
> color name h34-t 59,35,59,50
Color 'h34-t' is 50% transparent: rgba(59%, 35%, 59%, 50%) hex: #96599680
> color name h34-c 59,35,59,100
Color 'h34-c' is opaque: rgb(59%, 35%, 59%) hex: #965996
> color name h35-t 50,22,45,50
Color 'h35-t' is 50% transparent: rgba(50%, 22%, 45%, 50%) hex: #80387380
> color name h35-c 50,22,45,100
Color 'h35-c' is opaque: rgb(50%, 22%, 45%) hex: #803873
> color name h44-t 32,54,70,50
Color 'h44-t' is 50% transparent: rgba(32%, 54%, 70%, 50%) hex: #528ab380
> color name h44-c 32,54,70,100
Color 'h44-c' is opaque: rgb(32%, 54%, 70%) hex: #528ab3
> color name aploop-t 27,0,50,50
Color 'aploop-t' is 50% transparent: rgba(27%, 0%, 50%, 50%) hex: #45008080
> color name term16-t 40,64,64,50
Color 'term16-t' is 50% transparent: rgba(40%, 64%, 64%, 50%) hex: #66a3a380
> color name uS3-t 48,44,57,50
Color 'uS3-t' is 50% transparent: rgba(48%, 44%, 57%, 50%) hex: #7a709180
> color name uS3-c 48,44,57,100
Color 'uS3-c' is opaque: rgb(48%, 44%, 57%) hex: #7a7091
> color name uS3-dt 40,37,57,50
Color 'uS3-dt' is 50% transparent: rgba(40%, 37%, 57%, 50%) hex: #665e9180
> color name uS3-dc 40,37,57,100
Color 'uS3-dc' is opaque: rgb(40%, 37%, 57%) hex: #665e91
> color name uS5-t 0,50,45,50
Color 'uS5-t' is 50% transparent: rgba(0%, 50%, 45%, 50%) hex: #00807380
> color name gray-t 70,70,70,50
Color 'gray-t' is 50% transparent: rgba(70%, 70%, 70%, 50%) hex: #b3b3b380
> color name hx84-t 50,50,50,50
Color 'hx84-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name hx84-c 50,50,50,100
Color 'hx84-c' is opaque: gray(50%) hex: #808080
> color name hx84-dt 30,30,30,50
Color 'hx84-dt' is 50% transparent: rgba(30%, 30%, 30%, 50%) hex: #4d4d4d80
> color name hx84-dc 30,30,30,100
Color 'hx84-dc' is opaque: gray(30%) hex: #4d4d4d
> color name hx68-t 50,50,50,50
Color 'hx68-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name hx68-c 50,50,50,100
Color 'hx68-c' is opaque: gray(50%) hex: #808080
> color name hx69-t 40,40,40,50
Color 'hx69-t' is 50% transparent: rgba(40%, 40%, 40%, 50%) hex: #66666680
> color name hx69-c 40,40,40,100
Color 'hx69-c' is opaque: gray(40%) hex: #666666
> color name hx38-t 34,42,36,50
Color 'hx38-t' is 50% transparent: rgba(34%, 42%, 36%, 50%) hex: #576b5c80
> color name hx38-c 34,42,36,100
Color 'hx38-c' is opaque: rgb(34%, 42%, 36%) hex: #576b5c
> color name hx38-dt 34,42,36,50
Color 'hx38-dt' is 50% transparent: rgba(34%, 42%, 36%, 50%) hex: #576b5c80
> color name hx38-dc 34,42,36,100
Color 'hx38-dc' is opaque: rgb(34%, 42%, 36%) hex: #576b5c
> color name ul5-t 55,62,67,50
Color 'ul5-t' is 50% transparent: rgba(55%, 62%, 67%, 50%) hex: #8c9eab80
> color name ul5-c 55,62,67,100
Color 'ul5-c' is opaque: rgb(55%, 62%, 67%) hex: #8c9eab
> color name ul5-dt 38,47,52,50
Color 'ul5-dt' is 50% transparent: rgba(38%, 47%, 52%, 50%) hex: #61788580
> color name ul5-dc 38,47,52,100
Color 'ul5-dc' is opaque: rgb(38%, 47%, 52%) hex: #617885
> color name ul16-t 70,70,70,50
Color 'ul16-t' is 50% transparent: rgba(70%, 70%, 70%, 50%) hex: #b3b3b380
> color name ul16-c 70,70,70,100
Color 'ul16-c' is opaque: gray(70%) hex: #b3b3b3
> color name srl-t 50,50,50,50
Color 'srl-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name srl-t 50,50,50,100
Color 'srl-t' is opaque: gray(50%) hex: #808080
> color name highlight-t 92,78,8,50
Color 'highlight-t' is 50% transparent: rgba(92%, 78%, 8%, 50%) hex: #ebc71480
> color name highlight-c 92,78,8,100
Color 'highlight-c' is opaque: rgb(92%, 78%, 8%) hex: #ebc714
> color name tomato-t 100,39,28,50
Color 'tomato-t' is 50% transparent: rgba(100%, 39%, 28%, 50%) hex: #ff634780
> color name tomato-c 100,39,28,100
Color 'tomato-c' is opaque: rgb(100%, 39%, 28%) hex: #ff6347
> color name lightgrayt 83,83,83,50
Color 'lightgrayt' is 50% transparent: rgba(83%, 83%, 83%, 50%) hex: #d4d4d480
> color name silvert 75,75,75,50
Color 'silvert' is 50% transparent: rgba(75%, 75%, 75%, 50%) hex: #bfbfbf80
> color name grayt 50,50,50,50
Color 'grayt' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name lightcyant 88,100,100,50
Color 'lightcyant' is 50% transparent: rgba(88%, 100%, 100%, 50%) hex:
#e0ffff80
> color name yellowt 100,90,0,50
Color 'yellowt' is 50% transparent: rgba(100%, 90%, 0%, 50%) hex: #ffe60080
> color name deeppinkt 100,8,58,50
Color 'deeppinkt' is 50% transparent: rgba(100%, 8%, 58%, 50%) hex: #ff149480
> color name oranget 100,65,0,50
Color 'oranget' is 50% transparent: rgba(100%, 65%, 0%, 50%) hex: #ffa60080
> color name yellowgreent 60,80,20,50
Color 'yellowgreent' is 50% transparent: rgba(60%, 80%, 20%, 50%) hex:
#99cc3380
> color name darkmagentat 54,0,54,50
Color 'darkmagentat' is 50% transparent: rgba(54%, 0%, 54%, 50%) hex:
#8a008a80
> color name orchidt 86,44,84,50
Color 'orchidt' is 50% transparent: rgba(86%, 44%, 84%, 50%) hex: #db70d680
> color name paleturquoiset 69,93,93,50
Color 'paleturquoiset' is 50% transparent: rgba(69%, 93%, 93%, 50%) hex:
#b0eded80
> color name pinkt 100,75,80,50
Color 'pinkt' is 50% transparent: rgba(100%, 75%, 80%, 50%) hex: #ffbfcc80
> color name darkgreent 0,39,0,50
Color 'darkgreent' is 50% transparent: rgba(0%, 39%, 0%, 50%) hex: #00630080
> color name limegreent 20,80,20,50
Color 'limegreent' is 50% transparent: rgba(20%, 80%, 20%, 50%) hex: #33cc3380
> color name turquoiset 25,88,82,50
Color 'turquoiset' is 50% transparent: rgba(25%, 88%, 82%, 50%) hex: #40e0d180
> color name tealt 0,50,50,50
Color 'tealt' is 50% transparent: rgba(0%, 50%, 50%, 50%) hex: #00808080
> color name darkoranget 100,50,0,50
Color 'darkoranget' is 50% transparent: rgba(100%, 50%, 0%, 50%) hex:
#ff800080
> color name lightyellowt 100,100,50,50
Color 'lightyellowt' is 50% transparent: rgba(100%, 100%, 50%, 50%) hex:
#ffff8080
> color name goldt 100,75,0,50
Color 'goldt' is 50% transparent: rgba(100%, 75%, 0%, 50%) hex: #ffbf0080
> color name plumt 87,63,87,50
Color 'plumt' is 50% transparent: rgba(87%, 63%, 87%, 50%) hex: #dea1de80
> color name ssubluet 68,86,90,50
Color 'ssubluet' is 50% transparent: rgba(68%, 86%, 90%, 50%) hex: #addbe680
> color name p-prect 10,41,0,50
Color 'p-prect' is 50% transparent: rgba(10%, 41%, 0%, 50%) hex: #1a690080
> color name p-h2t 23,59,0,50
Color 'p-h2t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
> color name p-h1t 40,73,0,50
Color 'p-h1t' is 50% transparent: rgba(40%, 73%, 0%, 50%) hex: #66ba0080
> color name p-h1c 40,73,0,100
Color 'p-h1c' is opaque: rgb(40%, 73%, 0%) hex: #66ba00
> color name p-spct 68,81,0,50
Color 'p-spct' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
> color name p-spcc 68,81,0,100
Color 'p-spcc' is opaque: rgb(68%, 81%, 0%) hex: #adcf00
> color name p-fat 82,92,0,50
Color 'p-fat' is 50% transparent: rgba(82%, 92%, 0%, 50%) hex: #d1eb0080
> color name p-postt 100,92,0,50
Color 'p-postt' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
> color name d-t 100,80,4,50
Color 'd-t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
> color name d-prect 95,100,50,50
Color 'd-prect' is 50% transparent: rgba(95%, 100%, 50%, 50%) hex: #f2ff8080
> color name d-h2t 100,90,4,50
Color 'd-h2t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
> color name d-h1t 100,80,4,50
Color 'd-h1t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
> color name d-spct 100,70,4,50
Color 'd-spct' is 50% transparent: rgba(100%, 70%, 4%, 50%) hex: #ffb30a80
> color name d-fat 100,55,4,50
Color 'd-fat' is 50% transparent: rgba(100%, 55%, 4%, 50%) hex: #ff8c0a80
> color name d-fac 100,55,4,100
Color 'd-fac' is opaque: rgb(100%, 55%, 4%) hex: #ff8c0a
> color name d-postt 100,40,4,50
Color 'd-postt' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
> color name m-t 95,43,62,50
Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
> color name m-prect 100,85,95,50
Color 'm-prect' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex: #ffd9f280
> color name m-h2t 100,85,95,50
Color 'm-h2t' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex: #ffd9f280
> color name m-h1t 100,75,95,50
Color 'm-h1t' is 50% transparent: rgba(100%, 75%, 95%, 50%) hex: #ffbff280
> color name m-spct 89,63,75,50
Color 'm-spct' is 50% transparent: rgba(89%, 63%, 75%, 50%) hex: #e3a1bf80
> color name m-fat 95,51,75,50
Color 'm-fat' is 50% transparent: rgba(95%, 51%, 75%, 50%) hex: #f282bf80
> color name m-fac 95,51,75,100
Color 'm-fac' is opaque: rgb(95%, 51%, 75%) hex: #f282bf
> color name m-postt 95,43,62,50
Color 'm-postt' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
executed 70S_colors.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colorstandard.cxc
> color 100,100,100,50
> color lsu silvert
> color /3 lightgrayt
> color /5 lightgrayt
> color ssu ssu-t
> color head head-t
> color efg efg-t
> color dt d-t
> color pt p-t
> color pep p-t
> color mrna m-t
executed 70S_colorstandard.cxc
> windowsize 1000 1000
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_helices.cxc
> color h18 h18-t
> color h23 h23-t
> color h24 h24-t
> color h28 h28-t
> color h29 h29-t
> color h30 h30-t
> color h31 h31-t
> color h34 h34-t
> color h35 h35-t
> color h36 h36-t
> color h44 h44-t
> color H69 hx69-t
executed 70S_color_helices.cxc
> color h30|h36|h35 head-t
> view dc3
> surface cap true
> color zone #12.1 near #12.3,5 distance 5
> color zone #13.1 near #13.3,5 distance 5
> color zone #14.1 near #14.3,5 distance 5
> color zone #30.1 near #30.3,5 distance 5
> color zone #31.1 near #31.3,5 distance 5
> color zone #32.1 near #32.3,5 distance 5
> color zone #33.1 near #33.3,5 distance 5
> color zone #34.1 near #34.3,5 distance 5
> color zone #30.9 near #30.3,5 distance 5
> color zone #31.9 near #31.3,5 distance 5
> color zone #32.9 near #32.3,5 distance 5
> color zone #33.9 near #33.3,5 distance 5
> color zone #34.9 near #34.3,5 distance 5
> color h30|h36|h35 head-c
> color h28 h28-c
> color h29 h29-c
> color h34 h34-c
> color h23 h23-c
> color h24 h24-c
> color h31 h31-c
> hide #!100
> hide #101 models
> cartoon style nucleic xsection oval width 1.3 thickness 1.3
> transparency #*.3 0 target abc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_helices-s.cxc
> color h18 h18-c
> color h23 h23-c
> color h24 h24-c
> color h28 h28-c
> color h29 h29-c
> color h30 h30-c
> color h31 h31-c
> color h34 h34-c
> color h35 h35-c
> color h44 h44-c
> color H69 hx69-c
executed 70S_color_helices-s.cxc
> color /v d-c
> color /y p-c
> color /w m-c
executed gtpys_dc.cxc
> surface cap true
> lighting gentle
> lighting intensity .2
> size stickRadius 0.17
Changed 1744812 bond radii
> nucribthin
> style ringFill thin
Changed 122200 residue ring styles
> graphics silhouettes true color black
> ~select
Nothing selected
> ~select
Nothing selected
> ~ribbon
> ~display
> ribbon
> ~ribbon mrna
> display mrna
> display antiplus
> display /x:505-514,584
> display /6:1492,1493,530,532,1054,1400,1397
> display /3:1913
> display #*.3/L:44
> hide models
> show #31.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_ysH1b.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_ysH1b.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #32.3,5 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_ysH1c.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_ysH1c.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #12.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_H1apo.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_H1bapo.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #33.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_ysI1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_ysI1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #34.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_I1bys.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_I1bys.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #13.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_I1spc.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_I1spc.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #14.3,5 models
> ~display #14.3/w:38,49
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_I2fa.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_I2fa.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> graphics silhouettes true color 25,25,25,15
> style ringFill thick
Changed 122200 residue ring styles
> ~cartoon /6/3
> display /6/3
> ~cartoon trna
> display trna
> volume emmaps style surface step 1 level 3
> surface dust emmaps size 2
> volume emmaps surfaceSmoothing true
> view dc3
> hide models
> show #30 models
> select #30.3
60930 atoms, 65574 bonds, 3 pseudobonds, 4887 residues, 3 models selected
> hide #30.9 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_ysH1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #31 models
> select #31.3
60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected
> hide #31.9 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_ysH1b.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #32 models
> select #32.3
60097 atoms, 64722 bonds, 4 pseudobonds, 4779 residues, 3 models selected
> hide #32.9 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_ysH1c.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #12 models
> select #12.3
55765 atoms, 60298 bonds, 4230 residues, 1 model selected
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_H1apo.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #33 models
> select #33.3
61025 atoms, 65674 bonds, 2 pseudobonds, 4898 residues, 3 models selected
> hide #33.9 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_ysI1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #34 models
> select #34.3
61064 atoms, 65713 bonds, 3 pseudobonds, 4898 residues, 3 models selected
> hide #34.9 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_I1bys.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #13 models
> select #13.3
61103 atoms, 65762 bonds, 4902 residues, 1 model selected
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_I1spc.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #14 models
> ~display #14.3/w:38,49
> select #14.3
60702 atoms, 65388 bonds, 1 pseudobond, 4855 residues, 2 models selected
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_I2fa.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> volume emmaps style surface step 1 level 8
> surface dust emmaps size 2
> volume emmaps surfaceSmoothing true
> hide models
> show #30.3,5,9 models
> select #30.3
60930 atoms, 65574 bonds, 3 pseudobonds, 4887 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysH1a-FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #31.3,5,9 models
> select #31.3
60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysH1b-FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #32.3,5,9 models
> select #32.3
60097 atoms, 64722 bonds, 4 pseudobonds, 4779 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysH1c-FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #33.3,5,9 models
> select #33.3
61025 atoms, 65674 bonds, 2 pseudobonds, 4898 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysI1a-FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #34.3,5,9 models
> select #34.3
61064 atoms, 65713 bonds, 3 pseudobonds, 4898 residues, 3 models selected
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_I1bys-
> FR.tif format tiff width 1000 height 1000 supersample 20
> transparentBackground true
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
——— End of log from Thu Jul 20 18:51:54 2023 ———
opened ChimeraX session
> view dc2
> view dc1
> view dc3
> view dc2
> ui tool show "Side View"
> view name dc4
> hide models
> show #13 models
> view dc1
> display efg
> ui mousemode right pivot
> volume emmaps style surface step 1 level 3
> view name dc5
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
> color efg byhetero
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
——— End of log from Mon Jul 31 14:44:45 2023 ———
opened ChimeraX session
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_assign.cxc
> name atomods #*.3|#*.5
> name emmaps #*.1|#*.7|#*.8|#*.9
> name lsu #*.5
> name lsumap #*.8
> name ssu #*.3
> name ssumap #*.7
> name ligmap #*.9
> name rna /y,v,w,3,6,5
> name r23s /3
> name r16s /6
> name r5s /5
> name pt /y
> name dt /v
> name efg /x
> name pep /p
> name mrna /w
> name GSP :GSP
> name GDP :GDP
> name GTP :GTP
> name ntide :GTP|:GDP|:GSP
> name spc :SCM
> name fua :FUA
> name par :PAR
> name argb :LIG
> name drugs argb|par|fua|spc
> name D1 /x:start-293
> name D2 /x:294-410
> name D3 /x:411-489
> name D4 /x:490-612
> name D5 /x:613-end
> name sw1 /x:38-65
> name sw2 /x:89-108
> name pl /x:18-25
> name nkxd /x:142-146
> name mg /x:MG
> name trna /y,v
> name anticodon /y,v:34-36
> name antiplus /y,v:32-38
> name cca /y,v:74-76
> name astem /y,v:1-7,66-73
> name darm /y,v:8-25
> name aarm /y,v:26-43
> name varm /y,v:44-48
> name tarm /y,v:49-65
> name head #*.3/A/C/S/M/G/N/I/J/6:927-1390
> name arg-head #20.3/A/C/S/M/G/N/I/J/6:927-1390
> name post-head #15.3/A/C/S/M/G/N/I/J/6:927-1390
> name fa-head #14.3/A/C/S/M/G/N/I/J/6:927-1390
> name body #*.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name arg-body #20.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name post-body #15.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name fa-body #14.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name aploop /6:956-959
> name term16S /6:1503-end
> name aphelix /6:1228-1230
> name us2 #*.3/B
> name us3 #*.3/C
> name us4 #*.3/D
> name us5 #*.3/E
> name us6 #*.3/F
> name us7 #*.3/G
> name us8 #*.3/H
> name us9 #*.3/I
> name us10 #*.3/J
> name us11 #*.3/K
> name us12 #*.3/L
> name us13 #*.3/M
> name us14 #*.3/N
> name us15 #*.3/O
> name us16 #*.3/P
> name us17 #*.3/Q
> name us18 #*.3/R
> name us19 #*.3/S
> name us20 #*.3/T
> name us21 #*.3/U
> name us9-130 #*.3/I:130
> name l1stalk /3:2097-2191
> name srl /3:2652-2668
> name asf /3:863-910
> name l1stalk /3:2094-2195
> name ul1 #*.5/A
> name ul2 #*.5/B
> name ul3 #*.5/C
> name ul4 #*.5/D
> name ul5 #*.5/E
> name ul6 #*.5/F
> name ul7 #*.5/G
> name ul9 #*.5/I
> name ul10 #*.5/J
> name ul11 #*.5/K
> name ul13 #*.5/M
> name ul14 #*.5/N
> name ul15 #*.5/O
> name ul16 #*.5/P
> name ul17 #*.5/Q
> name ul18 #*.5/R
> name ul19 #*.5/S
> name ul20 #*.5/T
> name ul21 #*.5/U
> name ul22 #*.5/V
> name ul23 #*.5/W
> name ul24 #*.5/X
> name ul25 #*.5/Y
> name ul27 #*.5/a
> name ul28 #*.5/b
> name ul29 #*.5/c
> name ul30 #*.5/d
> name ul31 #*.5/e
> name ul32 #*.5/f
> name ul33 #*.5/g
> name ul34 #*.5/h
> name ul35 #*.5/i
> name ul36 #*.5/j
> name h1 #*.3/6:9-13|#*.3/6:21-25
> name h2 #*.3/6:17-19|#*.3/6:916-918
> name h3 #*.3/6:27-37|#*.3/6:547-556
> name h4 #*.3/6:39-46|#*.3/6:395-403
> name h5 #*.3/6:47-58|#*.3/6:354-360
> name h6 #*.3/6:61-106
> name h7 #*.3/6:122-142|#*.3/6:221-239
> name h8 #*.3/6:144-178
> name h9 #*.3/6:184-193
> name h10 #*.3/6:198-219
> name h11 #*.3/6:240-286
> name h12 #*.3/6:289-311
> name h13 #*.3/6:316-337
> name h14 #*.3/6:339-350
> name h15 #*.3/6:367-393
> name h16 #*.3/6:406-436
> name h17 #*.3/6:437-497
> name h18 #*.3/6:500-545
> name h19 #*.3/6:567-569|#*.3/6:881-88
> name h20 #*.3/6:577-586|#*.3/6:755-76
> name h21 #*.3/6:588-651
> name h22 #*.3/6:654-672|#*.3/6:734-75
> name h23 #*.3/6:673-733
> name h24 #*.3/6:769-810
> name h25 #*.3/6:821-827|#*.3/6:873-87
> name h26 #*.3/6:829-857
> name h26a #*.3/6:861-868
> name h27 #*.3/6:885-912
> name h28 #*.3/6:921-937|#*.3/6:1379-1400
> name h29 #*.3/6:938-943|#*.3/6:1337-1346
> name h30 #*.3/6:945-955|#*.3/6:1225-1236
> name h31 #*.3/6:956-975
> name h32 #*.3/6:984-991|#*.3/6:1212-1221
> name h33 #*.3/6:992-1045
> name h34 #*.3/6:1045-1065|#*.3/6:1188-1211
> name h35 #*.3/6:1066-1073|#*.3/6:1102-1110
> name h36 #*.3/6:1074-1083
> name h37 #*.3/6:1086-1099
> name h38 #*.3/6:1113-1117|#*.3/6:1183-1187
> name h39 #*.3/6:1118-1155
> name h40 #*.3/6:1161-1175
> name h41 #*.3/6:1241-1296
> name h42 #*.3/6:1303-1334
> name h43 #*.3/6:1350-1372
> name h44 #*.3/6:1401-1502
> name h45 #*.3/6:1506-1529
> name H1 #*.5/3:1-8|#*.5/3:2895-2904
> name H2 #*.5/3:15-24|#*.5/3:516-525
> name H3 #*.5/3:31-32|#*.5/3:473-474
> name H4 #*.5/3:35-45|#*.5/3:433-445
> name H5 #*.5/3:54-57|#*.5/3:114-117
> name H6 #*.5/3:58-69
> name H7 #*.5/3:75-110
> name H8 #*.5/3:121-130
> name H9 #*.5/3:131-148
> name H10 #*.5/3:150-176
> name H11 #*.5/3:183-213
> name H12 #*.5/3:224-231
> name H13 #*.5/3:235-262
> name H14 #*.5/3:265-268|#*.5/3:424-427
> name H16 #*.5/3:271-274|#*.5/3:363-366
> name H18 #*.5/3:281-297|#*.5/3:341-359
> name H19 #*.5/3:301-316
> name H20 #*.5/3:325-337
> name H21 #*.5/3:375-399
> name H22 #*.5/3:406-421
> name H23 #*.5/3:461-468
> name H24 #*.5/3:484-496
> name H25 #*.5/3:533-560
> name H26 #*.5/3:579-584|#*.5/3:1256-1261
> name H27 #*.5/3:589-601|#*.5/3:656-668
> name H28 #*.5/3:604-624
> name H29 #*.5/3:628-635
> name H31 #*.5/3:637-651
> name H32 #*.5/3:678-683|#*.5/3:794-799
> name H33 #*.5/3:687-698|#*.5/3:763-775
> name H34 #*.5/3:700-732
> name H35 #*.5/3:736-760
> name H35a #*.5/3:777-787
> name H36 #*.5/3:812-817|#*.5/3:1190-1195
> name H37 #*.5/3:822-835
> name H38 #*.5/3:838-940
> name H39 #*.5/3:946-971
> name H40 #*.5/3:976-987
> name H41 #*.5/3:991-1018|#*.5/3:1144-1163
> name H42 #*.5/3:1030-1055|#*.5/3:1104-1124
> name H43 #*.5/3:1057-1081
> name H44 #*.5/3:1087-1102
> name H45 #*.5/3:1164-1185
> name H46 #*.5/3:1198-1247
> name H47 #*.5/3:1276-1294
> name H48 #*.5/3:1295-1298|#*.5/3:1642-1646
> name H49 #*.5/3:1303-1306|#*.5/3:1622-1625
> name H50 #*.5/3:1314-1338
> name H51 #*.5/3:1345-1348|#*.5/3:1598-1601
> name H52 #*.5/3:1350-1381
> name H53 #*.5/3:1385-1402
> name H54 #*.5/3:1405-1417|#*.5/3:1581-1597
> name H55 #*.5/3:1420-1424|#*.5/3:1573-1578
> name H56 #*.5/3:1429-1444|#*.5/3:1547-1564
> name H57 #*.5/3:1445-1466
> name H58 #*.5/3:1467-1525
> name H59 #*.5/3:1527-1544
> name H60 #*.5/3:1627-1639
> name H61 #*.5/3:1647-1669|#*.5/3:1991-2009
> name H62 #*.5/3:1682-1706
> name H63 #*.5/3:1707-1751
> name H64 #*.5/3:1764-1772|#*.5/3:1979-1988
> name H65 #*.5/3:1775-1789
> name H66 #*.5/3:1792-1827
> name H67 #*.5/3:1830-1833|#*.5/3:1972-1975
> name H68 #*.5/3:1835-1905
> name H69 #*.5/3:1906-1924
> name H71 #*.5/3:1945-1960
> name H72 #*.5/3:2023-2040
> name H73 #*.5/3:2043-2057|#*.5/3:2611-2625
> name H74 #*.5/3:2064-2075|#*.5/3:2434-2446
> name H75 #*.5/3:2077-2090|#*.5/3:2229-2243
> name H76 #*.5/3:2093-2110|#*.5/3:2179-2196
> name H77 #*.5/3:2120-2124|#*.5/3:2174-2178
> name H78 #*.5/3:2127-2161
> name H79 #*.5/3:2200-2223
> name H80 #*.5/3:2246-2258
> name H81 #*.5/3:2259-2281
> name H82 #*.5/3:2284-2285|#*.5/3:2383-2384
> name H83 #*.5/3:2288-2295|#*.5/3:2337-2344
> name H84 #*.5/3:2296-2322
> name H85 #*.5/3:2323-2332
> name H86 #*.5/3:2347-2370
> name H87 #*.5/3:2372-2381
> name H88 #*.5/3:2395-2421
> name H89 #*.5/3:2453-2498
> name H90 #*.5/3:2507-2517|#*.5/3:2567-2582
> name H91 #*.5/3:2520-2545
> name H92 #*.5/3:2547-2561
> name H93 #*.5/3:2588-2606
> name H94 #*.5/3:2630-2643|#*.5/3:2771-2788
> name H95 #*.5/3:2646-2674
> name H96 #*.5/3:2675-2732
> name H97 #*.5/3:2735-2769
> name H98 #*.5/3:2791-2805
> name H99 #*.5/3:2811-2814|#*.5/3:2886-2889
> name H100 #*.5/3:2815-2831
executed 70S_assign.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_display.cxc
> alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6;
> alias nucribthin cartoon style nucleic xsect oval width 1.2 thick 1.2;
> alias cylinders cartoon style protein modeh tube rad 2 sides 24;
> alias licorice car style protein modeh default arrows f xsect oval width 1
> thick 1;
> dssp
> windowsize 1000 1000
> set bgColor white
> lighting full
> set silhouettes true
> set silhouetteWidth 1.7
> set silhouettes true
> set silhouetteDepthJump 0.02
> cartoon style width 2.5
> size atomRadius 2
Changed 1614330 atom radii
> nucleotides fill
> size ions atomRadius 1.6
Changed 31 atom radii
> size stickRadius 0.1
Changed 1744812 bond radii
> style stick ringFill thin
Changed 1614330 atom styles, 122200 residue ring styles
> show ribbons
> hide H
> hide :HOH
> hide target a
> show nucleic target a
> show drugs target a
> style drugs ball
Changed 106 atom styles
> graphics selection color black
> cartoon style protein xsection round width 2 thickness 0.6
> cartoon style modeHelix wrap
> cartoon style sides 24
> cartoon style strand xsection oval arrows false
> cartoon suppressBackboneDisplay true
> alias thinbois style ball;size ballscale 0.09; size stickradius 0.13;
> alias thickbois style stick;size stickradius 0.4;style stick ringFill thick;
> volume emmaps style surface step 1 level 4
> surface dust emmaps size 3
> volume surfaceSmoothing true
> cartoon tether trna shape cone opacity 1
> dssp
> thickbois
Changed 1614330 atom styles
Changed 1744812 bond radii
Changed 1614330 atom styles, 122200 residue ring styles
executed 70S_display.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colors.cxc
> color name efg-t 100,0,0,50
Color 'efg-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
> color name sw1-t 100,92,0,50
Color 'sw1-t' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
> color name sw2-t 68,81,0,50
Color 'sw2-t' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
> color name pl-t 23,59,0,50
Color 'pl-t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
> color name d1-t 100,18,4,50
Color 'd1-t' is 50% transparent: rgba(100%, 18%, 4%, 50%) hex: #ff2e0a80
> color name d2-t 100,40,4,50
Color 'd2-t' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
> color name d3-t 100,27,36,50
Color 'd3-t' is 50% transparent: rgba(100%, 27%, 36%, 50%) hex: #ff455c80
> color name d4-t 80,0,23,50
Color 'd4-t' is 50% transparent: rgba(80%, 0%, 23%, 50%) hex: #cc003b80
> color name d5-t 100,60,4,50
Color 'd5-t' is 50% transparent: rgba(100%, 60%, 4%, 50%) hex: #ff990a80
> color name fa-t 100,90,4,50
Color 'fa-t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
> color name gtp-t 45,53,60,50
Color 'gtp-t' is 50% transparent: rgba(45%, 53%, 60%, 50%) hex: #73879980
> color name mg-t 1,39,16,50
Color 'mg-t' is 50% transparent: rgba(1%, 39%, 16%, 50%) hex: #03632980
> color name spc-t 100,0,0,50
Color 'spc-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
> color name argb-t 50,0,50,50
Color 'argb-t' is 50% transparent: rgba(50%, 0%, 50%, 50%) hex: #80008080
> color name g-1t 98,42,30,50
Color 'g-1t' is 50% transparent: rgba(98%, 42%, 30%, 50%) hex: #fa6b4d80
> color name g-2t 95,35,25,50
Color 'g-2t' is 50% transparent: rgba(95%, 35%, 25%, 50%) hex: #f2594080
> color name g-3t 92,28,20,50
Color 'g-3t' is 50% transparent: rgba(92%, 28%, 20%, 50%) hex: #eb473380
> color name g-4t 89,21,15,50
Color 'g-4t' is 50% transparent: rgba(89%, 21%, 15%, 50%) hex: #e3362680
> color name g-5t 86,14,10,50
Color 'g-5t' is 50% transparent: rgba(86%, 14%, 10%, 50%) hex: #db241a80
> color name g-6t 83,7,5,50
Color 'g-6t' is 50% transparent: rgba(83%, 7%, 5%, 50%) hex: #d4120d80
> color name g-7t 80,0,0,50
Color 'g-7t' is 50% transparent: rgba(80%, 0%, 0%, 50%) hex: #cc000080
> color name p-t 44,59,2,50
Color 'p-t' is 50% transparent: rgba(44%, 59%, 2%, 50%) hex: #70960580
> color name p-c 44,59,2,100
Color 'p-c' is opaque: rgb(44%, 59%, 2%) hex: #709605
> color name p-1t 4,34,1,50
Color 'p-1t' is 50% transparent: rgba(4%, 34%, 1%, 50%) hex: #0a570380
> color name p-2t 12,39,1,50
Color 'p-2t' is 50% transparent: rgba(12%, 39%, 1%, 50%) hex: #1f630380
> color name p-3t 20,44,1,50
Color 'p-3t' is 50% transparent: rgba(20%, 44%, 1%, 50%) hex: #33700380
> color name p-4t 28,49,1,50
Color 'p-4t' is 50% transparent: rgba(28%, 49%, 1%, 50%) hex: #477d0380
> color name p-5t 36,54,2,50
Color 'p-5t' is 50% transparent: rgba(36%, 54%, 2%, 50%) hex: #5c8a0580
> color name p-6t 44,59,2,50
Color 'p-6t' is 50% transparent: rgba(44%, 59%, 2%, 50%) hex: #70960580
> color name p-7t 52,64,2,50
Color 'p-7t' is 50% transparent: rgba(52%, 64%, 2%, 50%) hex: #85a30580
> color name p-8t 60,69,2,50
Color 'p-8t' is 50% transparent: rgba(60%, 69%, 2%, 50%) hex: #99b00580
> color name p-9t 68,74,3,50
Color 'p-9t' is 50% transparent: rgba(68%, 74%, 3%, 50%) hex: #adbd0880
> color name p-10t 76,79,3,50
Color 'p-10t' is 50% transparent: rgba(76%, 79%, 3%, 50%) hex: #c2c90880
> color name p-11t 84,84,3,50
Color 'p-11t' is 50% transparent: rgba(84%, 84%, 3%, 50%) hex: #d6d60880
> color name d-t 100,65,4,50
Color 'd-t' is 50% transparent: rgba(100%, 65%, 4%, 50%) hex: #ffa60a80
> color name d-c 100,65,4,100
Color 'd-c' is opaque: rgb(100%, 65%, 4%) hex: #ffa60a
> color name d-1t 100,100,4,50
Color 'd-1t' is 50% transparent: rgba(100%, 100%, 4%, 50%) hex: #ffff0a80
> color name d-2t 100,93,4,50
Color 'd-2t' is 50% transparent: rgba(100%, 93%, 4%, 50%) hex: #ffed0a80
> color name d-3t 100,86,4,50
Color 'd-3t' is 50% transparent: rgba(100%, 86%, 4%, 50%) hex: #ffdb0a80
> color name d-4t 100,79,4,50
Color 'd-4t' is 50% transparent: rgba(100%, 79%, 4%, 50%) hex: #ffc90a80
> color name d-5t 100,72,4,50
Color 'd-5t' is 50% transparent: rgba(100%, 72%, 4%, 50%) hex: #ffb80a80
> color name d-6t 100,65,4,50
Color 'd-6t' is 50% transparent: rgba(100%, 65%, 4%, 50%) hex: #ffa60a80
> color name d-7t 100,58,4,50
Color 'd-7t' is 50% transparent: rgba(100%, 58%, 4%, 50%) hex: #ff940a80
> color name d-8t 100,51,4,50
Color 'd-8t' is 50% transparent: rgba(100%, 51%, 4%, 50%) hex: #ff820a80
> color name d-9t 100,44,4,50
Color 'd-9t' is 50% transparent: rgba(100%, 44%, 4%, 50%) hex: #ff700a80
> color name d-10t 100,37,4,50
Color 'd-10t' is 50% transparent: rgba(100%, 37%, 4%, 50%) hex: #ff5e0a80
> color name d-11t 100,30,4,50
Color 'd-11t' is 50% transparent: rgba(100%, 30%, 4%, 50%) hex: #ff4d0a80
> color name m-t 95,43,62,50
Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
> color name m-c 95,43,62,100
Color 'm-c' is opaque: rgb(95%, 43%, 62%) hex: #f26e9e
> color name m-1t 100,80,90,50
Color 'm-1t' is 50% transparent: rgba(100%, 80%, 90%, 50%) hex: #ffcce680
> color name m-2t 98,76,87,50
Color 'm-2t' is 50% transparent: rgba(98%, 76%, 87%, 50%) hex: #fac2de80
> color name m-3t 96,72,84,50
Color 'm-3t' is 50% transparent: rgba(96%, 72%, 84%, 50%) hex: #f5b8d680
> color name m-4t 94,68,81,50
Color 'm-4t' is 50% transparent: rgba(94%, 68%, 81%, 50%) hex: #f0adcf80
> color name m-5t 92,64,78,50
Color 'm-5t' is 50% transparent: rgba(92%, 64%, 78%, 50%) hex: #eba3c780
> color name m-6t 90,60,75,50
Color 'm-6t' is 50% transparent: rgba(90%, 60%, 75%, 50%) hex: #e699bf80
> color name m-7t 88,56,72,50
Color 'm-7t' is 50% transparent: rgba(88%, 56%, 72%, 50%) hex: #e08fb880
> color name m-8t 86,52,69,50
Color 'm-8t' is 50% transparent: rgba(86%, 52%, 69%, 50%) hex: #db85b080
> color name m-9t 84,48,66,50
Color 'm-9t' is 50% transparent: rgba(84%, 48%, 66%, 50%) hex: #d67aa880
> color name m-10t 82,44,63,50
Color 'm-10t' is 50% transparent: rgba(82%, 44%, 63%, 50%) hex: #d170a180
> color name m-11t 80,40,60,50
Color 'm-11t' is 50% transparent: rgba(80%, 40%, 60%, 50%) hex: #cc669980
> color name head-t 82,74,84,50
Color 'head-t' is 50% transparent: rgba(82%, 74%, 84%, 50%) hex: #d1bdd680
> color name head-c 82,74,84,100
Color 'head-c' is opaque: rgb(82%, 74%, 84%) hex: #d1bdd6
> color name headfa-t 54,41,54,50
Color 'headfa-t' is 50% transparent: rgba(54%, 41%, 54%, 50%) hex: #8a698a80
> color name headblue-t 59,78,94,50
Color 'headblue-t' is 50% transparent: rgba(59%, 78%, 94%, 50%) hex: #96c7f080
> color name headh1-t 41,64,100,50
Color 'headh1-t' is 50% transparent: rgba(41%, 64%, 100%, 50%) hex: #69a3ff80
> color name headh2-t 50,70,100,50
Color 'headh2-t' is 50% transparent: rgba(50%, 70%, 100%, 50%) hex: #80b3ff80
> color name headgray-t 60,60,60,50
Color 'headgray-t' is 50% transparent: rgba(60%, 60%, 60%, 50%) hex: #99999980
> color name darkhead-s 54,41,54,100
Color 'darkhead-s' is opaque: rgb(54%, 41%, 54%) hex: #8a698a
> color name bodywhite-t 90,90,90,50
Color 'bodywhite-t' is 50% transparent: rgba(90%, 90%, 90%, 50%) hex:
#e6e6e680
> color name rps-t 75,88,93,50
Color 'rps-t' is 50% transparent: rgba(75%, 88%, 93%, 50%) hex: #bfe0ed80
> color name ssu-t 69,79,82,50
Color 'ssu-t' is 50% transparent: rgba(69%, 79%, 82%, 50%) hex: #b0c9d180
> color name ssu-c 69,79,82,100
Color 'ssu-c' is opaque: rgb(69%, 79%, 82%) hex: #b0c9d1
> color name h16-t 79,85,89,50
Color 'h16-t' is 50% transparent: rgba(79%, 85%, 89%, 50%) hex: #c9d9e380
> color name h16-c 79,85,89,100
Color 'h16-c' is opaque: rgb(79%, 85%, 89%) hex: #c9d9e3
> color name h18-t 31,59,68,50
Color 'h18-t' is 50% transparent: rgba(31%, 59%, 68%, 50%) hex: #4f96ad80
> color name h18-dt 6,47,62,50
Color 'h18-dt' is 50% transparent: rgba(6%, 47%, 62%, 50%) hex: #0f789e80
> color name h18-dc 6,47,62,100
Color 'h18-dc' is opaque: rgb(6%, 47%, 62%) hex: #0f789e
> color name h18-c 31,59,68,100
Color 'h18-c' is opaque: rgb(31%, 59%, 68%) hex: #4f96ad
> color name h23-t 40,61,80,50
Color 'h23-t' is 50% transparent: rgba(40%, 61%, 80%, 50%) hex: #669ccc80
> color name h23-c 40,61,80,100
Color 'h23-c' is opaque: rgb(40%, 61%, 80%) hex: #669ccc
> color name h24-t 50,70,90,50
Color 'h24-t' is 50% transparent: rgba(50%, 70%, 90%, 50%) hex: #80b3e680
> color name h24-c 50,70,90,100
Color 'h24-c' is opaque: rgb(50%, 70%, 90%) hex: #80b3e6
> color name h28-t 21,27,56,50
Color 'h28-t' is 50% transparent: rgba(21%, 27%, 56%, 50%) hex: #36458f80
> color name h28-c 21,27,56,100
Color 'h28-c' is opaque: rgb(21%, 27%, 56%) hex: #36458f
> color name h29-t 80,69,92,50
Color 'h29-t' is 50% transparent: rgba(80%, 69%, 92%, 50%) hex: #ccb0eb80
> color name h29-c 80,69,92,100
Color 'h29-c' is opaque: rgb(80%, 69%, 92%) hex: #ccb0eb
> color name h30-t 40,40,59,50
Color 'h30-t' is 50% transparent: rgba(40%, 40%, 59%, 50%) hex: #66669680
> color name h30-c 40,40,59,100
Color 'h30-c' is opaque: rgb(40%, 40%, 59%) hex: #666696
> color name h31-t 45,35,55,50
Color 'h31-t' is 50% transparent: rgba(45%, 35%, 55%, 50%) hex: #73598c80
> color name h31-c 45,35,55,100
Color 'h31-c' is opaque: rgb(45%, 35%, 55%) hex: #73598c
> color name h32-t 75,62,79,50
Color 'h32-t' is 50% transparent: rgba(75%, 62%, 79%, 50%) hex: #bf9ec980
> color name h32-c 75,62,79,100
Color 'h32-c' is opaque: rgb(75%, 62%, 79%) hex: #bf9ec9
> color name h33-t 88,82,90,50
Color 'h33-t' is 50% transparent: rgba(88%, 82%, 90%, 50%) hex: #e0d1e680
> color name h33-c 88,82,90,100
Color 'h33-c' is opaque: rgb(88%, 82%, 90%) hex: #e0d1e6
> color name h34-t 59,35,59,50
Color 'h34-t' is 50% transparent: rgba(59%, 35%, 59%, 50%) hex: #96599680
> color name h34-c 59,35,59,100
Color 'h34-c' is opaque: rgb(59%, 35%, 59%) hex: #965996
> color name h35-t 50,22,45,50
Color 'h35-t' is 50% transparent: rgba(50%, 22%, 45%, 50%) hex: #80387380
> color name h35-c 50,22,45,100
Color 'h35-c' is opaque: rgb(50%, 22%, 45%) hex: #803873
> color name h44-t 32,54,70,50
Color 'h44-t' is 50% transparent: rgba(32%, 54%, 70%, 50%) hex: #528ab380
> color name h44-c 32,54,70,100
Color 'h44-c' is opaque: rgb(32%, 54%, 70%) hex: #528ab3
> color name aploop-t 27,0,50,50
Color 'aploop-t' is 50% transparent: rgba(27%, 0%, 50%, 50%) hex: #45008080
> color name term16-t 40,64,64,50
Color 'term16-t' is 50% transparent: rgba(40%, 64%, 64%, 50%) hex: #66a3a380
> color name uS3-t 48,44,57,50
Color 'uS3-t' is 50% transparent: rgba(48%, 44%, 57%, 50%) hex: #7a709180
> color name uS3-c 48,44,57,100
Color 'uS3-c' is opaque: rgb(48%, 44%, 57%) hex: #7a7091
> color name uS3-dt 40,37,57,50
Color 'uS3-dt' is 50% transparent: rgba(40%, 37%, 57%, 50%) hex: #665e9180
> color name uS3-dc 40,37,57,100
Color 'uS3-dc' is opaque: rgb(40%, 37%, 57%) hex: #665e91
> color name uS5-t 0,50,45,50
Color 'uS5-t' is 50% transparent: rgba(0%, 50%, 45%, 50%) hex: #00807380
> color name gray-t 70,70,70,50
Color 'gray-t' is 50% transparent: rgba(70%, 70%, 70%, 50%) hex: #b3b3b380
> color name hx84-t 50,50,50,50
Color 'hx84-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name hx84-c 50,50,50,100
Color 'hx84-c' is opaque: gray(50%) hex: #808080
> color name hx84-dt 30,30,30,50
Color 'hx84-dt' is 50% transparent: rgba(30%, 30%, 30%, 50%) hex: #4d4d4d80
> color name hx84-dc 30,30,30,100
Color 'hx84-dc' is opaque: gray(30%) hex: #4d4d4d
> color name hx68-t 50,50,50,50
Color 'hx68-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name hx68-c 50,50,50,100
Color 'hx68-c' is opaque: gray(50%) hex: #808080
> color name hx69-t 40,40,40,50
Color 'hx69-t' is 50% transparent: rgba(40%, 40%, 40%, 50%) hex: #66666680
> color name hx69-c 40,40,40,100
Color 'hx69-c' is opaque: gray(40%) hex: #666666
> color name hx38-t 34,42,36,50
Color 'hx38-t' is 50% transparent: rgba(34%, 42%, 36%, 50%) hex: #576b5c80
> color name hx38-c 34,42,36,100
Color 'hx38-c' is opaque: rgb(34%, 42%, 36%) hex: #576b5c
> color name hx38-dt 34,42,36,50
Color 'hx38-dt' is 50% transparent: rgba(34%, 42%, 36%, 50%) hex: #576b5c80
> color name hx38-dc 34,42,36,100
Color 'hx38-dc' is opaque: rgb(34%, 42%, 36%) hex: #576b5c
> color name ul5-t 55,62,67,50
Color 'ul5-t' is 50% transparent: rgba(55%, 62%, 67%, 50%) hex: #8c9eab80
> color name ul5-c 55,62,67,100
Color 'ul5-c' is opaque: rgb(55%, 62%, 67%) hex: #8c9eab
> color name ul5-dt 38,47,52,50
Color 'ul5-dt' is 50% transparent: rgba(38%, 47%, 52%, 50%) hex: #61788580
> color name ul5-dc 38,47,52,100
Color 'ul5-dc' is opaque: rgb(38%, 47%, 52%) hex: #617885
> color name ul16-t 70,70,70,50
Color 'ul16-t' is 50% transparent: rgba(70%, 70%, 70%, 50%) hex: #b3b3b380
> color name ul16-c 70,70,70,100
Color 'ul16-c' is opaque: gray(70%) hex: #b3b3b3
> color name srl-t 50,50,50,50
Color 'srl-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name srl-t 50,50,50,100
Color 'srl-t' is opaque: gray(50%) hex: #808080
> color name highlight-t 92,78,8,50
Color 'highlight-t' is 50% transparent: rgba(92%, 78%, 8%, 50%) hex: #ebc71480
> color name highlight-c 92,78,8,100
Color 'highlight-c' is opaque: rgb(92%, 78%, 8%) hex: #ebc714
> color name tomato-t 100,39,28,50
Color 'tomato-t' is 50% transparent: rgba(100%, 39%, 28%, 50%) hex: #ff634780
> color name tomato-c 100,39,28,100
Color 'tomato-c' is opaque: rgb(100%, 39%, 28%) hex: #ff6347
> color name lightgrayt 83,83,83,50
Color 'lightgrayt' is 50% transparent: rgba(83%, 83%, 83%, 50%) hex: #d4d4d480
> color name silvert 75,75,75,50
Color 'silvert' is 50% transparent: rgba(75%, 75%, 75%, 50%) hex: #bfbfbf80
> color name grayt 50,50,50,50
Color 'grayt' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name lightcyant 88,100,100,50
Color 'lightcyant' is 50% transparent: rgba(88%, 100%, 100%, 50%) hex:
#e0ffff80
> color name yellowt 100,90,0,50
Color 'yellowt' is 50% transparent: rgba(100%, 90%, 0%, 50%) hex: #ffe60080
> color name deeppinkt 100,8,58,50
Color 'deeppinkt' is 50% transparent: rgba(100%, 8%, 58%, 50%) hex: #ff149480
> color name oranget 100,65,0,50
Color 'oranget' is 50% transparent: rgba(100%, 65%, 0%, 50%) hex: #ffa60080
> color name yellowgreent 60,80,20,50
Color 'yellowgreent' is 50% transparent: rgba(60%, 80%, 20%, 50%) hex:
#99cc3380
> color name darkmagentat 54,0,54,50
Color 'darkmagentat' is 50% transparent: rgba(54%, 0%, 54%, 50%) hex:
#8a008a80
> color name orchidt 86,44,84,50
Color 'orchidt' is 50% transparent: rgba(86%, 44%, 84%, 50%) hex: #db70d680
> color name paleturquoiset 69,93,93,50
Color 'paleturquoiset' is 50% transparent: rgba(69%, 93%, 93%, 50%) hex:
#b0eded80
> color name pinkt 100,75,80,50
Color 'pinkt' is 50% transparent: rgba(100%, 75%, 80%, 50%) hex: #ffbfcc80
> color name darkgreent 0,39,0,50
Color 'darkgreent' is 50% transparent: rgba(0%, 39%, 0%, 50%) hex: #00630080
> color name limegreent 20,80,20,50
Color 'limegreent' is 50% transparent: rgba(20%, 80%, 20%, 50%) hex: #33cc3380
> color name turquoiset 25,88,82,50
Color 'turquoiset' is 50% transparent: rgba(25%, 88%, 82%, 50%) hex: #40e0d180
> color name tealt 0,50,50,50
Color 'tealt' is 50% transparent: rgba(0%, 50%, 50%, 50%) hex: #00808080
> color name darkoranget 100,50,0,50
Color 'darkoranget' is 50% transparent: rgba(100%, 50%, 0%, 50%) hex:
#ff800080
> color name lightyellowt 100,100,50,50
Color 'lightyellowt' is 50% transparent: rgba(100%, 100%, 50%, 50%) hex:
#ffff8080
> color name goldt 100,75,0,50
Color 'goldt' is 50% transparent: rgba(100%, 75%, 0%, 50%) hex: #ffbf0080
> color name plumt 87,63,87,50
Color 'plumt' is 50% transparent: rgba(87%, 63%, 87%, 50%) hex: #dea1de80
> color name ssubluet 68,86,90,50
Color 'ssubluet' is 50% transparent: rgba(68%, 86%, 90%, 50%) hex: #addbe680
> color name p-prect 10,41,0,50
Color 'p-prect' is 50% transparent: rgba(10%, 41%, 0%, 50%) hex: #1a690080
> color name p-h2t 23,59,0,50
Color 'p-h2t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
> color name p-h1t 40,73,0,50
Color 'p-h1t' is 50% transparent: rgba(40%, 73%, 0%, 50%) hex: #66ba0080
> color name p-h1c 40,73,0,100
Color 'p-h1c' is opaque: rgb(40%, 73%, 0%) hex: #66ba00
> color name p-spct 68,81,0,50
Color 'p-spct' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
> color name p-spcc 68,81,0,100
Color 'p-spcc' is opaque: rgb(68%, 81%, 0%) hex: #adcf00
> color name p-fat 82,92,0,50
Color 'p-fat' is 50% transparent: rgba(82%, 92%, 0%, 50%) hex: #d1eb0080
> color name p-postt 100,92,0,50
Color 'p-postt' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
> color name d-t 100,80,4,50
Color 'd-t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
> color name d-prect 95,100,50,50
Color 'd-prect' is 50% transparent: rgba(95%, 100%, 50%, 50%) hex: #f2ff8080
> color name d-h2t 100,90,4,50
Color 'd-h2t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
> color name d-h1t 100,80,4,50
Color 'd-h1t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
> color name d-spct 100,70,4,50
Color 'd-spct' is 50% transparent: rgba(100%, 70%, 4%, 50%) hex: #ffb30a80
> color name d-fat 100,55,4,50
Color 'd-fat' is 50% transparent: rgba(100%, 55%, 4%, 50%) hex: #ff8c0a80
> color name d-fac 100,55,4,100
Color 'd-fac' is opaque: rgb(100%, 55%, 4%) hex: #ff8c0a
> color name d-postt 100,40,4,50
Color 'd-postt' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
> color name m-t 95,43,62,50
Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
> color name m-prect 100,85,95,50
Color 'm-prect' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex: #ffd9f280
> color name m-h2t 100,85,95,50
Color 'm-h2t' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex: #ffd9f280
> color name m-h1t 100,75,95,50
Color 'm-h1t' is 50% transparent: rgba(100%, 75%, 95%, 50%) hex: #ffbff280
> color name m-spct 89,63,75,50
Color 'm-spct' is 50% transparent: rgba(89%, 63%, 75%, 50%) hex: #e3a1bf80
> color name m-fat 95,51,75,50
Color 'm-fat' is 50% transparent: rgba(95%, 51%, 75%, 50%) hex: #f282bf80
> color name m-fac 95,51,75,100
Color 'm-fac' is opaque: rgb(95%, 51%, 75%) hex: #f282bf
> color name m-postt 95,43,62,50
Color 'm-postt' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
executed 70S_colors.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colorstandard.cxc
> color 100,100,100,50
> color lsu silvert
> color /3 lightgrayt
> color /5 lightgrayt
> color ssu ssu-t
> color head head-t
> color efg efg-t
> color dt d-t
> color pt p-t
> color pep p-t
> color mrna m-t
executed 70S_colorstandard.cxc
> windowsize 1000 1000
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_helices.cxc
> color h18 h18-t
> color h23 h23-t
> color h24 h24-t
> color h28 h28-t
> color h29 h29-t
> color h30 h30-t
> color h31 h31-t
> color h34 h34-t
> color h35 h35-t
> color h36 h36-t
> color h44 h44-t
> color H69 hx69-t
executed 70S_color_helices.cxc
> color h30|h36|h35 head-t
> view dc3
> surface cap true
> color zone #12.1 near #12.3,5 distance 5
> color zone #13.1 near #13.3,5 distance 5
> color zone #14.1 near #14.3,5 distance 5
> color zone #30.1 near #30.3,5 distance 5
> color zone #31.1 near #31.3,5 distance 5
> color zone #32.1 near #32.3,5 distance 5
> color zone #33.1 near #33.3,5 distance 5
> color zone #34.1 near #34.3,5 distance 5
> color zone #30.9 near #30.3,5 distance 5
> color zone #31.9 near #31.3,5 distance 5
> color zone #32.9 near #32.3,5 distance 5
> color zone #33.9 near #33.3,5 distance 5
> color zone #34.9 near #34.3,5 distance 5
> color h30|h36|h35 head-c
> color h28 h28-c
> color h29 h29-c
> color h34 h34-c
> color h23 h23-c
> color h24 h24-c
> color h31 h31-c
> hide #!100
> hide #101 models
> cartoon style nucleic xsection oval width 1.3 thickness 1.3
> transparency #*.3 0 target abc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_helices-s.cxc
> color h18 h18-c
> color h23 h23-c
> color h24 h24-c
> color h28 h28-c
> color h29 h29-c
> color h30 h30-c
> color h31 h31-c
> color h34 h34-c
> color h35 h35-c
> color h44 h44-c
> color H69 hx69-c
executed 70S_color_helices-s.cxc
> color /v d-c
> color /y p-c
> color /w m-c
executed gtpys_dc.cxc
> surface cap true
> lighting gentle
> lighting intensity .2
> size stickRadius 0.17
Changed 1744812 bond radii
> nucribthin
> style ringFill thin
Changed 122200 residue ring styles
> graphics silhouettes true color black
> ~select
Nothing selected
> ~select
Nothing selected
> ~ribbon
> ~display
> ribbon
> ~ribbon mrna
> display mrna
> display antiplus
> display /x:504-514,584
> display /6:1492,1493,530,532,1054,1400,1397
> display /3:1913
> display #*.3/L:44
> color efg byhetero
> select efg
36728 atoms, 37417 bonds, 9 pseudobonds, 4797 residues, 16 models selected
> hide models
> show #30.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_ysH1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_ysH1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #31.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_ysH1b.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_ysH1b.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #32.3,5 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_ysH1c.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_ysH1c.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #12.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_H1apo.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_H1bapo.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #33.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_ysI1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_ysI1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #34.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_I1bys.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_I1bys.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #13.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_I1spc.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_I1spc.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #14.3,5 models
> ~display #14.3/w:38,49
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_I2fa.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_I2fa.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> graphics silhouettes true color 25,25,25,15
> style ringFill thick
Changed 122200 residue ring styles
> ~cartoon /6/3
> display /6/3
> ~cartoon trna
> display trna
> volume emmaps style surface step 1 level 3
> surface dust emmaps size 2
> volume emmaps surfaceSmoothing true
> view dc3
> hide models
> show #30 models
> select #30.3
60930 atoms, 65574 bonds, 3 pseudobonds, 4887 residues, 3 models selected
> hide #30.9 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_ysH1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #31 models
> select #31.3
60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected
> hide #31.9 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_ysH1b.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #32 models
> select #32.3
60097 atoms, 64722 bonds, 4 pseudobonds, 4779 residues, 3 models selected
> hide #32.9 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_ysH1c.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #12 models
> select #12.3
55765 atoms, 60298 bonds, 4230 residues, 1 model selected
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_H1apo.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #33 models
> select #33.3
61025 atoms, 65674 bonds, 2 pseudobonds, 4898 residues, 3 models selected
> hide #33.9 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_ysI1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #34 models
> select #34.3
61064 atoms, 65713 bonds, 3 pseudobonds, 4898 residues, 3 models selected
> hide #34.9 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_I1bys.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #13 models
> select #13.3
61103 atoms, 65762 bonds, 4902 residues, 1 model selected
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_I1spc.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #14 models
> ~display #14.3/w:38,49
> select #14.3
60702 atoms, 65388 bonds, 1 pseudobond, 4855 residues, 2 models selected
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_I2fa.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> view dc4
> hide models
> show #30 models
> select #30.3
60930 atoms, 65574 bonds, 3 pseudobonds, 4887 residues, 3 models selected
> hide #30.9 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig3_ysH1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #31 models
> select #31.3
60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected
> hide #31.9 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig3_ysH1b.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #32 models
> select #32.3
60097 atoms, 64722 bonds, 4 pseudobonds, 4779 residues, 3 models selected
> hide #32.9 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig3_ysH1c.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #12 models
> select #12.3
55765 atoms, 60298 bonds, 4230 residues, 1 model selected
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig3_H1apo.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #33 models
> select #33.3
61025 atoms, 65674 bonds, 2 pseudobonds, 4898 residues, 3 models selected
> hide #33.9 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig3_ysI1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #34 models
> select #34.3
61064 atoms, 65713 bonds, 3 pseudobonds, 4898 residues, 3 models selected
> hide #34.9 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig3_I1bys.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #13 models
> select #13.3
61103 atoms, 65762 bonds, 4902 residues, 1 model selected
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig3_I1spc.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #14 models
> ~display #14.3/w:38,49
> select #14.3
60702 atoms, 65388 bonds, 1 pseudobond, 4855 residues, 2 models selected
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig3_I2fa.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> view dc5
> hide models
> show #30 models
> select #30.3
60930 atoms, 65574 bonds, 3 pseudobonds, 4887 residues, 3 models selected
> hide #30.9 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig3_ysH1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #31 models
> select #31.3
60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected
> hide #31.9 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig3_ysH1b.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #32 models
> select #32.3
60097 atoms, 64722 bonds, 4 pseudobonds, 4779 residues, 3 models selected
> hide #32.9 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig3_ysH1c.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #12 models
> select #12.3
55765 atoms, 60298 bonds, 4230 residues, 1 model selected
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig3_H1apo.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #33 models
> select #33.3
61025 atoms, 65674 bonds, 2 pseudobonds, 4898 residues, 3 models selected
> hide #33.9 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig3_ysI1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #34 models
> select #34.3
61064 atoms, 65713 bonds, 3 pseudobonds, 4898 residues, 3 models selected
> hide #34.9 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig3_I1bys.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #13 models
> select #13.3
61103 atoms, 65762 bonds, 4902 residues, 1 model selected
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig3_I1spc.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #14 models
> ~display #14.3/w:38,49
> select #14.3
60702 atoms, 65388 bonds, 1 pseudobond, 4855 residues, 2 models selected
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig3_I2fa.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> volume emmaps style surface step 1 level 8
> surface dust emmaps size 2
> volume emmaps surfaceSmoothing true
> hide models
> show #30.3,5,9 models
> select #30.3
60930 atoms, 65574 bonds, 3 pseudobonds, 4887 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysH1a-FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #31.3,5,9 models
> select #31.3
60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysH1b-FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #32.3,5,9 models
> select #32.3
60097 atoms, 64722 bonds, 4 pseudobonds, 4779 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysH1c-FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #33.3,5,9 models
> select #33.3
61025 atoms, 65674 bonds, 2 pseudobonds, 4898 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysI1a-FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #34.3,5,9 models
> select #34.3
61064 atoms, 65713 bonds, 3 pseudobonds, 4898 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysI1b-FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> view dc4
> hide models
> show #30.3,5,9 models
> select #30.3
60930 atoms, 65574 bonds, 3 pseudobonds, 4887 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig8_ysH1a-FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #31.3,5,9 models
> select #31.3
60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig8_ysH1b-FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #32.3,5,9 models
> select #32.3
60097 atoms, 64722 bonds, 4 pseudobonds, 4779 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig8_ysH1c-FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #33.3,5,9 models
> select #33.3
61025 atoms, 65674 bonds, 2 pseudobonds, 4898 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig8_ysI1a-FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #34.3,5,9 models
> select #34.3
61064 atoms, 65713 bonds, 3 pseudobonds, 4898 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig8_ysI1b-FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> view dc4
> hide models
> show #30.3,5,9 models
> select #30.3
60930 atoms, 65574 bonds, 3 pseudobonds, 4887 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig8_ysH1a-FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #31.3,5,9 models
> select #31.3
60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig8_ysH1b-FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #32.3,5,9 models
> select #32.3
60097 atoms, 64722 bonds, 4 pseudobonds, 4779 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig8_ysH1c-FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #33.3,5,9 models
> select #33.3
61025 atoms, 65674 bonds, 2 pseudobonds, 4898 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig8_ysI1a-FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> hide models
> show #34.3,5,9 models
> select #34.3
61064 atoms, 65713 bonds, 3 pseudobonds, 4898 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig8_ysI1b-FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground true
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Unable to save 'nucleotides' -> <chimerax.nucleotides._data.NucleotideState
object at 0x7f33faefe1c0>". Session might not restore properly.
——— End of log from Mon Jul 31 16:31:22 2023 ———
opened ChimeraX session
OpenGL version: 4.5 (Core Profile) Mesa 23.1.0
OpenGL renderer: llvmpipe (LLVM 15.0.7, 256 bits)
OpenGL vendor: Mesa
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb
XDG_SESSION_TYPE=
DESKTOP_SESSION=
XDG_SESSION_DESKTOP=
XDG_CURRENT_DESKTOP=
DISPLAY=localhost:10.0
Manufacturer: TYAN
Model: B7105F48TV4HR-2T-N
OS: CentOS Stream 8 n/a
Architecture: 64bit ELF
Virtual Machine: none
CPU: 72 Intel(R) Xeon(R) Gold 5220 CPU @ 2.20GHz
Cache Size: 25344 KB
Memory:
total used free shared buff/cache available
Mem: 376Gi 22Gi 296Gi 327Mi 57Gi 351Gi
Swap: 9Gi 0B 9Gi
Graphics:
04:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)
Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000]
Kernel driver in use: ast
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (5)
comment:1 by , 2 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Nucleotide restore state is None |
comment:2 by , 2 years ago
| Description: | modified (diff) |
|---|---|
| Status: | assigned → feedback |
comment:3 by , 2 years ago
The session is too large to send over email as an attachment, can we send by dropbox?
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Thursday, August 3, 2023 at 5:43 PM
To: gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>, Rundlet, Emily <Emily.Rundlet@STJUDE.ORG>
Subject: Re: [ChimeraX] #9513: Nucleotide restore state is None
Caution: External Sender. Do not open unless you know the content is safe.
#9513: Nucleotide restore state is None
--------------------------------------+------------------------
Reporter: Emily.Rundlet@… | Owner: Greg Couch
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: Sessions | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------------+------------------------
Changes (by Greg Couch):
* status: assigned => feedback
Old description:
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New description:
{{{
The following bug report has been submitted:
Platform: Linux-4.18.0-500.el8.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
}}}
The error occurs upon attempting to load a session file previously written
by ChimeraX 1.6.1. Limited local debugging suggests that it is associated
with loading "NucleotideState" data. The issue manifested after upgrading
from ChimeraX 1.3. We can provide a session file with which we can
reliably reproduce the issue, but not via e-mail, on account of file size.
In addition to a bug fix, we hope you can provide advice and / or
assistance with recovering the seemingly-corrupted session files.
{{{
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
format
> session
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at
level
8, step 1, values float32
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 734, in restore
obj = sm.restore_snapshot(self, data)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/nucleotides/_data.py", line 472, in restore_snapshot
if data['version'] != 1:
TypeError: 'NoneType' object is not subscriptable
Log from Mon Jul 31 16:31:22 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at level 3,
step 1, values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at level 3,
step 1, values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at level 3, step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at level
3,
step 1, values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at level 3,
step
1, values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at level
3,
step 1, values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at
level
3, step 1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at level
3,
step 1, values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at
level
3, step 1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at level
3,
step 1, values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at
level
3, step 1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at level
3,
step 1, values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at
level
3, step 1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at level
3,
step 1, values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at
level
3, step 1, values float32
Log from Mon Jul 31 14:44:45 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at
level
8, step 1, values float32
Log from Thu Jul 20 18:51:54 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at
level
8, step 1, values float32
Log from Wed Jul 19 18:31:44 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at
level
8, step 1, values float32
Log from Tue Jul 18 13:01:32 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at
level
8, step 1, values float32
Log from Tue Jul 18 11:01:24 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at
level
8, step 1, values float32
Log from Thu Jun 15 17:34:19 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at
level
8, step 1, values float32
Log from Thu Jun 15 13:56:32 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at
level
8, step 1, values float32
Log from Mon Jun 12 17:35:46 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at
level
6, step 1, values float32
Log from Mon Jun 12 15:39:44 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at level 3, step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Log from Tue May 23 15:01:38 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at level 4, step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Log from Mon May 22 15:00:55 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at level 4, step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Log from Mon May 22 11:11:24 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at level
4,
step 1, values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Log from Tue May 16 16:53:33 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open gtpys/helix/gtpys_helix.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at level 0.000164, step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at level 4,
step 1, values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at level 4,
step 1, values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at level 4, step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at level
4,
step 1, values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at level 4,
step
1, values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at level
4,
step 1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at level
4,
step 1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at level
4,
step 1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at level
4,
step 1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at level
4,
step 1, values float32
Log from Tue May 16 16:15:28 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open gtpys/helix/argb_helix.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at step 1, values float32
Opened arg_j152.mrc as #20.1, grid size 380,380,380, pixel 1.05, shown at
step
1, values float32
Opened arg-apo.mrc as #21.1, grid size 360,360,360, pixel 1.08, shown at
step
1, values float32
Opened POST_j93ct15_pplocal_g0_n.mrc as #15.1, grid size 576,576,576,
pixel
1.06, shown at step 1, values float32
Opened PREC_job225_ct14_pplocal_g0_n.mrc as #10.1, grid size 576,576,576,
pixel 1.06, shown at step 1, values float32
opened ChimeraX session
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_startup_gtpys.cxc
> close all
> open /data/EmilyRundlet/ChimeraX_70S/Maps/4ybb_50Score_3A.mrc
Opened 4ybb_50Score_3A.mrc as #1, grid size 576,576,576, pixel 1.06, shown
at
level 0.000164, step 4, values float32
> rename #1 id #100
> open /data/EmilyRundlet/ChimeraX_70S/Models/prec_7n1p_50S.pdb
Chain information for prec_7n1p_50S.pdb #1
---
Chain | Description
3 | No description available
5 | No description available
P | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #101
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_post.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/post_50S.pdb
name
> post5
Chain information for post5 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #15.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/post_30S.pdb
name
> post3
Chain information for post3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
y | No description available
> rename #1 id #15.3
> open
>
/data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/POST_j93ct15_pplocal_g0_n.mrc
> name post
Opened post as #1, grid size 576,576,576, pixel 1.06, shown at level 1.16,
step 4, values float32
> rename #1 id #15.1
> rename #15 post
> matchmaker #15.5 to #101 matrix Nucleic bring #15.1#15.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with post5, chain 3 (#15.5),
sequence alignment score = 11580.3
RMSD between 2766 pruned atom pairs is 0.341 angstroms; (across all 2904
pairs: 2.745)
> fitmap #15.1 inMap #100
Fit map post in map 4ybb_50Score_3A.mrc using 29937 points
correlation = 0.7033, correlation about mean = 0.6059, overlap = 7.619e+04
steps = 48, shift = 0.0376, angle = 0.0465 degrees
Position of post (#15.1) relative to 4ybb_50Score_3A.mrc (#100)
coordinates:
Matrix rotation and translation
0.99999983 0.00051499 -0.00026539 -0.07015622
-0.00051501 0.99999986 -0.00009768 0.21094928
0.00026534 0.00009781 0.99999996 -0.12735627
Axis 0.16636276 -0.45165257 -0.87654628
Axis point 413.67366807 137.87803145 0.00000000
Rotation angle (degrees) 0.03366312
Shift along axis 0.00468650
> fitmap #15.5 inMap #15.1
Fit molecule post5 (#15.5) to map post (#15.1) using 90903 atoms
average map value = 15.29, steps = 40
shifted from previous position = 0.0173
rotated from previous position = 0.0481 degrees
atoms outside contour = 27101, contour level = 1.1571
Position of post5 (#15.5) relative to post (#15.1) coordinates:
Matrix rotation and translation
1.00000000 0.00007488 -0.00001293 -0.00984527
-0.00007488 1.00000000 0.00003964 0.01927617
0.00001293 -0.00003964 1.00000000 0.00608995
Axis -0.46249937 -0.15083335 -0.87369539
Axis point 250.02744189 154.19286933 0.00000000
Rotation angle (degrees) 0.00491036
Shift along axis -0.00367482
> fitmap #15.3 inMap #15.1
Fit molecule post3 (#15.3) to map post (#15.1) using 55643 atoms
average map value = 11.56, steps = 40
shifted from previous position = 0.0883
rotated from previous position = 0.0476 degrees
atoms outside contour = 13831, contour level = 1.1571
Position of post3 (#15.3) relative to post (#15.1) coordinates:
Matrix rotation and translation
1.00000000 -0.00005318 -0.00004310 0.02635100
0.00005318 1.00000000 -0.00000125 -0.02050708
0.00004310 0.00000124 1.00000000 -0.01832489
Axis 0.01818364 -0.62958007 0.77672279
Axis point 395.65049914 495.82230346 0.00000000
Rotation angle (degrees) 0.00392252
Shift along axis -0.00084336
executed 70S_open_post.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_prec.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/prec_50S.pdb
name
> prec5
Chain information for prec5 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #10.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/prec_30S.pdb
name
> prec3
Chain information for prec3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
y | No description available
> rename #1 id #10.3
> open
>
/data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/PREC*local*.mrc
> name prec
Opened prec as #1, grid size 576,576,576, pixel 1.06, shown at level
0.719,
step 4, values float32
> rename #1 id #10.1
> rename #10 prec
> matchmaker #10.5 to #101 matrix Nucleic bring #10.1#10.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with prec5, chain 3 (#10.5),
sequence alignment score = 11585.2
RMSD between 2904 pruned atom pairs is 0.000 angstroms; (across all 2904
pairs: 0.000)
> fitmap #10.1 inMap #100
Fit map prec in map 4ybb_50Score_3A.mrc using 29930 points
correlation = 0.705, correlation about mean = 0.6153, overlap = 7.403e+04
steps = 100, shift = 0.0276, angle = 0.0213 degrees
Position of prec (#10.1) relative to 4ybb_50Score_3A.mrc (#100)
coordinates:
Matrix rotation and translation
0.99999993 0.00023597 -0.00028739 0.01666834
-0.00023597 0.99999997 0.00000377 0.08653163
0.00028739 -0.00000370 0.99999996 -0.10871255
Axis -0.01003658 -0.77282074 -0.63454501
Axis point 373.98904576 -0.00000000 57.97612114
Rotation angle (degrees) 0.02130699
Shift along axis 0.00194228
> fitmap #10.5 inMap #10.1
Fit molecule prec5 (#10.5) to map prec (#10.1) using 93196 atoms
average map value = 15.31, steps = 40
shifted from previous position = 0.0241
rotated from previous position = 0.0378 degrees
atoms outside contour = 32220, contour level = 0.71858
Position of prec5 (#10.5) relative to prec (#10.1) coordinates:
Matrix rotation and translation
0.99999996 0.00028462 -0.00008450 -0.07054285
-0.00028461 0.99999995 0.00015462 0.06036830
0.00008454 -0.00015460 0.99999998 0.02731692
Axis -0.46188152 -0.25249170 -0.85024314
Axis point 206.84210925 257.43360450 0.00000000
Rotation angle (degrees) 0.01917937
Shift along axis -0.00588608
> fitmap #10.3 inMap #10.1
Fit molecule prec3 (#10.3) to map prec (#10.1) using 56259 atoms
average map value = 11.39, steps = 48
shifted from previous position = 0.0796
rotated from previous position = 0.0392 degrees
atoms outside contour = 16720, contour level = 0.71858
Position of prec3 (#10.3) relative to prec (#10.1) coordinates:
Matrix rotation and translation
0.99999994 0.00035395 -0.00002496 -0.09187678
-0.00035394 0.99999993 0.00014842 0.08455945
0.00002502 -0.00014841 0.99999999 0.04385687
Axis -0.38587760 -0.06497510 -0.92025905
Axis point 236.94211808 270.96015369 0.00000000
Rotation angle (degrees) 0.02203670
Shift along axis -0.01040075
executed 70S_open_prec.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_fa.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/fa_50S.pdb name
> i2fa5
Chain information for i2fa5 #1
---
Chain | Description
3 | No description available
5 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
K | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #14.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/fa_30S.pdb name
> i2fa3
Chain information for i2fa3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
x | No description available
y | No description available
> rename #1 id #14.3
> open
> /data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/FA*local*.mrc
Opened FA_j118_localres_filt_g0_n.mrc as #1, grid size 576,576,576, pixel
1.06, shown at level 0.555, step 4, values float32
> rename #1 id #14.1
> matchmaker #14.5 to #101 matrix Nucleic bring #14.1#14.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with i2fa5, chain 3 (#14.5),
sequence alignment score = 11567.9
RMSD between 2675 pruned atom pairs is 0.458 angstroms; (across all 2903
pairs: 3.500)
> rename #14 fa
> fitmap #14.1 inMap #100
Fit map FA_j118_localres_filt_g0_n.mrc in map 4ybb_50Score_3A.mrc using
29876
points
correlation = 0.7652, correlation about mean = 0.6917, overlap = 8.026e+04
steps = 124, shift = 0.0674, angle = 0.0469 degrees
Position of FA_j118_localres_filt_g0_n.mrc (#14.1) relative to
4ybb_50Score_3A.mrc (#100) coordinates:
Matrix rotation and translation
0.99999951 0.00082837 -0.00054821 -0.07721517
-0.00082823 0.99999963 0.00024790 0.22483688
0.00054841 -0.00024745 0.99999982 -0.11895947
Axis -0.24193109 -0.53558675 -0.80908354
Axis point 267.87230737 94.97670830 0.00000000
Rotation angle (degrees) 0.05865666
Shift along axis -0.00549075
> fitmap #14.5 inMap #14.1
Fit molecule i2fa5 (#14.5) to map FA_j118_localres_filt_g0_n.mrc (#14.1)
using
94455 atoms
average map value = 14.71, steps = 44
shifted from previous position = 0.0492
rotated from previous position = 0.0489 degrees
atoms outside contour = 26009, contour level = 0.5555
Position of i2fa5 (#14.5) relative to FA_j118_localres_filt_g0_n.mrc
(#14.1)
coordinates:
Matrix rotation and translation
0.99999999 0.00013549 0.00005439 -0.05910674
-0.00013549 0.99999999 -0.00008462 0.07061428
-0.00005440 0.00008461 0.99999999 -0.01606966
Axis 0.50141948 0.32233497 -0.80291884
Axis point 506.79859217 458.57499403 0.00000000
Rotation angle (degrees) 0.00966859
Shift along axis 0.00602682
> fitmap #14.3 inMap #14.1
Fit molecule i2fa3 (#14.3) to map FA_j118_localres_filt_g0_n.mrc (#14.1)
using
60702 atoms
average map value = 7.538, steps = 40
shifted from previous position = 0.104
rotated from previous position = 0.0489 degrees
atoms outside contour = 11367, contour level = 0.5555
Position of i2fa3 (#14.3) relative to FA_j118_localres_filt_g0_n.mrc
(#14.1)
coordinates:
Matrix rotation and translation
0.99999996 0.00022144 0.00016174 -0.14067075
-0.00022141 0.99999996 -0.00017040 0.12305826
-0.00016178 0.00017037 0.99999997 -0.00200513
Axis 0.52777238 0.50104898 -0.68586167
Axis point 581.05763080 608.65192133 0.00000000
Rotation angle (degrees) 0.01849719
Shift along axis -0.01120868
executed 70S_open_fa.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_spc.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/spc_50S.pdb
name
> i1spc5
Chain information for i1spc5 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #13.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/spc_30S.pdb
name
> i1spc3
Chain information for i1spc3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
x | No description available
y | No description available
> rename #1 id #13.3
> open
>
/data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/INT1_spc*local*.mrc
> name i1spc
Opened i1spc as #1, grid size 576,576,576, pixel 1.06, shown at level
0.527,
step 4, values float32
> rename #1 id #13.1
> rename #13 i1spc
> matchmaker #13.5 to #101 matrix Nucleic bring #13.1#13.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with i1spc5, chain 3 (#13.5),
sequence alignment score = 11576.1
RMSD between 2613 pruned atom pairs is 0.440 angstroms; (across all 2904
pairs: 4.190)
> fitmap #13.1 inMap #100
Fit map i1spc in map 4ybb_50Score_3A.mrc using 29799 points
correlation = 0.7329, correlation about mean = 0.6398, overlap = 7.208e+04
steps = 104, shift = 0.0985, angle = 0.0628 degrees
Position of i1spc (#13.1) relative to 4ybb_50Score_3A.mrc (#100)
coordinates:
Matrix rotation and translation
0.99999127 -0.00305790 -0.00284733 1.91534327
0.00305942 0.99999518 0.00052889 -1.13631859
0.00284570 -0.00053760 0.99999581 -1.01117770
Axis -0.12659581 -0.67578369 0.72614730
Axis point 418.51647841 616.51914515 0.00000000
Rotation angle (degrees) 0.24134036
Shift along axis -0.20883282
> fitmap #13.5 inMap #13.1
Fit molecule i1spc5 (#13.5) to map i1spc (#13.1) using 93017 atoms
average map value = 14.57, steps = 48
shifted from previous position = 0.0733
rotated from previous position = 0.0651 degrees
atoms outside contour = 27434, contour level = 0.52653
Position of i1spc5 (#13.5) relative to i1spc (#13.1) coordinates:
Matrix rotation and translation
1.00000000 -0.00000053 -0.00005875 0.01737643
0.00000053 1.00000000 -0.00002655 0.00255801
0.00005875 0.00002655 1.00000000 -0.03456253
Axis 0.41177423 -0.91124934 0.00816220
Axis point 588.98331322 0.00000000 263.93669119
Rotation angle (degrees) 0.00369369
Shift along axis 0.00454208
> fitmap #13.3 inMap #13.1
Fit molecule i1spc3 (#13.3) to map i1spc (#13.1) using 61103 atoms
average map value = 9.699, steps = 60
shifted from previous position = 0.162
rotated from previous position = 0.0627 degrees
atoms outside contour = 14669, contour level = 0.52653
Position of i1spc3 (#13.3) relative to i1spc (#13.1) coordinates:
Matrix rotation and translation
0.99999999 0.00006855 -0.00007419 -0.00808096
-0.00006856 1.00000000 -0.00003421 0.02476248
0.00007419 0.00003421 1.00000000 -0.04490669
Axis 0.32075098 -0.69563238 -0.64281755
Axis point 526.89840240 0.00000000 -148.08272269
Rotation angle (degrees) 0.00611054
Shift along axis 0.00904925
executed 70S_open_spc.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_h1.cxc
> open
>
/data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/apo_H1*local*.mrc
> name hy1
Opened hy1 as #1, grid size 576,576,576, pixel 1.06, shown at level 0.822,
step 4, values float32
> rename #1 id #12.1
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/h1_50S.pdb name
> hy15
Chain information for hy15 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #12.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/h1_30S.pdb name
> hy13
Chain information for hy13 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
y | No description available
> rename #1 id #12.3
> matchmaker #12.5 to #101 matrix Nucleic bring #12.1#12.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with hy15, chain 3 (#12.5),
sequence alignment score = 11572.3
RMSD between 2683 pruned atom pairs is 0.437 angstroms; (across all 2902
pairs: 4.227)
> fitmap #12.1 inMap #100
Fit map hy1 in map 4ybb_50Score_3A.mrc using 29865 points
correlation = 0.7182, correlation about mean = 0.6351, overlap = 7.48e+04
steps = 80, shift = 0.0539, angle = 0.0362 degrees
Position of hy1 (#12.1) relative to 4ybb_50Score_3A.mrc (#100)
coordinates:
Matrix rotation and translation
0.99999993 0.00033939 -0.00014651 -0.03967194
-0.00033939 0.99999994 0.00003379 0.08904027
0.00014652 -0.00003374 0.99999999 -0.04209798
Axis -0.09096206 -0.39471037 -0.91429187
Axis point 270.42268136 115.08181596 0.00000000
Rotation angle (degrees) 0.02126851
Shift along axis 0.00695336
> fitmap #12.5 inMap #12.1
Fit molecule hy15 (#12.5) to map hy1 (#12.1) using 91053 atoms
average map value = 15.92, steps = 40
shifted from previous position = 0.0355
rotated from previous position = 0.0365 degrees
atoms outside contour = 31662, contour level = 0.82202
Position of hy15 (#12.5) relative to hy1 (#12.1) coordinates:
Matrix rotation and translation
1.00000000 0.00001739 -0.00003452 0.00191493
-0.00001738 1.00000000 0.00005119 -0.00075625
0.00003452 -0.00005119 1.00000000 0.00373129
Axis -0.79805293 -0.53818813 -0.27104440
Axis point 0.00000000 61.60073087 37.19705100
Rotation angle (degrees) 0.00367501
Shift along axis -0.00213255
> fitmap #12.3 inMap #12.1
Fit molecule hy13 (#12.3) to map hy1 (#12.1) using 55765 atoms
average map value = 9.817, steps = 44
shifted from previous position = 0.0694
rotated from previous position = 0.0332 degrees
atoms outside contour = 14540, contour level = 0.82202
Position of hy13 (#12.3) relative to hy1 (#12.1) coordinates:
Matrix rotation and translation
1.00000000 -0.00000897 0.00000895 -0.00690250
0.00000897 0.99999999 0.00011154 -0.02727097
-0.00000895 -0.00011154 0.99999999 0.03999319
Axis -0.99361126 0.07969592 0.07990759
Axis point 0.00000000 352.90975575 250.15609103
Rotation angle (degrees) 0.00643159
Shift along axis 0.00788078
executed 70S_open_h1.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_ys.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1a_50S.pdb
name
> ys-H1a5
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1a_50S.pdb
---
warnings | Ignored bad PDB record found on line 4
LINK ZN ZN Le0201 SG CY 04
Ignored bad PDB record found on line 5
LINK ZN ZN Le0201 SG CY 03
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 01
Ignored bad PDB record found on line 7
LINK ZN ZN Le0201 SG CY 01
Ignored bad PDB record found on line 8
LINK ZN ZN Lj0101 ND1 HI 03
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue ASP (2432820)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-H1a5 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #30.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1a_30S.pdb
name
> ys-H1a3
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1a_30S.pdb
---
warnings | Ignored bad PDB record found on line 4
LINK ZN ZN Le0201 SG CY 04
Ignored bad PDB record found on line 5
LINK ZN ZN Le0201 SG CY 03
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 01
Ignored bad PDB record found on line 7
LINK ZN ZN Le0201 SG CY 01
Ignored bad PDB record found on line 8
LINK ZN ZN Lj0101 ND1 HI 03
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue ASP (2432820)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-H1a3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
x | No description available
y | No description available
> rename #1 id #30.3
> open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/ys-H1a*.mrc name
ys-H1a
Opened ys-H1a as #1, grid size 512,512,512, pixel 0.826, shown at level
3.13,
step 2, values float32
> rename #1 id #30.1
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1b_50S.pdb
name
> ys-H1b5
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1b_50S.pdb
---
warnings | Ignored bad PDB record found on line 5
LINK ZN ZN Le0201 SG CY 04
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 03
Ignored bad PDB record found on line 7
LINK ZN ZN Le0201 SG CY 01
Ignored bad PDB record found on line 8
LINK ZN ZN Le0201 SG CY 01
Ignored bad PDB record found on line 9
LINK ZN ZN Lj0101 ND1 HI 03
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue LYS (2432823)
Cannot find LINK/SSBOND residue THR (2432824)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-H1b5 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #31.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1b_30S.pdb
name
> ys-H1b3
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1b_30S.pdb
---
warnings | Ignored bad PDB record found on line 5
LINK ZN ZN Le0201 SG CY 04
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 03
Ignored bad PDB record found on line 7
LINK ZN ZN Le0201 SG CY 01
Ignored bad PDB record found on line 8
LINK ZN ZN Le0201 SG CY 01
Ignored bad PDB record found on line 9
LINK ZN ZN Lj0101 ND1 HI 03
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue LYS (2432823)
Cannot find LINK/SSBOND residue THR (2432824)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-H1b3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
x | No description available
y | No description available
> rename #1 id #31.3
> open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/ys-H1b*.mrc name
ys-H1b
Opened ys-H1b as #1, grid size 512,512,512, pixel 0.826, shown at level
3.16,
step 2, values float32
> rename #1 id #31.1
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1c_50S.pdb
name
> ys-H1c5
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1c_50S.pdb
---
warnings | Ignored bad PDB record found on line 2
LINK ZN ZN Lj0101 ND1 HI 03
Ignored bad PDB record found on line 3
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 4
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 5
LINK ZN ZN Lj0101 SG CY 02
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 04
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-H1c5 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #32.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1c_30S.pdb
name
> ys-H1c3
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1c_30S.pdb
---
warnings | Ignored bad PDB record found on line 2
LINK ZN ZN Lj0101 ND1 HI 03
Ignored bad PDB record found on line 3
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 4
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 5
LINK ZN ZN Lj0101 SG CY 02
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 04
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-H1c3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
x | No description available
y | No description available
> rename #1 id #32.3
> open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/ys-H1c*.mrc name
ys-H1c
Opened ys-H1c as #1, grid size 512,512,512, pixel 0.826, shown at level
3.11,
step 2, values float32
> rename #1 id #32.1
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1a_50S.pdb
name
> ys-I1a5
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1a_50S.pdb
---
warnings | Ignored bad PDB record found on line 2
LINK ZN ZN Lj0101 ND1 HI 03
Ignored bad PDB record found on line 3
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 4
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 5
LINK ZN ZN Lj0101 SG CY 02
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 04
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-I1a5 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #33.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1a_30S.pdb
name
> ys-I1a3
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1a_30S.pdb
---
warnings | Ignored bad PDB record found on line 2
LINK ZN ZN Lj0101 ND1 HI 03
Ignored bad PDB record found on line 3
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 4
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 5
LINK ZN ZN Lj0101 SG CY 02
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 04
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-I1a3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
x | No description available
y | No description available
> rename #1 id #33.3
> open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/ys-I1a*.mrc name
ys-I1a
Opened ys-I1a as #1, grid size 512,512,512, pixel 0.826, shown at level
3.09,
step 2, values float32
> rename #1 id #33.1
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1b_50S.pdb
name
> ys-I1b5
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1b_50S.pdb
---
warnings | Ignored bad PDB record found on line 2
LINK ZN ZN Lj0101 ND1 HI 03
Ignored bad PDB record found on line 3
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 4
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 5
LINK ZN ZN Lj0101 SG CY 02
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 04
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-I1b5 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #34.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1b_30S.pdb
name
> ys-I1b3
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1b_30S.pdb
---
warnings | Ignored bad PDB record found on line 2
LINK ZN ZN Lj0101 ND1 HI 03
Ignored bad PDB record found on line 3
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 4
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 5
LINK ZN ZN Lj0101 SG CY 02
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 04
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-I1b3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
x | No description available
y | No description available
> rename #1 id #34.3
> open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/ys-I1b*.mrc name
ys-I1b
Opened ys-I1b as #1, grid size 512,512,512, pixel 0.826, shown at level
3.09,
step 2, values float32
> rename #1 id #34.1
> matchmaker #30.5 to #101 matrix Nucleic bring #30.1#30.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with ys-H1a5, chain 3
(#30.5),
sequence alignment score = 11576.1
RMSD between 2631 pruned atom pairs is 0.435 angstroms; (across all 2904
pairs: 4.260)
> matchmaker #31.5 to #101 matrix Nucleic bring #31.1#31.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with ys-H1b5, chain 3
(#31.5),
sequence alignment score = 11576.1
RMSD between 2629 pruned atom pairs is 0.438 angstroms; (across all 2904
pairs: 4.264)
> matchmaker #32.5 to #101 matrix Nucleic bring #32.1#32.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with ys-H1c5, chain 3
(#32.5),
sequence alignment score = 11576.1
RMSD between 2600 pruned atom pairs is 0.428 angstroms; (across all 2904
pairs: 4.256)
> matchmaker #33.5 to #101 matrix Nucleic bring #33.1#33.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with ys-I1a5, chain 3
(#33.5),
sequence alignment score = 11576.1
RMSD between 2595 pruned atom pairs is 0.428 angstroms; (across all 2904
pairs: 4.252)
> matchmaker #34.5 to #101 matrix Nucleic bring #34.1#34.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with ys-I1b5, chain 3
(#34.5),
sequence alignment score = 11576.1
RMSD between 2617 pruned atom pairs is 0.432 angstroms; (across all 2904
pairs: 4.229)
> fitmap #30.1 inMap #100
Fit map ys-H1a in map 4ybb_50Score_3A.mrc using 167516 points
correlation = 0.7712, correlation about mean = 0.5068, overlap = 5.636e+05
steps = 116, shift = 0.0431, angle = 0.06 degrees
Position of ys-H1a (#30.1) relative to 4ybb_50Score_3A.mrc (#100)
coordinates:
Matrix rotation and translation
-0.16096874 0.07054784 0.98443490 117.93148350
-0.09736653 -0.99371151 0.05529186 532.16401993
0.98214501 -0.08695075 0.16682549 84.98416227
Axis -0.64633407 0.01040498 -0.76298362
Axis point 42.26680055 265.56440366 0.00000000
Rotation angle (degrees) 173.68249450
Shift along axis -135.52750571
> fitmap #30.5 inMap #30.1
Fit molecule ys-H1a5 (#30.5) to map ys-H1a (#30.1) using 92994 atoms
average map value = 7.904, steps = 44
shifted from previous position = 0.0158
rotated from previous position = 0.0583 degrees
atoms outside contour = 20674, contour level = 3.1252
Position of ys-H1a5 (#30.5) relative to ys-H1a (#30.1) coordinates:
Matrix rotation and translation
1.00000000 0.00007896 0.00002842 -0.01618923
-0.00007896 1.00000000 0.00000766 0.01408032
-0.00002842 -0.00000766 1.00000000 0.00064511
Axis -0.09088428 0.33726732 -0.93701163
Axis point 154.32943537 198.57692600 0.00000000
Rotation angle (degrees) 0.00482813
Shift along axis 0.00561570
> fitmap #30.3 inMap #30.1
Fit molecule ys-H1a3 (#30.3) to map ys-H1a (#30.1) using 60930 atoms
average map value = 5.423, steps = 44
shifted from previous position = 0.107
rotated from previous position = 0.0638 degrees
atoms outside contour = 21357, contour level = 3.1252
Position of ys-H1a3 (#30.3) relative to ys-H1a (#30.1) coordinates:
Matrix rotation and translation
1.00000000 -0.00007009 0.00004160 -0.00010326
0.00007009 1.00000000 -0.00003531 -0.00429301
-0.00004159 0.00003531 1.00000000 -0.00573932
Axis 0.39752790 0.46828522 0.78910108
Axis point 17.28659253 35.84690625 0.00000000
Rotation angle (degrees) 0.00508928
Shift along axis -0.00658030
> fitmap #31.1 inMap #100
Fit map ys-H1b in map 4ybb_50Score_3A.mrc using 167746 points
correlation = 0.7557, correlation about mean = 0.4732, overlap = 4.809e+05
steps = 104, shift = 0.0913, angle = 0.169 degrees
Position of ys-H1b (#31.1) relative to 4ybb_50Score_3A.mrc (#100)
coordinates:
Matrix rotation and translation
-0.16402794 0.07279267 0.98376626 117.06968879
-0.09958269 -0.99340097 0.05690170 531.99178964
0.98141639 -0.08863262 0.17019441 84.62198725
Axis -0.64507570 0.01041575 -0.76404768
Axis point 42.56283115 265.45365415 0.00000000
Rotation angle (degrees) 173.52301718
Shift along axis -134.63295191
> fitmap #31.5 inMap #31.1
Fit molecule ys-H1b5 (#31.5) to map ys-H1b (#31.1) using 92994 atoms
average map value = 6.419, steps = 48
shifted from previous position = 0.0121
rotated from previous position = 0.0631 degrees
atoms outside contour = 25942, contour level = 3.1558
Position of ys-H1b5 (#31.5) relative to ys-H1b (#31.1) coordinates:
Matrix rotation and translation
0.99999984 0.00056889 -0.00006451 -0.12124833
-0.00056878 0.99999829 0.00175780 -0.12851585
0.00006551 -0.00175777 0.99999845 0.36559707
Axis -0.95083394 -0.03516616 -0.30769816
Axis point 0.00000000 209.20515420 73.16839244
Rotation angle (degrees) 0.10592152
Shift along axis 0.00731289
> fitmap #31.3 inMap #31.1
Fit molecule ys-H1b3 (#31.3) to map ys-H1b (#31.1) using 60958 atoms
average map value = 4.602, steps = 44
shifted from previous position = 0.0971
rotated from previous position = 0.114 degrees
atoms outside contour = 25030, contour level = 3.1558
Position of ys-H1b3 (#31.3) relative to ys-H1b (#31.1) coordinates:
Matrix rotation and translation
0.99999972 -0.00035593 0.00066202 -0.06165935
0.00035492 0.99999877 0.00152816 -0.29466909
-0.00066256 -0.00152792 0.99999861 0.44538378
Axis -0.89731715 0.38891986 0.20871819
Axis point 0.00000000 286.71155040 201.62993409
Rotation angle (degrees) 0.09756906
Shift along axis 0.03368503
> fitmap #32.1 inMap #100
Fit map ys-H1c in map 4ybb_50Score_3A.mrc using 167598 points
correlation = 0.7687, correlation about mean = 0.5028, overlap = 5.462e+05
steps = 64, shift = 0.174, angle = 0.0444 degrees
Position of ys-H1c (#32.1) relative to 4ybb_50Score_3A.mrc (#100)
coordinates:
Matrix rotation and translation
-0.16402649 0.07085424 0.98390802 117.46660733
-0.09904792 -0.99355948 0.05503707 532.18633927
0.98147074 -0.08842650 0.16998804 84.56695102
Axis -0.64511751 0.01095977 -0.76400477
Axis point 42.50698240 265.58065026 0.00000000
Rotation angle (degrees) 173.61597695
Shift along axis -134.55667780
> fitmap #32.5 inMap #32.1
Fit molecule ys-H1c5 (#32.5) to map ys-H1c (#32.1) using 92992 atoms
average map value = 7.486, steps = 36
shifted from previous position = 0.0219
rotated from previous position = 0.0647 degrees
atoms outside contour = 22168, contour level = 3.1136
Position of ys-H1c5 (#32.5) relative to ys-H1c (#32.1) coordinates:
Matrix rotation and translation
0.99999983 -0.00057175 0.00006040 0.12367865
0.00057186 0.99999823 -0.00179030 0.13731617
-0.00005938 0.00179034 0.99999840 -0.36604473
Axis 0.95211000 0.03184871 0.30409245
Axis point 0.00000000 206.36170644 76.30401858
Rotation angle (degrees) 0.10773729
Shift along axis 0.01081758
> fitmap #32.3 inMap #32.1
Fit molecule ys-H1c3 (#32.3) to map ys-H1c (#32.1) using 60097 atoms
average map value = 5.192, steps = 48
shifted from previous position = 0.133
rotated from previous position = 0.0654 degrees
atoms outside contour = 21804, contour level = 3.1136
Position of ys-H1c3 (#32.3) relative to ys-H1c (#32.1) coordinates:
Matrix rotation and translation
0.99999975 0.00002916 -0.00070103 0.13056968
-0.00003034 0.99999858 -0.00168673 0.26834816
0.00070098 0.00168675 0.99999833 -0.48614194
Axis 0.92330390 -0.38372472 -0.01628638
Axis point 0.00000000 288.12835311 164.65187972
Rotation angle (degrees) 0.10467114
Shift along axis 0.02550116
> fitmap #33.1 inMap #100
Fit map ys-I1a in map 4ybb_50Score_3A.mrc using 167703 points
correlation = 0.7667, correlation about mean = 0.498, overlap = 5.302e+05
steps = 104, shift = 0.0538, angle = 0.0755 degrees
Position of ys-I1a (#33.1) relative to 4ybb_50Score_3A.mrc (#100)
coordinates:
Matrix rotation and translation
-0.16092884 0.07096607 0.98441136 117.88246252
-0.09669854 -0.99374659 0.05583104 532.06291528
0.98221754 -0.08620632 0.16678480 84.75523562
Axis -0.64635360 0.00998316 -0.76297271
Axis point 42.30362323 265.49282475 0.00000000
Rotation angle (degrees) 173.69183881
Shift along axis -135.54801612
> fitmap #33.5 inMap #33.1
Fit molecule ys-I1a5 (#33.5) to map ys-I1a (#33.1) using 92992 atoms
average map value = 7.334, steps = 36
shifted from previous position = 0.0203
rotated from previous position = 0.0746 degrees
atoms outside contour = 22072, contour level = 3.0948
Position of ys-I1a5 (#33.5) relative to ys-I1a (#33.1) coordinates:
Matrix rotation and translation
1.00000000 0.00006785 0.00002158 -0.01571402
-0.00006785 1.00000000 0.00000247 0.01394877
-0.00002158 -0.00000247 1.00000000 0.00028445
Axis -0.03462129 0.30294566 -0.95237875
Axis point 185.47857319 229.29962927 0.00000000
Rotation angle (degrees) 0.00408210
Shift along axis 0.00449885
> fitmap #33.3 inMap #33.1
Fit molecule ys-I1a3 (#33.3) to map ys-I1a (#33.1) using 61025 atoms
average map value = 5.134, steps = 60
shifted from previous position = 0.135
rotated from previous position = 0.08 degrees
atoms outside contour = 22330, contour level = 3.0948
Position of ys-I1a3 (#33.3) relative to ys-I1a (#33.1) coordinates:
Matrix rotation and translation
0.99999998 -0.00017787 0.00003522 0.02444707
0.00017787 0.99999998 -0.00002049 -0.02796573
-0.00003522 0.00002050 1.00000000 0.00287850
Axis 0.11232351 0.19300468 0.97474747
Axis point 157.40269238 137.32963987 0.00000000
Rotation angle (degrees) 0.01045538
Shift along axis 0.00015427
> fitmap #34.1 inMap #100
Fit map ys-I1b in map 4ybb_50Score_3A.mrc using 167622 points
correlation = 0.7694, correlation about mean = 0.5021, overlap = 5.244e+05
steps = 48, shift = 0.0515, angle = 0.0695 degrees
Position of ys-I1b (#34.1) relative to 4ybb_50Score_3A.mrc (#100)
coordinates:
Matrix rotation and translation
-0.15974764 0.06847542 0.98478008 118.03715648
-0.09853124 -0.99371554 0.05311334 533.28558991
0.98222822 -0.08854688 0.16549068 85.54764208
Axis -0.64682093 0.01165178 -0.76255290
Axis point 41.99640823 266.19892413 0.00000000
Rotation angle (degrees) 173.71321980
Shift along axis -135.36977768
> fitmap #34.5 inMap #34.1
Fit molecule ys-I1b5 (#34.5) to map ys-I1b (#34.1) using 92992 atoms
average map value = 7.158, steps = 44
shifted from previous position = 0.014
rotated from previous position = 0.0687 degrees
atoms outside contour = 22660, contour level = 3.0873
Position of ys-I1b5 (#34.5) relative to ys-I1b (#34.1) coordinates:
Matrix rotation and translation
1.00000000 -0.00003647 0.00000880 0.00851051
0.00003647 1.00000000 0.00003193 -0.01982466
-0.00000880 -0.00003193 1.00000000 0.00942241
Axis -0.64817747 0.17854187 0.74026263
Axis point 533.41299576 196.36486997 0.00000000
Rotation angle (degrees) 0.00282273
Shift along axis -0.00208080
> fitmap #34.3 inMap #34.1
Fit molecule ys-I1b3 (#34.3) to map ys-I1b (#34.1) using 61064 atoms
average map value = 4.951, steps = 48
shifted from previous position = 0.125
rotated from previous position = 0.0753 degrees
atoms outside contour = 23372, contour level = 3.0873
Position of ys-I1b3 (#34.3) relative to ys-I1b (#34.1) coordinates:
Matrix rotation and translation
0.99999999 -0.00013951 0.00000938 0.01771739
0.00013951 0.99999999 -0.00004705 -0.01825677
-0.00000937 0.00004706 1.00000000 -0.00740427
Axis 0.31895163 0.06356485 0.94563702
Axis point 129.73074307 132.73108386 0.00000000
Rotation angle (degrees) 0.00845277
Shift along axis -0.00251125
> rename #30 ys-H1a
> rename #31 ys-H1b
> rename #32 ys-H1c
> rename #33 ys-I1a
> rename #34 ys-I1b
executed 70S_open_ys.cxc
executed 70S_startup_gtpys.cxc
> open
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/helix/gtpys_helix.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_assign.cxc
> name atomods #*.3,5,7
> name emmaps #*.1
> name lsu #*.5
> name ssu #*.3
> name rna /y,v,w,3,6,5
> name r23s /3
> name r16s /6
> name r5s /5
> name pt /y
> name dt /v
> name efg /x
> name pep /p
> name mrna /w
> name GSP :GSP
> name GDP :GDP
> name GTP :GTP
> name ntide :GTP|:GDP|:GSP
> name spc :SCM
> name fua :FUA
> name par :PAR
> name argb :LIG | #20.7/b
> name drugs argb|par|fua|spc
> name D1 /x:start-293
> name D2 /x:294-410
> name D3 /x:411-489
> name D4 /x:490-612
> name D5 /x:613-end
> name sw1 /x:38-65
> name sw2 /x:89-108
> name pl /x:18-25
> name nkxd /x:142-146
> name kirby #20.7
> name mg /x:MG
> name trna /y,v
> name anticodon /y,v:34-36
> name antiplus /y,v:32-38
> name cca /y,v:74-76
> name astem /y,v:1-7,66-73
> name darm /y,v:8-25
> name aarm /y,v:26-43
> name varm /y,v:44-48
> name tarm /y,v:49-65
> name head #*.3/A/C/S/M/G/N/I/J/6:927-1390
> name arg-head #20.3/A/C/S/M/G/N/I/J/6:927-1390
> name post-head #15.3/A/C/S/M/G/N/I/J/6:927-1390
> name fa-head #14.3/A/C/S/M/G/N/I/J/6:927-1390
> name body #*.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name arg-body #20.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name post-body #15.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name fa-body #14.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name h8 /6:144-178
> name h14 /6:339-350
> name h18 /6:511-540
> name h23 /6:674-716
> name h24 /6:769-810
> name h27 /6:894-905
> name h28 /6:921-937,1379-1400
> name h29 /6:938-943,1337-1346
> name h30 /6:945-955,1225-1235
> name h31 /6:956-975
> name h32 /6:984-990,1215-1221
> name h34 /6:1045-1065,1188-1211
> name h35 /6:1066-1073,1102-1110
> name h36 /6:1074-1083
> name h44 /6:1401-1502
> name h45 /6:1506-1529
> name aploop /6:956-959
> name term16S /6:1503-end
> name aphelix /6:1228-1230
> name us3 #*.3/C
> name us5 #*.3/E
> name us7 #*.3/G
> name us9 #*.3/I
> name us11 #*.3/K
> name us12 #*.3/L
> name us13 #*.3/M
> name us14 #*.3/N
> name us15 #*.3/O
> name us9-130 #*.3/I:130
> name l1stalk /3:2097-2191
> name srl /3:2652-2668
> name H68 /3:1832-1906
> name H69 /3:1907-1924
> name H95 /3:2647-2673
> name ul2 #*.5/B
> name ul5 #*.5/E
> name ul14 #*.5/N
> name ul19 #*.5/S
> name ul31 #*.5/e
executed 70S_assign.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_display.cxc
> alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6;
> alias nucribthin cartoon style nucleic xsect oval width 1.2 thick 1.2;
> alias cylinders cartoon style protein modeh tube rad 2 sides 24;
> alias licorice car style protein modeh default arrows f xsect oval width
1
> thick 1;
> dssp
> windowsize 1000 1000
> set bgColor white
> lighting full
> set silhouettes true
> set silhouetteWidth 1.7
> set silhouettes true
> set silhouetteDepthJump 0.02
> cartoon style width 2.5
> size atomRadius 2
Changed 1614330 atom radii
> nucleotides fill
> size ions atomRadius 1.6
Changed 31 atom radii
> size stickRadius 0.1
Changed 1744812 bond radii
> style stick ringFill thin
Changed 1614330 atom styles, 122200 residue ring styles
> show ribbons
> hide H
> hide :HOH
> hide target a
> show nucleic target a
> show drugs target a
> style drugs ball
Changed 106 atom styles
> nucrib
> graphics selection color black
> volume emmaps style surface step 1 level 4
> surface dust emmaps size 3
> volume surfaceSmoothing true
> cartoon tether trna shape cone opacity 1
> dssp
executed 70S_display.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colors.cxc
> color name efg-t 100,0,0,50
Color 'efg-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
> color name sw1-t 100,92,0,50
Color 'sw1-t' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
> color name sw2-t 68,81,0,50
Color 'sw2-t' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
> color name pl-t 23,59,0,50
Color 'pl-t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
> color name d1-t 100,18,4,50
Color 'd1-t' is 50% transparent: rgba(100%, 18%, 4%, 50%) hex: #ff2e0a80
> color name d2-t 100,40,4,50
Color 'd2-t' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
> color name d3-t 100,27,36,50
Color 'd3-t' is 50% transparent: rgba(100%, 27%, 36%, 50%) hex: #ff455c80
> color name d4-t 80,0,23,50
Color 'd4-t' is 50% transparent: rgba(80%, 0%, 23%, 50%) hex: #cc003b80
> color name d5-t 100,60,4,50
Color 'd5-t' is 50% transparent: rgba(100%, 60%, 4%, 50%) hex: #ff990a80
> color name fa-t 100,90,4,50
Color 'fa-t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
> color name gtp-t 45,53,60,50
Color 'gtp-t' is 50% transparent: rgba(45%, 53%, 60%, 50%) hex: #73879980
> color name mg-t 1,39,16,50
Color 'mg-t' is 50% transparent: rgba(1%, 39%, 16%, 50%) hex: #03632980
> color name spc-t 100,0,0,50
Color 'spc-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
> color name argb-t 50,0,50,50
Color 'argb-t' is 50% transparent: rgba(50%, 0%, 50%, 50%) hex: #80008080
> color name g-1t 98,42,30,50
Color 'g-1t' is 50% transparent: rgba(98%, 42%, 30%, 50%) hex: #fa6b4d80
> color name g-2t 95,35,25,50
Color 'g-2t' is 50% transparent: rgba(95%, 35%, 25%, 50%) hex: #f2594080
> color name g-3t 92,28,20,50
Color 'g-3t' is 50% transparent: rgba(92%, 28%, 20%, 50%) hex: #eb473380
> color name g-4t 89,21,15,50
Color 'g-4t' is 50% transparent: rgba(89%, 21%, 15%, 50%) hex: #e3362680
> color name g-5t 86,14,10,50
Color 'g-5t' is 50% transparent: rgba(86%, 14%, 10%, 50%) hex: #db241a80
> color name g-6t 83,7,5,50
Color 'g-6t' is 50% transparent: rgba(83%, 7%, 5%, 50%) hex: #d4120d80
> color name g-7t 80,0,0,50
Color 'g-7t' is 50% transparent: rgba(80%, 0%, 0%, 50%) hex: #cc000080
> color name p-t 40,60,2,50
Color 'p-t' is 50% transparent: rgba(40%, 60%, 2%, 50%) hex: #66990580
> color name p-1t 4,34,1,50
Color 'p-1t' is 50% transparent: rgba(4%, 34%, 1%, 50%) hex: #0a570380
> color name p-2t 12,39,1,50
Color 'p-2t' is 50% transparent: rgba(12%, 39%, 1%, 50%) hex: #1f630380
> color name p-3t 20,44,1,50
Color 'p-3t' is 50% transparent: rgba(20%, 44%, 1%, 50%) hex: #33700380
> color name p-4t 28,49,1,50
Color 'p-4t' is 50% transparent: rgba(28%, 49%, 1%, 50%) hex: #477d0380
> color name p-5t 36,54,2,50
Color 'p-5t' is 50% transparent: rgba(36%, 54%, 2%, 50%) hex: #5c8a0580
> color name p-6t 44,59,2,50
Color 'p-6t' is 50% transparent: rgba(44%, 59%, 2%, 50%) hex: #70960580
> color name p-7t 52,64,2,50
Color 'p-7t' is 50% transparent: rgba(52%, 64%, 2%, 50%) hex: #85a30580
> color name p-8t 60,69,2,50
Color 'p-8t' is 50% transparent: rgba(60%, 69%, 2%, 50%) hex: #99b00580
> color name p-9t 68,74,3,50
Color 'p-9t' is 50% transparent: rgba(68%, 74%, 3%, 50%) hex: #adbd0880
> color name p-10t 76,79,3,50
Color 'p-10t' is 50% transparent: rgba(76%, 79%, 3%, 50%) hex: #c2c90880
> color name p-11t 84,84,3,50
Color 'p-11t' is 50% transparent: rgba(84%, 84%, 3%, 50%) hex: #d6d60880
> color name d-t 100,75,4,50
Color 'd-t' is 50% transparent: rgba(100%, 75%, 4%, 50%) hex: #ffbf0a80
> color name d-1t 100,100,4,50
Color 'd-1t' is 50% transparent: rgba(100%, 100%, 4%, 50%) hex: #ffff0a80
> color name d-2t 100,93,4,50
Color 'd-2t' is 50% transparent: rgba(100%, 93%, 4%, 50%) hex: #ffed0a80
> color name d-3t 100,86,4,50
Color 'd-3t' is 50% transparent: rgba(100%, 86%, 4%, 50%) hex: #ffdb0a80
> color name d-4t 100,79,4,50
Color 'd-4t' is 50% transparent: rgba(100%, 79%, 4%, 50%) hex: #ffc90a80
> color name d-5t 100,72,4,50
Color 'd-5t' is 50% transparent: rgba(100%, 72%, 4%, 50%) hex: #ffb80a80
> color name d-6t 100,65,4,50
Color 'd-6t' is 50% transparent: rgba(100%, 65%, 4%, 50%) hex: #ffa60a80
> color name d-7t 100,58,4,50
Color 'd-7t' is 50% transparent: rgba(100%, 58%, 4%, 50%) hex: #ff940a80
> color name d-8t 100,51,4,50
Color 'd-8t' is 50% transparent: rgba(100%, 51%, 4%, 50%) hex: #ff820a80
> color name d-9t 100,44,4,50
Color 'd-9t' is 50% transparent: rgba(100%, 44%, 4%, 50%) hex: #ff700a80
> color name d-10t 100,37,4,50
Color 'd-10t' is 50% transparent: rgba(100%, 37%, 4%, 50%) hex: #ff5e0a80
> color name d-11t 100,30,4,50
Color 'd-11t' is 50% transparent: rgba(100%, 30%, 4%, 50%) hex: #ff4d0a80
> color name m-t 95,43,62,50
Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
> color name m-1t 100,80,90,50
Color 'm-1t' is 50% transparent: rgba(100%, 80%, 90%, 50%) hex: #ffcce680
> color name m-2t 98,76,87,50
Color 'm-2t' is 50% transparent: rgba(98%, 76%, 87%, 50%) hex: #fac2de80
> color name m-3t 96,72,84,50
Color 'm-3t' is 50% transparent: rgba(96%, 72%, 84%, 50%) hex: #f5b8d680
> color name m-4t 94,68,81,50
Color 'm-4t' is 50% transparent: rgba(94%, 68%, 81%, 50%) hex: #f0adcf80
> color name m-5t 92,64,78,50
Color 'm-5t' is 50% transparent: rgba(92%, 64%, 78%, 50%) hex: #eba3c780
> color name m-6t 90,60,75,50
Color 'm-6t' is 50% transparent: rgba(90%, 60%, 75%, 50%) hex: #e699bf80
> color name m-7t 88,56,72,50
Color 'm-7t' is 50% transparent: rgba(88%, 56%, 72%, 50%) hex: #e08fb880
> color name m-8t 86,52,69,50
Color 'm-8t' is 50% transparent: rgba(86%, 52%, 69%, 50%) hex: #db85b080
> color name m-9t 84,48,66,50
Color 'm-9t' is 50% transparent: rgba(84%, 48%, 66%, 50%) hex: #d67aa880
> color name m-10t 82,44,63,50
Color 'm-10t' is 50% transparent: rgba(82%, 44%, 63%, 50%) hex: #d170a180
> color name m-11t 80,40,60,50
Color 'm-11t' is 50% transparent: rgba(80%, 40%, 60%, 50%) hex: #cc669980
> color name head-t 71,51,66,50
Color 'head-t' is 50% transparent: rgba(71%, 51%, 66%, 50%) hex: #b582a880
> color name head-c 89,89,100,100
Color 'head-c' is opaque: rgb(89%, 89%, 100%) hex: #e3e3ff
> color name headfa-t 80,79,100,50
Color 'headfa-t' is 50% transparent: rgba(80%, 79%, 100%, 50%) hex:
#ccc9ff80
> color name headblue-t 59,78,94,50
Color 'headblue-t' is 50% transparent: rgba(59%, 78%, 94%, 50%) hex:
#96c7f080
> color name headh1-t 41,64,100,50
Color 'headh1-t' is 50% transparent: rgba(41%, 64%, 100%, 50%) hex:
#69a3ff80
> color name headh2-t 50,70,100,50
Color 'headh2-t' is 50% transparent: rgba(50%, 70%, 100%, 50%) hex:
#80b3ff80
> color name headgray-t 60,60,60,50
Color 'headgray-t' is 50% transparent: rgba(60%, 60%, 60%, 50%) hex:
#99999980
> color name darkhead-s 58,34,52,100
Color 'darkhead-s' is opaque: rgb(58%, 34%, 52%) hex: #945785
> color name bodywhite-t 90,90,90,50
Color 'bodywhite-t' is 50% transparent: rgba(90%, 90%, 90%, 50%) hex:
#e6e6e680
> color name rps-t 75,88,93,50
Color 'rps-t' is 50% transparent: rgba(75%, 88%, 93%, 50%) hex: #bfe0ed80
> color name ssu-t 57,71,75,50
Color 'ssu-t' is 50% transparent: rgba(57%, 71%, 75%, 50%) hex: #91b5bf80
> color name h18-t 31,59,68,50
Color 'h18-t' is 50% transparent: rgba(31%, 59%, 68%, 50%) hex: #4f96ad80
> color name h23-t 18,36,100,50
Color 'h23-t' is 50% transparent: rgba(18%, 36%, 100%, 50%) hex: #2e5cff80
> color name h23-c 18,36,100,100
Color 'h23-c' is opaque: rgb(18%, 36%, 100%) hex: #2e5cff
> color name h24-t 50,70,90,50
Color 'h24-t' is 50% transparent: rgba(50%, 70%, 90%, 50%) hex: #80b3e680
> color name h24-c 50,70,90,100
Color 'h24-c' is opaque: rgb(50%, 70%, 90%) hex: #80b3e6
> color name h28-t 0,24,57,50
Color 'h28-t' is 50% transparent: rgba(0%, 24%, 57%, 50%) hex: #003d9180
> color name h28-c 0,24,57,100
Color 'h28-c' is opaque: rgb(0%, 24%, 57%) hex: #003d91
> color name h29-t 80,69,92,50
Color 'h29-t' is 50% transparent: rgba(80%, 69%, 92%, 50%) hex: #ccb0eb80
> color name h29-c 80,69,92,100
Color 'h29-c' is opaque: rgb(80%, 69%, 92%) hex: #ccb0eb
> color name h30-t 40,40,59,50
Color 'h30-t' is 50% transparent: rgba(40%, 40%, 59%, 50%) hex: #66669680
> color name h31-t 45,18,59,50
Color 'h31-t' is 50% transparent: rgba(45%, 18%, 59%, 50%) hex: #732e9680
> color name h31-c 45,18,59,100
Color 'h31-c' is opaque: rgb(45%, 18%, 59%) hex: #732e96
> color name h34-t 59,18,59,50
Color 'h34-t' is 50% transparent: rgba(59%, 18%, 59%, 50%) hex: #962e9680
> color name h34-c 59,18,59,100
Color 'h34-c' is opaque: rgb(59%, 18%, 59%) hex: #962e96
> color name h35-t 50,22,45,50
Color 'h35-t' is 50% transparent: rgba(50%, 22%, 45%, 50%) hex: #80387380
> color name h44-t 27,50,80,50
Color 'h44-t' is 50% transparent: rgba(27%, 50%, 80%, 50%) hex: #4580cc80
> color name aploop-t 27,0,50,50
Color 'aploop-t' is 50% transparent: rgba(27%, 0%, 50%, 50%) hex:
#45008080
> color name term16-t 40,64,64,50
Color 'term16-t' is 50% transparent: rgba(40%, 64%, 64%, 50%) hex:
#66a3a380
> color name uS3-t 64,41,82,50
Color 'uS3-t' is 50% transparent: rgba(64%, 41%, 82%, 50%) hex: #a369d180
> color name uS5-t 0,50,45,50
Color 'uS5-t' is 50% transparent: rgba(0%, 50%, 45%, 50%) hex: #00807380
> color name gray-t 70,70,70,50
Color 'gray-t' is 50% transparent: rgba(70%, 70%, 70%, 50%) hex: #b3b3b380
> color name hx68-t 50,50,50,50
Color 'hx68-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name hx69-t 30,30,30,50
Color 'hx69-t' is 50% transparent: rgba(30%, 30%, 30%, 50%) hex: #4d4d4d80
> color name srl-t 50,50,50,50
Color 'srl-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name lightgrayt 83,83,83,50
Color 'lightgrayt' is 50% transparent: rgba(83%, 83%, 83%, 50%) hex:
#d4d4d480
> color name silvert 75,75,75,50
Color 'silvert' is 50% transparent: rgba(75%, 75%, 75%, 50%) hex:
#bfbfbf80
> color name grayt 50,50,50,50
Color 'grayt' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name lightcyant 88,100,100,50
Color 'lightcyant' is 50% transparent: rgba(88%, 100%, 100%, 50%) hex:
#e0ffff80
> color name yellowt 100,90,0,50
Color 'yellowt' is 50% transparent: rgba(100%, 90%, 0%, 50%) hex:
#ffe60080
> color name deeppinkt 100,8,58,50
Color 'deeppinkt' is 50% transparent: rgba(100%, 8%, 58%, 50%) hex:
#ff149480
> color name oranget 100,65,0,50
Color 'oranget' is 50% transparent: rgba(100%, 65%, 0%, 50%) hex:
#ffa60080
> color name yellowgreent 60,80,20,50
Color 'yellowgreent' is 50% transparent: rgba(60%, 80%, 20%, 50%) hex:
#99cc3380
> color name darkmagentat 54,0,54,50
Color 'darkmagentat' is 50% transparent: rgba(54%, 0%, 54%, 50%) hex:
#8a008a80
> color name orchidt 86,44,84,50
Color 'orchidt' is 50% transparent: rgba(86%, 44%, 84%, 50%) hex:
#db70d680
> color name paleturquoiset 69,93,93,50
Color 'paleturquoiset' is 50% transparent: rgba(69%, 93%, 93%, 50%) hex:
#b0eded80
> color name pinkt 100,75,80,50
Color 'pinkt' is 50% transparent: rgba(100%, 75%, 80%, 50%) hex: #ffbfcc80
> color name darkgreent 0,39,0,50
Color 'darkgreent' is 50% transparent: rgba(0%, 39%, 0%, 50%) hex:
#00630080
> color name limegreent 20,80,20,50
Color 'limegreent' is 50% transparent: rgba(20%, 80%, 20%, 50%) hex:
#33cc3380
> color name turquoiset 25,88,82,50
Color 'turquoiset' is 50% transparent: rgba(25%, 88%, 82%, 50%) hex:
#40e0d180
> color name tealt 0,50,50,50
Color 'tealt' is 50% transparent: rgba(0%, 50%, 50%, 50%) hex: #00808080
> color name darkoranget 100,50,0,50
Color 'darkoranget' is 50% transparent: rgba(100%, 50%, 0%, 50%) hex:
#ff800080
> color name lightyellowt 100,100,50,50
Color 'lightyellowt' is 50% transparent: rgba(100%, 100%, 50%, 50%) hex:
#ffff8080
> color name goldt 100,75,0,50
Color 'goldt' is 50% transparent: rgba(100%, 75%, 0%, 50%) hex: #ffbf0080
> color name plumt 87,63,87,50
Color 'plumt' is 50% transparent: rgba(87%, 63%, 87%, 50%) hex: #dea1de80
> color name ssubluet 68,86,90,50
Color 'ssubluet' is 50% transparent: rgba(68%, 86%, 90%, 50%) hex:
#addbe680
> color name p-prect 10,41,0,50
Color 'p-prect' is 50% transparent: rgba(10%, 41%, 0%, 50%) hex: #1a690080
> color name p-h2t 23,59,0,50
Color 'p-h2t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
> color name p-h1t 40,73,0,50
Color 'p-h1t' is 50% transparent: rgba(40%, 73%, 0%, 50%) hex: #66ba0080
> color name p-h1c 40,73,0,100
Color 'p-h1c' is opaque: rgb(40%, 73%, 0%) hex: #66ba00
> color name p-spct 68,81,0,50
Color 'p-spct' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
> color name p-spcc 68,81,0,100
Color 'p-spcc' is opaque: rgb(68%, 81%, 0%) hex: #adcf00
> color name p-fat 82,92,0,50
Color 'p-fat' is 50% transparent: rgba(82%, 92%, 0%, 50%) hex: #d1eb0080
> color name p-postt 100,92,0,50
Color 'p-postt' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex:
#ffeb0080
> color name d-t 100,80,4,50
Color 'd-t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
> color name d-prect 95,100,50,50
Color 'd-prect' is 50% transparent: rgba(95%, 100%, 50%, 50%) hex:
#f2ff8080
> color name d-h2t 100,90,4,50
Color 'd-h2t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
> color name d-h1t 100,80,4,50
Color 'd-h1t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
> color name d-spct 100,70,4,50
Color 'd-spct' is 50% transparent: rgba(100%, 70%, 4%, 50%) hex: #ffb30a80
> color name d-fat 100,55,4,50
Color 'd-fat' is 50% transparent: rgba(100%, 55%, 4%, 50%) hex: #ff8c0a80
> color name d-fac 100,55,4,100
Color 'd-fac' is opaque: rgb(100%, 55%, 4%) hex: #ff8c0a
> color name d-postt 100,40,4,50
Color 'd-postt' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex:
#ff660a80
> color name m-t 95,43,62,50
Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
> color name m-prect 100,85,95,50
Color 'm-prect' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex:
#ffd9f280
> color name m-h2t 100,85,95,50
Color 'm-h2t' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex: #ffd9f280
> color name m-h1t 100,75,95,50
Color 'm-h1t' is 50% transparent: rgba(100%, 75%, 95%, 50%) hex: #ffbff280
> color name m-spct 89,63,75,50
Color 'm-spct' is 50% transparent: rgba(89%, 63%, 75%, 50%) hex: #e3a1bf80
> color name m-fat 95,51,75,50
Color 'm-fat' is 50% transparent: rgba(95%, 51%, 75%, 50%) hex: #f282bf80
> color name m-fac 95,51,75,100
Color 'm-fac' is opaque: rgb(95%, 51%, 75%) hex: #f282bf
> color name m-postt 95,43,62,50
Color 'm-postt' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex:
#f26e9e80
executed 70S_colors.cxc
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colorstandard.cxc
> color 100,100,100,50
> color lsu silvert
> color /3 lightgrayt
> color /5 lightgrayt
> color ssu ssu-t
> color head head-t
> color efg efg-t
> color dt d-t
> color pt p-t
> color pep p-t
> color mrna m-t
executed 70S_colorstandard.cxc
> windowsize 1000 1000
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_helices.cxc
> color h18 h18-t
> color h23 h23-t
> color h24 h24-t
> color h28 h28-t
> color h29 h29-t
> color h30 h30-t
> color h31 h31-t
> color h34 h34-t
> color h35 h35-t
> color h36 h36-t
> color h44 h44-t
executed 70S_color_helices.cxc
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_helices.cxc
> color h18 h18-t
> color h23 h23-t
> color h24 h24-t
> color h28 h28-t
> color h29 h29-t
> color h30 h30-t
> color h31 h31-t
> color h34 h34-t
> color h35 h35-t
> color h36 h36-t
> color h44 h44-t
executed 70S_color_helices.cxc
> color h30|h36|h35 head-t
> color zone #12.1 near #12.3,5 distance 5
> color zone #13.1 near #13.3,5 distance 5
> color zone #14.1 near #14.3,5 distance 5
> color zone #30.1 near #30.3,5 distance 5
> color zone #31.1 near #31.3,5 distance 5
> color zone #32.1 near #32.3,5 distance 5
> color zone #33.1 near #33.3,5 distance 5
> color zone #34.1 near #34.3,5 distance 5
> color h30|h36|h35 head-c
> color h28 h28-c
> color h29 h29-c
> color h34 h34-c
> color h23 h23-c
> color h24 h24-c
> color h31 h31-c
> hide #!100
> hide #101 models
> cartoon style nucleic xsection oval width 1.3 thickness 1.3
> transparency #*.3 0 target abc
executed gtpys_helix.cxc
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/helix/gtpys_helix.cxs
——— End of log from Tue May 16 16:15:28 2023 ———
opened ChimeraX session
> hide models
> show #13.3,5 models
> ui mousemode right pivot
> color h69 hx69-t
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or
'random'
or a keyword
> color H69 hx69-t
> ui tool show "Side View"
> view name dc1
> view name dc2
[Repeated 1 time(s)]
> show #13.1 models
> view name dc3
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
——— End of log from Tue May 16 16:53:33 2023 ———
opened ChimeraX session
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_assign.cxc
> name atomods #*.3,5,7
> name emmaps #*.1
> name lsu #*.5
> name ssu #*.3
> name rna /y,v,w,3,6,5
> name r23s /3
> name r16s /6
> name r5s /5
> name pt /y
> name dt /v
> name efg /x
> name pep /p
> name mrna /w
> name GSP :GSP
> name GDP :GDP
> name GTP :GTP
> name ntide :GTP|:GDP|:GSP
> name spc :SCM
> name fua :FUA
> name par :PAR
> name argb :LIG | #20.7/b
> name drugs argb|par|fua|spc
> name D1 /x:start-293
> name D2 /x:294-410
> name D3 /x:411-489
> name D4 /x:490-612
> name D5 /x:613-end
> name sw1 /x:38-65
> name sw2 /x:89-108
> name pl /x:18-25
> name nkxd /x:142-146
> name kirby #20.7
> name mg /x:MG
> name trna /y,v
> name anticodon /y,v:34-36
> name antiplus /y,v:32-38
> name cca /y,v:74-76
> name astem /y,v:1-7,66-73
> name darm /y,v:8-25
> name aarm /y,v:26-43
> name varm /y,v:44-48
> name tarm /y,v:49-65
> name head #*.3/A/C/S/M/G/N/I/J/6:927-1390
> name arg-head #20.3/A/C/S/M/G/N/I/J/6:927-1390
> name post-head #15.3/A/C/S/M/G/N/I/J/6:927-1390
> name fa-head #14.3/A/C/S/M/G/N/I/J/6:927-1390
> name body #*.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name arg-body #20.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name post-body #15.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name fa-body #14.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name h8 /6:144-178
> name h14 /6:339-350
> name h18 /6:511-540
> name h23 /6:674-716
> name h24 /6:769-810
> name h27 /6:894-905
> name h28 /6:921-937,1379-1400
> name h29 /6:938-943,1337-1346
> name h30 /6:945-955,1225-1235
> name h31 /6:956-975
> name h32 /6:984-990,1215-1221
> name h34 /6:1045-1065,1188-1211
> name h35 /6:1066-1073,1102-1110
> name h36 /6:1074-1083
> name h44 /6:1401-1502
> name h45 /6:1506-1529
> name aploop /6:956-959
> name term16S /6:1503-end
> name aphelix /6:1228-1230
> name us3 #*.3/C
> name us5 #*.3/E
> name us7 #*.3/G
> name us9 #*.3/I
> name us11 #*.3/K
> name us12 #*.3/L
> name us13 #*.3/M
> name us14 #*.3/N
> name us15 #*.3/O
> name us9-130 #*.3/I:130
> name l1stalk /3:2097-2191
> name srl /3:2652-2668
> name H68 /3:1832-1906
> name H69 /3:1907-1924
> name H95 /3:2647-2673
> name ul2 #*.5/B
> name ul5 #*.5/E
> name ul14 #*.5/N
> name ul19 #*.5/S
> name ul31 #*.5/e
executed 70S_assign.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_display.cxc
> alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6;
> alias nucribthin cartoon style nucleic xsect oval width 1.2 thick 1.2;
> alias cylinders cartoon style protein modeh tube rad 2 sides 24;
> alias licorice car style protein modeh default arrows f xsect oval width
1
> thick 1;
> dssp
> windowsize 1000 1000
> set bgColor white
> lighting full
> set silhouettes true
> set silhouetteWidth 1.7
> set silhouettes true
> set silhouetteDepthJump 0.02
> cartoon style width 2.5
> size atomRadius 2
Changed 1614330 atom radii
> nucleotides fill
> size ions atomRadius 1.6
Changed 31 atom radii
> size stickRadius 0.1
Changed 1744812 bond radii
> style stick ringFill thin
Changed 1614330 atom styles, 122200 residue ring styles
> show ribbons
> hide H
> hide :HOH
> hide target a
> show nucleic target a
> show drugs target a
> style drugs ball
Changed 106 atom styles
> nucrib
> graphics selection color black
> volume emmaps style surface step 1 level 4
> surface dust emmaps size 3
> volume surfaceSmoothing true
> cartoon tether trna shape cone opacity 1
> dssp
executed 70S_display.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colors.cxc
> color name efg-t 100,0,0,50
Color 'efg-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
> color name sw1-t 100,92,0,50
Color 'sw1-t' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
> color name sw2-t 68,81,0,50
Color 'sw2-t' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
> color name pl-t 23,59,0,50
Color 'pl-t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
> color name d1-t 100,18,4,50
Color 'd1-t' is 50% transparent: rgba(100%, 18%, 4%, 50%) hex: #ff2e0a80
> color name d2-t 100,40,4,50
Color 'd2-t' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
> color name d3-t 100,27,36,50
Color 'd3-t' is 50% transparent: rgba(100%, 27%, 36%, 50%) hex: #ff455c80
> color name d4-t 80,0,23,50
Color 'd4-t' is 50% transparent: rgba(80%, 0%, 23%, 50%) hex: #cc003b80
> color name d5-t 100,60,4,50
Color 'd5-t' is 50% transparent: rgba(100%, 60%, 4%, 50%) hex: #ff990a80
> color name fa-t 100,90,4,50
Color 'fa-t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
> color name gtp-t 45,53,60,50
Color 'gtp-t' is 50% transparent: rgba(45%, 53%, 60%, 50%) hex: #73879980
> color name mg-t 1,39,16,50
Color 'mg-t' is 50% transparent: rgba(1%, 39%, 16%, 50%) hex: #03632980
> color name spc-t 100,0,0,50
Color 'spc-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
> color name argb-t 50,0,50,50
Color 'argb-t' is 50% transparent: rgba(50%, 0%, 50%, 50%) hex: #80008080
> color name g-1t 98,42,30,50
Color 'g-1t' is 50% transparent: rgba(98%, 42%, 30%, 50%) hex: #fa6b4d80
> color name g-2t 95,35,25,50
Color 'g-2t' is 50% transparent: rgba(95%, 35%, 25%, 50%) hex: #f2594080
> color name g-3t 92,28,20,50
Color 'g-3t' is 50% transparent: rgba(92%, 28%, 20%, 50%) hex: #eb473380
> color name g-4t 89,21,15,50
Color 'g-4t' is 50% transparent: rgba(89%, 21%, 15%, 50%) hex: #e3362680
> color name g-5t 86,14,10,50
Color 'g-5t' is 50% transparent: rgba(86%, 14%, 10%, 50%) hex: #db241a80
> color name g-6t 83,7,5,50
Color 'g-6t' is 50% transparent: rgba(83%, 7%, 5%, 50%) hex: #d4120d80
> color name g-7t 80,0,0,50
Color 'g-7t' is 50% transparent: rgba(80%, 0%, 0%, 50%) hex: #cc000080
> color name p-t 40,60,2,50
Color 'p-t' is 50% transparent: rgba(40%, 60%, 2%, 50%) hex: #66990580
> color name p-c 40,60,2,100
Color 'p-c' is opaque: rgb(40%, 60%, 2%) hex: #669905
> color name p-1t 4,34,1,50
Color 'p-1t' is 50% transparent: rgba(4%, 34%, 1%, 50%) hex: #0a570380
> color name p-2t 12,39,1,50
Color 'p-2t' is 50% transparent: rgba(12%, 39%, 1%, 50%) hex: #1f630380
> color name p-3t 20,44,1,50
Color 'p-3t' is 50% transparent: rgba(20%, 44%, 1%, 50%) hex: #33700380
> color name p-4t 28,49,1,50
Color 'p-4t' is 50% transparent: rgba(28%, 49%, 1%, 50%) hex: #477d0380
> color name p-5t 36,54,2,50
Color 'p-5t' is 50% transparent: rgba(36%, 54%, 2%, 50%) hex: #5c8a0580
> color name p-6t 44,59,2,50
Color 'p-6t' is 50% transparent: rgba(44%, 59%, 2%, 50%) hex: #70960580
> color name p-7t 52,64,2,50
Color 'p-7t' is 50% transparent: rgba(52%, 64%, 2%, 50%) hex: #85a30580
> color name p-8t 60,69,2,50
Color 'p-8t' is 50% transparent: rgba(60%, 69%, 2%, 50%) hex: #99b00580
> color name p-9t 68,74,3,50
Color 'p-9t' is 50% transparent: rgba(68%, 74%, 3%, 50%) hex: #adbd0880
> color name p-10t 76,79,3,50
Color 'p-10t' is 50% transparent: rgba(76%, 79%, 3%, 50%) hex: #c2c90880
> color name p-11t 84,84,3,50
Color 'p-11t' is 50% transparent: rgba(84%, 84%, 3%, 50%) hex: #d6d60880
> color name d-t 100,75,4,50
Color 'd-t' is 50% transparent: rgba(100%, 75%, 4%, 50%) hex: #ffbf0a80
> color name d-c 100,75,4,100
Color 'd-c' is opaque: rgb(100%, 75%, 4%) hex: #ffbf0a
> color name d-1t 100,100,4,50
Color 'd-1t' is 50% transparent: rgba(100%, 100%, 4%, 50%) hex: #ffff0a80
> color name d-2t 100,93,4,50
Color 'd-2t' is 50% transparent: rgba(100%, 93%, 4%, 50%) hex: #ffed0a80
> color name d-3t 100,86,4,50
Color 'd-3t' is 50% transparent: rgba(100%, 86%, 4%, 50%) hex: #ffdb0a80
> color name d-4t 100,79,4,50
Color 'd-4t' is 50% transparent: rgba(100%, 79%, 4%, 50%) hex: #ffc90a80
> color name d-5t 100,72,4,50
Color 'd-5t' is 50% transparent: rgba(100%, 72%, 4%, 50%) hex: #ffb80a80
> color name d-6t 100,65,4,50
Color 'd-6t' is 50% transparent: rgba(100%, 65%, 4%, 50%) hex: #ffa60a80
> color name d-7t 100,58,4,50
Color 'd-7t' is 50% transparent: rgba(100%, 58%, 4%, 50%) hex: #ff940a80
> color name d-8t 100,51,4,50
Color 'd-8t' is 50% transparent: rgba(100%, 51%, 4%, 50%) hex: #ff820a80
> color name d-9t 100,44,4,50
Color 'd-9t' is 50% transparent: rgba(100%, 44%, 4%, 50%) hex: #ff700a80
> color name d-10t 100,37,4,50
Color 'd-10t' is 50% transparent: rgba(100%, 37%, 4%, 50%) hex: #ff5e0a80
> color name d-11t 100,30,4,50
Color 'd-11t' is 50% transparent: rgba(100%, 30%, 4%, 50%) hex: #ff4d0a80
> color name m-t 95,43,62,50
Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
> color name m-c 95,43,62,100
Color 'm-c' is opaque: rgb(95%, 43%, 62%) hex: #f26e9e
> color name m-1t 100,80,90,50
Color 'm-1t' is 50% transparent: rgba(100%, 80%, 90%, 50%) hex: #ffcce680
> color name m-2t 98,76,87,50
Color 'm-2t' is 50% transparent: rgba(98%, 76%, 87%, 50%) hex: #fac2de80
> color name m-3t 96,72,84,50
Color 'm-3t' is 50% transparent: rgba(96%, 72%, 84%, 50%) hex: #f5b8d680
> color name m-4t 94,68,81,50
Color 'm-4t' is 50% transparent: rgba(94%, 68%, 81%, 50%) hex: #f0adcf80
> color name m-5t 92,64,78,50
Color 'm-5t' is 50% transparent: rgba(92%, 64%, 78%, 50%) hex: #eba3c780
> color name m-6t 90,60,75,50
Color 'm-6t' is 50% transparent: rgba(90%, 60%, 75%, 50%) hex: #e699bf80
> color name m-7t 88,56,72,50
Color 'm-7t' is 50% transparent: rgba(88%, 56%, 72%, 50%) hex: #e08fb880
> color name m-8t 86,52,69,50
Color 'm-8t' is 50% transparent: rgba(86%, 52%, 69%, 50%) hex: #db85b080
> color name m-9t 84,48,66,50
Color 'm-9t' is 50% transparent: rgba(84%, 48%, 66%, 50%) hex: #d67aa880
> color name m-10t 82,44,63,50
Color 'm-10t' is 50% transparent: rgba(82%, 44%, 63%, 50%) hex: #d170a180
> color name m-11t 80,40,60,50
Color 'm-11t' is 50% transparent: rgba(80%, 40%, 60%, 50%) hex: #cc669980
> color name head-t 71,51,66,50
Color 'head-t' is 50% transparent: rgba(71%, 51%, 66%, 50%) hex: #b582a880
> color name head-c 89,89,100,100
Color 'head-c' is opaque: rgb(89%, 89%, 100%) hex: #e3e3ff
> color name headfa-t 80,79,100,50
Color 'headfa-t' is 50% transparent: rgba(80%, 79%, 100%, 50%) hex:
#ccc9ff80
> color name headblue-t 59,78,94,50
Color 'headblue-t' is 50% transparent: rgba(59%, 78%, 94%, 50%) hex:
#96c7f080
> color name headh1-t 41,64,100,50
Color 'headh1-t' is 50% transparent: rgba(41%, 64%, 100%, 50%) hex:
#69a3ff80
> color name headh2-t 50,70,100,50
Color 'headh2-t' is 50% transparent: rgba(50%, 70%, 100%, 50%) hex:
#80b3ff80
> color name headgray-t 60,60,60,50
Color 'headgray-t' is 50% transparent: rgba(60%, 60%, 60%, 50%) hex:
#99999980
> color name darkhead-s 58,34,52,100
Color 'darkhead-s' is opaque: rgb(58%, 34%, 52%) hex: #945785
> color name bodywhite-t 90,90,90,50
Color 'bodywhite-t' is 50% transparent: rgba(90%, 90%, 90%, 50%) hex:
#e6e6e680
> color name rps-t 75,88,93,50
Color 'rps-t' is 50% transparent: rgba(75%, 88%, 93%, 50%) hex: #bfe0ed80
> color name ssu-t 57,71,75,50
Color 'ssu-t' is 50% transparent: rgba(57%, 71%, 75%, 50%) hex: #91b5bf80
> color name h18-t 31,59,68,50
Color 'h18-t' is 50% transparent: rgba(31%, 59%, 68%, 50%) hex: #4f96ad80
> color name h18-c 31,59,68,100
Color 'h18-c' is opaque: rgb(31%, 59%, 68%) hex: #4f96ad
> color name h23-t 18,36,100,50
Color 'h23-t' is 50% transparent: rgba(18%, 36%, 100%, 50%) hex: #2e5cff80
> color name h23-c 18,36,100,100
Color 'h23-c' is opaque: rgb(18%, 36%, 100%) hex: #2e5cff
> color name h24-t 50,70,90,50
Color 'h24-t' is 50% transparent: rgba(50%, 70%, 90%, 50%) hex: #80b3e680
> color name h24-c 50,70,90,100
Color 'h24-c' is opaque: rgb(50%, 70%, 90%) hex: #80b3e6
> color name h28-t 0,24,57,50
Color 'h28-t' is 50% transparent: rgba(0%, 24%, 57%, 50%) hex: #003d9180
> color name h28-c 0,24,57,100
Color 'h28-c' is opaque: rgb(0%, 24%, 57%) hex: #003d91
> color name h29-t 80,69,92,50
Color 'h29-t' is 50% transparent: rgba(80%, 69%, 92%, 50%) hex: #ccb0eb80
> color name h29-c 80,69,92,100
Color 'h29-c' is opaque: rgb(80%, 69%, 92%) hex: #ccb0eb
> color name h30-t 40,40,59,50
Color 'h30-t' is 50% transparent: rgba(40%, 40%, 59%, 50%) hex: #66669680
> color name h30-c 40,40,59,100
Color 'h30-c' is opaque: rgb(40%, 40%, 59%) hex: #666696
> color name h31-t 45,18,59,50
Color 'h31-t' is 50% transparent: rgba(45%, 18%, 59%, 50%) hex: #732e9680
> color name h31-c 45,18,59,100
Color 'h31-c' is opaque: rgb(45%, 18%, 59%) hex: #732e96
> color name h34-t 59,18,59,50
Color 'h34-t' is 50% transparent: rgba(59%, 18%, 59%, 50%) hex: #962e9680
> color name h34-c 59,18,59,100
Color 'h34-c' is opaque: rgb(59%, 18%, 59%) hex: #962e96
> color name h35-t 50,22,45,50
Color 'h35-t' is 50% transparent: rgba(50%, 22%, 45%, 50%) hex: #80387380
> color name h35-c 50,22,45,100
Color 'h35-c' is opaque: rgb(50%, 22%, 45%) hex: #803873
> color name h44-t 27,50,80,50
Color 'h44-t' is 50% transparent: rgba(27%, 50%, 80%, 50%) hex: #4580cc80
> color name h44-c 27,50,80,100
Color 'h44-c' is opaque: rgb(27%, 50%, 80%) hex: #4580cc
> color name aploop-t 27,0,50,50
Color 'aploop-t' is 50% transparent: rgba(27%, 0%, 50%, 50%) hex:
#45008080
> color name term16-t 40,64,64,50
Color 'term16-t' is 50% transparent: rgba(40%, 64%, 64%, 50%) hex:
#66a3a380
> color name uS3-t 64,41,82,50
Color 'uS3-t' is 50% transparent: rgba(64%, 41%, 82%, 50%) hex: #a369d180
> color name uS5-t 0,50,45,50
Color 'uS5-t' is 50% transparent: rgba(0%, 50%, 45%, 50%) hex: #00807380
> color name gray-t 70,70,70,50
Color 'gray-t' is 50% transparent: rgba(70%, 70%, 70%, 50%) hex: #b3b3b380
> color name hx68-t 50,50,50,50
Color 'hx68-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name hx68-c 50,50,50,100
Color 'hx68-c' is opaque: gray(50%) hex: #808080
> color name hx69-t 40,40,40,50
Color 'hx69-t' is 50% transparent: rgba(40%, 40%, 40%, 50%) hex: #66666680
> color name hx69-c 40,40,40,100
Color 'hx69-c' is opaque: gray(40%) hex: #666666
> color name srl-t 50,50,50,50
Color 'srl-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name srl-t 50,50,50,100
Color 'srl-t' is opaque: gray(50%) hex: #808080
> color name lightgrayt 83,83,83,50
Color 'lightgrayt' is 50% transparent: rgba(83%, 83%, 83%, 50%) hex:
#d4d4d480
> color name silvert 75,75,75,50
Color 'silvert' is 50% transparent: rgba(75%, 75%, 75%, 50%) hex:
#bfbfbf80
> color name grayt 50,50,50,50
Color 'grayt' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name lightcyant 88,100,100,50
Color 'lightcyant' is 50% transparent: rgba(88%, 100%, 100%, 50%) hex:
#e0ffff80
> color name yellowt 100,90,0,50
Color 'yellowt' is 50% transparent: rgba(100%, 90%, 0%, 50%) hex:
#ffe60080
> color name deeppinkt 100,8,58,50
Color 'deeppinkt' is 50% transparent: rgba(100%, 8%, 58%, 50%) hex:
#ff149480
> color name oranget 100,65,0,50
Color 'oranget' is 50% transparent: rgba(100%, 65%, 0%, 50%) hex:
#ffa60080
> color name yellowgreent 60,80,20,50
Color 'yellowgreent' is 50% transparent: rgba(60%, 80%, 20%, 50%) hex:
#99cc3380
> color name darkmagentat 54,0,54,50
Color 'darkmagentat' is 50% transparent: rgba(54%, 0%, 54%, 50%) hex:
#8a008a80
> color name orchidt 86,44,84,50
Color 'orchidt' is 50% transparent: rgba(86%, 44%, 84%, 50%) hex:
#db70d680
> color name paleturquoiset 69,93,93,50
Color 'paleturquoiset' is 50% transparent: rgba(69%, 93%, 93%, 50%) hex:
#b0eded80
> color name pinkt 100,75,80,50
Color 'pinkt' is 50% transparent: rgba(100%, 75%, 80%, 50%) hex: #ffbfcc80
> color name darkgreent 0,39,0,50
Color 'darkgreent' is 50% transparent: rgba(0%, 39%, 0%, 50%) hex:
#00630080
> color name limegreent 20,80,20,50
Color 'limegreent' is 50% transparent: rgba(20%, 80%, 20%, 50%) hex:
#33cc3380
> color name turquoiset 25,88,82,50
Color 'turquoiset' is 50% transparent: rgba(25%, 88%, 82%, 50%) hex:
#40e0d180
> color name tealt 0,50,50,50
Color 'tealt' is 50% transparent: rgba(0%, 50%, 50%, 50%) hex: #00808080
> color name darkoranget 100,50,0,50
Color 'darkoranget' is 50% transparent: rgba(100%, 50%, 0%, 50%) hex:
#ff800080
> color name lightyellowt 100,100,50,50
Color 'lightyellowt' is 50% transparent: rgba(100%, 100%, 50%, 50%) hex:
#ffff8080
> color name goldt 100,75,0,50
Color 'goldt' is 50% transparent: rgba(100%, 75%, 0%, 50%) hex: #ffbf0080
> color name plumt 87,63,87,50
Color 'plumt' is 50% transparent: rgba(87%, 63%, 87%, 50%) hex: #dea1de80
> color name ssubluet 68,86,90,50
Color 'ssubluet' is 50% transparent: rgba(68%, 86%, 90%, 50%) hex:
#addbe680
> color name p-prect 10,41,0,50
Color 'p-prect' is 50% transparent: rgba(10%, 41%, 0%, 50%) hex: #1a690080
> color name p-h2t 23,59,0,50
Color 'p-h2t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
> color name p-h1t 40,73,0,50
Color 'p-h1t' is 50% transparent: rgba(40%, 73%, 0%, 50%) hex: #66ba0080
> color name p-h1c 40,73,0,100
Color 'p-h1c' is opaque: rgb(40%, 73%, 0%) hex: #66ba00
> color name p-spct 68,81,0,50
Color 'p-spct' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
> color name p-spcc 68,81,0,100
Color 'p-spcc' is opaque: rgb(68%, 81%, 0%) hex: #adcf00
> color name p-fat 82,92,0,50
Color 'p-fat' is 50% transparent: rgba(82%, 92%, 0%, 50%) hex: #d1eb0080
> color name p-postt 100,92,0,50
Color 'p-postt' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex:
#ffeb0080
> color name d-t 100,80,4,50
Color 'd-t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
> color name d-prect 95,100,50,50
Color 'd-prect' is 50% transparent: rgba(95%, 100%, 50%, 50%) hex:
#f2ff8080
> color name d-h2t 100,90,4,50
Color 'd-h2t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
> color name d-h1t 100,80,4,50
Color 'd-h1t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
> color name d-spct 100,70,4,50
Color 'd-spct' is 50% transparent: rgba(100%, 70%, 4%, 50%) hex: #ffb30a80
> color name d-fat 100,55,4,50
Color 'd-fat' is 50% transparent: rgba(100%, 55%, 4%, 50%) hex: #ff8c0a80
> color name d-fac 100,55,4,100
Color 'd-fac' is opaque: rgb(100%, 55%, 4%) hex: #ff8c0a
> color name d-postt 100,40,4,50
Color 'd-postt' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex:
#ff660a80
> color name m-t 95,43,62,50
Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
> color name m-prect 100,85,95,50
Color 'm-prect' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex:
#ffd9f280
> color name m-h2t 100,85,95,50
Color 'm-h2t' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex: #ffd9f280
> color name m-h1t 100,75,95,50
Color 'm-h1t' is 50% transparent: rgba(100%, 75%, 95%, 50%) hex: #ffbff280
> color name m-spct 89,63,75,50
Color 'm-spct' is 50% transparent: rgba(89%, 63%, 75%, 50%) hex: #e3a1bf80
> color name m-fat 95,51,75,50
Color 'm-fat' is 50% transparent: rgba(95%, 51%, 75%, 50%) hex: #f282bf80
> color name m-fac 95,51,75,100
Color 'm-fac' is opaque: rgb(95%, 51%, 75%) hex: #f282bf
> color name m-postt 95,43,62,50
Color 'm-postt' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex:
#f26e9e80
executed 70S_colors.cxc
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colorstandard.cxc
> color 100,100,100,50
> color lsu silvert
> color /3 lightgrayt
> color /5 lightgrayt
> color ssu ssu-t
> color head head-t
> color efg efg-t
> color dt d-t
> color pt p-t
> color pep p-t
> color mrna m-t
executed 70S_colorstandard.cxc
> windowsize 1000 1000
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_helices.cxc
> color h18 h18-t
> color h23 h23-t
> color h24 h24-t
> color h28 h28-t
> color h29 h29-t
> color h30 h30-t
> color h31 h31-t
> color h34 h34-t
> color h35 h35-t
> color h36 h36-t
> color h44 h44-t
> color H69 hx69-t
executed 70S_color_helices.cxc
> color h30|h36|h35 head-t
> view dc3
> surface cap true
> color zone #12.1 near #12.3,5 distance 5
> color zone #13.1 near #13.3,5 distance 5
> color zone #14.1 near #14.3,5 distance 5
> color zone #30.1 near #30.3,5 distance 5
> color zone #31.1 near #31.3,5 distance 5
> color zone #32.1 near #32.3,5 distance 5
> color zone #33.1 near #33.3,5 distance 5
> color zone #34.1 near #34.3,5 distance 5
> color h30|h36|h35 head-c
> color h28 h28-c
> color h29 h29-c
> color h34 h34-c
> color h23 h23-c
> color h24 h24-c
> color h31 h31-c
> hide #!100
> hide #101 models
> cartoon style nucleic xsection oval width 1.3 thickness 1.3
> transparency #*.3 0 target abc
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_helices-s.cxc
> color h18 h18-c
> color h23 h23-c
> color h24 h24-c
[had to delete some of the log to fit within ticket length limits]
> name H79 #*.5/3:2200-2223
> name H80 #*.5/3:2246-2258
> name H81 #*.5/3:2259-2281
> name H82 #*.5/3:2284-2285|#*.5/3:2383-2384
> name H83 #*.5/3:2288-2295|#*.5/3:2337-2344
> name H84 #*.5/3:2296-2322
> name H85 #*.5/3:2323-2332
> name H86 #*.5/3:2347-2370
> name H87 #*.5/3:2372-2381
> name H88 #*.5/3:2395-2421
> name H89 #*.5/3:2453-2498
> name H90 #*.5/3:2507-2517|#*.5/3:2567-2582
> name H91 #*.5/3:2520-2545
> name H92 #*.5/3:2547-2561
> name H93 #*.5/3:2588-2606
> name H94 #*.5/3:2630-2643|#*.5/3:2771-2788
> name H95 #*.5/3:2646-2674
> name H96 #*.5/3:2675-2732
> name H97 #*.5/3:2735-2769
> name H98 #*.5/3:2791-2805
> name H99 #*.5/3:2811-2814|#*.5/3:2886-2889
> name H100 #*.5/3:2815-2831
executed 70S_assign.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_display.cxc
> alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6;
> alias nucribthin cartoon style nucleic xsect oval width 1.2 thick 1.2;
> alias cylinders cartoon style protein modeh tube rad 2 sides 24;
> alias licorice car style protein modeh default arrows f xsect oval width
1
> thick 1;
> dssp
> windowsize 1000 1000
> set bgColor white
> lighting full
> set silhouettes true
> set silhouetteWidth 1.7
> set silhouettes true
> set silhouetteDepthJump 0.02
> cartoon style width 2.5
> size atomRadius 2
Changed 1614330 atom radii
> nucleotides fill
> size ions atomRadius 1.6
Changed 31 atom radii
> size stickRadius 0.1
Changed 1744812 bond radii
> style stick ringFill thin
Changed 1614330 atom styles, 122200 residue ring styles
> show ribbons
> hide H
> hide :HOH
> hide target a
> show nucleic target a
> show drugs target a
> style drugs ball
Changed 106 atom styles
> graphics selection color black
> cartoon style protein xsection round width 2 thickness 0.6
> cartoon style modeHelix wrap
> cartoon style sides 24
> cartoon style strand xsection oval arrows false
> cartoon suppressBackboneDisplay true
> alias thinbois style ball;size ballscale 0.09; size stickradius 0.13;
> alias thickbois style stick;size stickradius 0.4;style stick ringFill
thick;
> volume emmaps style surface step 1 level 4
> surface dust emmaps size 3
> volume surfaceSmoothing true
> cartoon tether trna shape cone opacity 1
> dssp
> thickbois
Changed 1614330 atom styles
Changed 1744812 bond radii
Changed 1614330 atom styles, 122200 residue ring styles
executed 70S_display.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colors.cxc
> color name efg-t 100,0,0,50
Color 'efg-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
> color name sw1-t 100,92,0,50
Color 'sw1-t' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
> color name sw2-t 68,81,0,50
Color 'sw2-t' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
> color name pl-t 23,59,0,50
Color 'pl-t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
> color name d1-t 100,18,4,50
Color 'd1-t' is 50% transparent: rgba(100%, 18%, 4%, 50%) hex: #ff2e0a80
> color name d2-t 100,40,4,50
Color 'd2-t' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
> color name d3-t 100,27,36,50
Color 'd3-t' is 50% transparent: rgba(100%, 27%, 36%, 50%) hex: #ff455c80
> color name d4-t 80,0,23,50
Color 'd4-t' is 50% transparent: rgba(80%, 0%, 23%, 50%) hex: #cc003b80
> color name d5-t 100,60,4,50
Color 'd5-t' is 50% transparent: rgba(100%, 60%, 4%, 50%) hex: #ff990a80
> color name fa-t 100,90,4,50
Color 'fa-t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
> color name gtp-t 45,53,60,50
Color 'gtp-t' is 50% transparent: rgba(45%, 53%, 60%, 50%) hex: #73879980
> color name mg-t 1,39,16,50
Color 'mg-t' is 50% transparent: rgba(1%, 39%, 16%, 50%) hex: #03632980
> color name spc-t 100,0,0,50
Color 'spc-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
> color name argb-t 50,0,50,50
Color 'argb-t' is 50% transparent: rgba(50%, 0%, 50%, 50%) hex: #80008080
> color name g-1t 98,42,30,50
Color 'g-1t' is 50% transparent: rgba(98%, 42%, 30%, 50%) hex: #fa6b4d80
> color name g-2t 95,35,25,50
Color 'g-2t' is 50% transparent: rgba(95%, 35%, 25%, 50%) hex: #f2594080
> color name g-3t 92,28,20,50
Color 'g-3t' is 50% transparent: rgba(92%, 28%, 20%, 50%) hex: #eb473380
> color name g-4t 89,21,15,50
Color 'g-4t' is 50% transparent: rgba(89%, 21%, 15%, 50%) hex: #e3362680
> color name g-5t 86,14,10,50
Color 'g-5t' is 50% transparent: rgba(86%, 14%, 10%, 50%) hex: #db241a80
> color name g-6t 83,7,5,50
Color 'g-6t' is 50% transparent: rgba(83%, 7%, 5%, 50%) hex: #d4120d80
> color name g-7t 80,0,0,50
Color 'g-7t' is 50% transparent: rgba(80%, 0%, 0%, 50%) hex: #cc000080
> color name p-t 44,59,2,50
Color 'p-t' is 50% transparent: rgba(44%, 59%, 2%, 50%) hex: #70960580
> color name p-c 44,59,2,100
Color 'p-c' is opaque: rgb(44%, 59%, 2%) hex: #709605
> color name p-1t 4,34,1,50
Color 'p-1t' is 50% transparent: rgba(4%, 34%, 1%, 50%) hex: #0a570380
> color name p-2t 12,39,1,50
Color 'p-2t' is 50% transparent: rgba(12%, 39%, 1%, 50%) hex: #1f630380
> color name p-3t 20,44,1,50
Color 'p-3t' is 50% transparent: rgba(20%, 44%, 1%, 50%) hex: #33700380
> color name p-4t 28,49,1,50
Color 'p-4t' is 50% transparent: rgba(28%, 49%, 1%, 50%) hex: #477d0380
> color name p-5t 36,54,2,50
Color 'p-5t' is 50% transparent: rgba(36%, 54%, 2%, 50%) hex: #5c8a0580
> color name p-6t 44,59,2,50
Color 'p-6t' is 50% transparent: rgba(44%, 59%, 2%, 50%) hex: #70960580
> color name p-7t 52,64,2,50
Color 'p-7t' is 50% transparent: rgba(52%, 64%, 2%, 50%) hex: #85a30580
> color name p-8t 60,69,2,50
Color 'p-8t' is 50% transparent: rgba(60%, 69%, 2%, 50%) hex: #99b00580
> color name p-9t 68,74,3,50
Color 'p-9t' is 50% transparent: rgba(68%, 74%, 3%, 50%) hex: #adbd0880
> color name p-10t 76,79,3,50
Color 'p-10t' is 50% transparent: rgba(76%, 79%, 3%, 50%) hex: #c2c90880
> color name p-11t 84,84,3,50
Color 'p-11t' is 50% transparent: rgba(84%, 84%, 3%, 50%) hex: #d6d60880
> color name d-t 100,65,4,50
Color 'd-t' is 50% transparent: rgba(100%, 65%, 4%, 50%) hex: #ffa60a80
> color name d-c 100,65,4,100
Color 'd-c' is opaque: rgb(100%, 65%, 4%) hex: #ffa60a
> color name d-1t 100,100,4,50
Color 'd-1t' is 50% transparent: rgba(100%, 100%, 4%, 50%) hex: #ffff0a80
> color name d-2t 100,93,4,50
Color 'd-2t' is 50% transparent: rgba(100%, 93%, 4%, 50%) hex: #ffed0a80
> color name d-3t 100,86,4,50
Color 'd-3t' is 50% transparent: rgba(100%, 86%, 4%, 50%) hex: #ffdb0a80
> color name d-4t 100,79,4,50
Color 'd-4t' is 50% transparent: rgba(100%, 79%, 4%, 50%) hex: #ffc90a80
> color name d-5t 100,72,4,50
Color 'd-5t' is 50% transparent: rgba(100%, 72%, 4%, 50%) hex: #ffb80a80
> color name d-6t 100,65,4,50
Color 'd-6t' is 50% transparent: rgba(100%, 65%, 4%, 50%) hex: #ffa60a80
> color name d-7t 100,58,4,50
Color 'd-7t' is 50% transparent: rgba(100%, 58%, 4%, 50%) hex: #ff940a80
> color name d-8t 100,51,4,50
Color 'd-8t' is 50% transparent: rgba(100%, 51%, 4%, 50%) hex: #ff820a80
> color name d-9t 100,44,4,50
Color 'd-9t' is 50% transparent: rgba(100%, 44%, 4%, 50%) hex: #ff700a80
> color name d-10t 100,37,4,50
Color 'd-10t' is 50% transparent: rgba(100%, 37%, 4%, 50%) hex: #ff5e0a80
> color name d-11t 100,30,4,50
Color 'd-11t' is 50% transparent: rgba(100%, 30%, 4%, 50%) hex: #ff4d0a80
> color name m-t 95,43,62,50
Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
> color name m-c 95,43,62,100
Color 'm-c' is opaque: rgb(95%, 43%, 62%) hex: #f26e9e
> color name m-1t 100,80,90,50
Color 'm-1t' is 50% transparent: rgba(100%, 80%, 90%, 50%) hex: #ffcce680
> color name m-2t 98,76,87,50
Color 'm-2t' is 50% transparent: rgba(98%, 76%, 87%, 50%) hex: #fac2de80
> color name m-3t 96,72,84,50
Color 'm-3t' is 50% transparent: rgba(96%, 72%, 84%, 50%) hex: #f5b8d680
> color name m-4t 94,68,81,50
Color 'm-4t' is 50% transparent: rgba(94%, 68%, 81%, 50%) hex: #f0adcf80
> color name m-5t 92,64,78,50
Color 'm-5t' is 50% transparent: rgba(92%, 64%, 78%, 50%) hex: #eba3c780
> color name m-6t 90,60,75,50
Color 'm-6t' is 50% transparent: rgba(90%, 60%, 75%, 50%) hex: #e699bf80
> color name m-7t 88,56,72,50
Color 'm-7t' is 50% transparent: rgba(88%, 56%, 72%, 50%) hex: #e08fb880
> color name m-8t 86,52,69,50
Color 'm-8t' is 50% transparent: rgba(86%, 52%, 69%, 50%) hex: #db85b080
> color name m-9t 84,48,66,50
Color 'm-9t' is 50% transparent: rgba(84%, 48%, 66%, 50%) hex: #d67aa880
> color name m-10t 82,44,63,50
Color 'm-10t' is 50% transparent: rgba(82%, 44%, 63%, 50%) hex: #d170a180
> color name m-11t 80,40,60,50
Color 'm-11t' is 50% transparent: rgba(80%, 40%, 60%, 50%) hex: #cc669980
> color name head-t 82,74,84,50
Color 'head-t' is 50% transparent: rgba(82%, 74%, 84%, 50%) hex: #d1bdd680
> color name head-c 82,74,84,100
Color 'head-c' is opaque: rgb(82%, 74%, 84%) hex: #d1bdd6
> color name headfa-t 54,41,54,50
Color 'headfa-t' is 50% transparent: rgba(54%, 41%, 54%, 50%) hex:
#8a698a80
> color name headblue-t 59,78,94,50
Color 'headblue-t' is 50% transparent: rgba(59%, 78%, 94%, 50%) hex:
#96c7f080
> color name headh1-t 41,64,100,50
Color 'headh1-t' is 50% transparent: rgba(41%, 64%, 100%, 50%) hex:
#69a3ff80
> color name headh2-t 50,70,100,50
Color 'headh2-t' is 50% transparent: rgba(50%, 70%, 100%, 50%) hex:
#80b3ff80
> color name headgray-t 60,60,60,50
Color 'headgray-t' is 50% transparent: rgba(60%, 60%, 60%, 50%) hex:
#99999980
> color name darkhead-s 54,41,54,100
Color 'darkhead-s' is opaque: rgb(54%, 41%, 54%) hex: #8a698a
> color name bodywhite-t 90,90,90,50
Color 'bodywhite-t' is 50% transparent: rgba(90%, 90%, 90%, 50%) hex:
#e6e6e680
> color name rps-t 75,88,93,50
Color 'rps-t' is 50% transparent: rgba(75%, 88%, 93%, 50%) hex: #bfe0ed80
> color name ssu-t 69,79,82,50
Color 'ssu-t' is 50% transparent: rgba(69%, 79%, 82%, 50%) hex: #b0c9d180
> color name ssu-c 69,79,82,100
Color 'ssu-c' is opaque: rgb(69%, 79%, 82%) hex: #b0c9d1
> color name h16-t 79,85,89,50
Color 'h16-t' is 50% transparent: rgba(79%, 85%, 89%, 50%) hex: #c9d9e380
> color name h16-c 79,85,89,100
Color 'h16-c' is opaque: rgb(79%, 85%, 89%) hex: #c9d9e3
> color name h18-t 31,59,68,50
Color 'h18-t' is 50% transparent: rgba(31%, 59%, 68%, 50%) hex: #4f96ad80
> color name h18-dt 6,47,62,50
Color 'h18-dt' is 50% transparent: rgba(6%, 47%, 62%, 50%) hex: #0f789e80
> color name h18-dc 6,47,62,100
Color 'h18-dc' is opaque: rgb(6%, 47%, 62%) hex: #0f789e
> color name h18-c 31,59,68,100
Color 'h18-c' is opaque: rgb(31%, 59%, 68%) hex: #4f96ad
> color name h23-t 40,61,80,50
Color 'h23-t' is 50% transparent: rgba(40%, 61%, 80%, 50%) hex: #669ccc80
> color name h23-c 40,61,80,100
Color 'h23-c' is opaque: rgb(40%, 61%, 80%) hex: #669ccc
> color name h24-t 50,70,90,50
Color 'h24-t' is 50% transparent: rgba(50%, 70%, 90%, 50%) hex: #80b3e680
> color name h24-c 50,70,90,100
Color 'h24-c' is opaque: rgb(50%, 70%, 90%) hex: #80b3e6
> color name h28-t 21,27,56,50
Color 'h28-t' is 50% transparent: rgba(21%, 27%, 56%, 50%) hex: #36458f80
> color name h28-c 21,27,56,100
Color 'h28-c' is opaque: rgb(21%, 27%, 56%) hex: #36458f
> color name h29-t 80,69,92,50
Color 'h29-t' is 50% transparent: rgba(80%, 69%, 92%, 50%) hex: #ccb0eb80
> color name h29-c 80,69,92,100
Color 'h29-c' is opaque: rgb(80%, 69%, 92%) hex: #ccb0eb
> color name h30-t 40,40,59,50
Color 'h30-t' is 50% transparent: rgba(40%, 40%, 59%, 50%) hex: #66669680
> color name h30-c 40,40,59,100
Color 'h30-c' is opaque: rgb(40%, 40%, 59%) hex: #666696
> color name h31-t 45,35,55,50
Color 'h31-t' is 50% transparent: rgba(45%, 35%, 55%, 50%) hex: #73598c80
> color name h31-c 45,35,55,100
Color 'h31-c' is opaque: rgb(45%, 35%, 55%) hex: #73598c
> color name h32-t 75,62,79,50
Color 'h32-t' is 50% transparent: rgba(75%, 62%, 79%, 50%) hex: #bf9ec980
> color name h32-c 75,62,79,100
Color 'h32-c' is opaque: rgb(75%, 62%, 79%) hex: #bf9ec9
> color name h33-t 88,82,90,50
Color 'h33-t' is 50% transparent: rgba(88%, 82%, 90%, 50%) hex: #e0d1e680
> color name h33-c 88,82,90,100
Color 'h33-c' is opaque: rgb(88%, 82%, 90%) hex: #e0d1e6
> color name h34-t 59,35,59,50
Color 'h34-t' is 50% transparent: rgba(59%, 35%, 59%, 50%) hex: #96599680
> color name h34-c 59,35,59,100
Color 'h34-c' is opaque: rgb(59%, 35%, 59%) hex: #965996
> color name h35-t 50,22,45,50
Color 'h35-t' is 50% transparent: rgba(50%, 22%, 45%, 50%) hex: #80387380
> color name h35-c 50,22,45,100
Color 'h35-c' is opaque: rgb(50%, 22%, 45%) hex: #803873
> color name h44-t 32,54,70,50
Color 'h44-t' is 50% transparent: rgba(32%, 54%, 70%, 50%) hex: #528ab380
> color name h44-c 32,54,70,100
Color 'h44-c' is opaque: rgb(32%, 54%, 70%) hex: #528ab3
> color name aploop-t 27,0,50,50
Color 'aploop-t' is 50% transparent: rgba(27%, 0%, 50%, 50%) hex:
#45008080
> color name term16-t 40,64,64,50
Color 'term16-t' is 50% transparent: rgba(40%, 64%, 64%, 50%) hex:
#66a3a380
> color name uS3-t 48,44,57,50
Color 'uS3-t' is 50% transparent: rgba(48%, 44%, 57%, 50%) hex: #7a709180
> color name uS3-c 48,44,57,100
Color 'uS3-c' is opaque: rgb(48%, 44%, 57%) hex: #7a7091
> color name uS3-dt 40,37,57,50
Color 'uS3-dt' is 50% transparent: rgba(40%, 37%, 57%, 50%) hex: #665e9180
> color name uS3-dc 40,37,57,100
Color 'uS3-dc' is opaque: rgb(40%, 37%, 57%) hex: #665e91
> color name uS5-t 0,50,45,50
Color 'uS5-t' is 50% transparent: rgba(0%, 50%, 45%, 50%) hex: #00807380
> color name gray-t 70,70,70,50
Color 'gray-t' is 50% transparent: rgba(70%, 70%, 70%, 50%) hex: #b3b3b380
> color name hx84-t 50,50,50,50
Color 'hx84-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name hx84-c 50,50,50,100
Color 'hx84-c' is opaque: gray(50%) hex: #808080
> color name hx84-dt 30,30,30,50
Color 'hx84-dt' is 50% transparent: rgba(30%, 30%, 30%, 50%) hex:
#4d4d4d80
> color name hx84-dc 30,30,30,100
Color 'hx84-dc' is opaque: gray(30%) hex: #4d4d4d
> color name hx68-t 50,50,50,50
Color 'hx68-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name hx68-c 50,50,50,100
Color 'hx68-c' is opaque: gray(50%) hex: #808080
> color name hx69-t 40,40,40,50
Color 'hx69-t' is 50% transparent: rgba(40%, 40%, 40%, 50%) hex: #66666680
> color name hx69-c 40,40,40,100
Color 'hx69-c' is opaque: gray(40%) hex: #666666
> color name hx38-t 34,42,36,50
Color 'hx38-t' is 50% transparent: rgba(34%, 42%, 36%, 50%) hex: #576b5c80
> color name hx38-c 34,42,36,100
Color 'hx38-c' is opaque: rgb(34%, 42%, 36%) hex: #576b5c
> color name hx38-dt 34,42,36,50
Color 'hx38-dt' is 50% transparent: rgba(34%, 42%, 36%, 50%) hex:
#576b5c80
> color name hx38-dc 34,42,36,100
Color 'hx38-dc' is opaque: rgb(34%, 42%, 36%) hex: #576b5c
> color name ul5-t 55,62,67,50
Color 'ul5-t' is 50% transparent: rgba(55%, 62%, 67%, 50%) hex: #8c9eab80
> color name ul5-c 55,62,67,100
Color 'ul5-c' is opaque: rgb(55%, 62%, 67%) hex: #8c9eab
> color name ul5-dt 38,47,52,50
Color 'ul5-dt' is 50% transparent: rgba(38%, 47%, 52%, 50%) hex: #61788580
> color name ul5-dc 38,47,52,100
Color 'ul5-dc' is opaque: rgb(38%, 47%, 52%) hex: #617885
> color name ul16-t 70,70,70,50
Color 'ul16-t' is 50% transparent: rgba(70%, 70%, 70%, 50%) hex: #b3b3b380
> color name ul16-c 70,70,70,100
Color 'ul16-c' is opaque: gray(70%) hex: #b3b3b3
> color name srl-t 50,50,50,50
Color 'srl-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name srl-t 50,50,50,100
Color 'srl-t' is opaque: gray(50%) hex: #808080
> color name highlight-t 92,78,8,50
Color 'highlight-t' is 50% transparent: rgba(92%, 78%, 8%, 50%) hex:
#ebc71480
> color name highlight-c 92,78,8,100
Color 'highlight-c' is opaque: rgb(92%, 78%, 8%) hex: #ebc714
> color name tomato-t 100,39,28,50
Color 'tomato-t' is 50% transparent: rgba(100%, 39%, 28%, 50%) hex:
#ff634780
> color name tomato-c 100,39,28,100
Color 'tomato-c' is opaque: rgb(100%, 39%, 28%) hex: #ff6347
> color name lightgrayt 83,83,83,50
Color 'lightgrayt' is 50% transparent: rgba(83%, 83%, 83%, 50%) hex:
#d4d4d480
> color name silvert 75,75,75,50
Color 'silvert' is 50% transparent: rgba(75%, 75%, 75%, 50%) hex:
#bfbfbf80
> color name grayt 50,50,50,50
Color 'grayt' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name lightcyant 88,100,100,50
Color 'lightcyant' is 50% transparent: rgba(88%, 100%, 100%, 50%) hex:
#e0ffff80
> color name yellowt 100,90,0,50
Color 'yellowt' is 50% transparent: rgba(100%, 90%, 0%, 50%) hex:
#ffe60080
> color name deeppinkt 100,8,58,50
Color 'deeppinkt' is 50% transparent: rgba(100%, 8%, 58%, 50%) hex:
#ff149480
> color name oranget 100,65,0,50
Color 'oranget' is 50% transparent: rgba(100%, 65%, 0%, 50%) hex:
#ffa60080
> color name yellowgreent 60,80,20,50
Color 'yellowgreent' is 50% transparent: rgba(60%, 80%, 20%, 50%) hex:
#99cc3380
> color name darkmagentat 54,0,54,50
Color 'darkmagentat' is 50% transparent: rgba(54%, 0%, 54%, 50%) hex:
#8a008a80
> color name orchidt 86,44,84,50
Color 'orchidt' is 50% transparent: rgba(86%, 44%, 84%, 50%) hex:
#db70d680
> color name paleturquoiset 69,93,93,50
Color 'paleturquoiset' is 50% transparent: rgba(69%, 93%, 93%, 50%) hex:
#b0eded80
> color name pinkt 100,75,80,50
Color 'pinkt' is 50% transparent: rgba(100%, 75%, 80%, 50%) hex: #ffbfcc80
> color name darkgreent 0,39,0,50
Color 'darkgreent' is 50% transparent: rgba(0%, 39%, 0%, 50%) hex:
#00630080
> color name limegreent 20,80,20,50
Color 'limegreent' is 50% transparent: rgba(20%, 80%, 20%, 50%) hex:
#33cc3380
> color name turquoiset 25,88,82,50
Color 'turquoiset' is 50% transparent: rgba(25%, 88%, 82%, 50%) hex:
#40e0d180
> color name tealt 0,50,50,50
Color 'tealt' is 50% transparent: rgba(0%, 50%, 50%, 50%) hex: #00808080
> color name darkoranget 100,50,0,50
Color 'darkoranget' is 50% transparent: rgba(100%, 50%, 0%, 50%) hex:
#ff800080
> color name lightyellowt 100,100,50,50
Color 'lightyellowt' is 50% transparent: rgba(100%, 100%, 50%, 50%) hex:
#ffff8080
> color name goldt 100,75,0,50
Color 'goldt' is 50% transparent: rgba(100%, 75%, 0%, 50%) hex: #ffbf0080
> color name plumt 87,63,87,50
Color 'plumt' is 50% transparent: rgba(87%, 63%, 87%, 50%) hex: #dea1de80
> color name ssubluet 68,86,90,50
Color 'ssubluet' is 50% transparent: rgba(68%, 86%, 90%, 50%) hex:
#addbe680
> color name p-prect 10,41,0,50
Color 'p-prect' is 50% transparent: rgba(10%, 41%, 0%, 50%) hex: #1a690080
> color name p-h2t 23,59,0,50
Color 'p-h2t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
> color name p-h1t 40,73,0,50
Color 'p-h1t' is 50% transparent: rgba(40%, 73%, 0%, 50%) hex: #66ba0080
> color name p-h1c 40,73,0,100
Color 'p-h1c' is opaque: rgb(40%, 73%, 0%) hex: #66ba00
> color name p-spct 68,81,0,50
Color 'p-spct' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
> color name p-spcc 68,81,0,100
Color 'p-spcc' is opaque: rgb(68%, 81%, 0%) hex: #adcf00
> color name p-fat 82,92,0,50
Color 'p-fat' is 50% transparent: rgba(82%, 92%, 0%, 50%) hex: #d1eb0080
> color name p-postt 100,92,0,50
Color 'p-postt' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex:
#ffeb0080
> color name d-t 100,80,4,50
Color 'd-t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
> color name d-prect 95,100,50,50
Color 'd-prect' is 50% transparent: rgba(95%, 100%, 50%, 50%) hex:
#f2ff8080
> color name d-h2t 100,90,4,50
Color 'd-h2t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
> color name d-h1t 100,80,4,50
Color 'd-h1t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
> color name d-spct 100,70,4,50
Color 'd-spct' is 50% transparent: rgba(100%, 70%, 4%, 50%) hex: #ffb30a80
> color name d-fat 100,55,4,50
Color 'd-fat' is 50% transparent: rgba(100%, 55%, 4%, 50%) hex: #ff8c0a80
> color name d-fac 100,55,4,100
Color 'd-fac' is opaque: rgb(100%, 55%, 4%) hex: #ff8c0a
> color name d-postt 100,40,4,50
Color 'd-postt' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex:
#ff660a80
> color name m-t 95,43,62,50
Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
> color name m-prect 100,85,95,50
Color 'm-prect' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex:
#ffd9f280
> color name m-h2t 100,85,95,50
Color 'm-h2t' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex: #ffd9f280
> color name m-h1t 100,75,95,50
Color 'm-h1t' is 50% transparent: rgba(100%, 75%, 95%, 50%) hex: #ffbff280
> color name m-spct 89,63,75,50
Color 'm-spct' is 50% transparent: rgba(89%, 63%, 75%, 50%) hex: #e3a1bf80
> color name m-fat 95,51,75,50
Color 'm-fat' is 50% transparent: rgba(95%, 51%, 75%, 50%) hex: #f282bf80
> color name m-fac 95,51,75,100
Color 'm-fac' is opaque: rgb(95%, 51%, 75%) hex: #f282bf
> color name m-postt 95,43,62,50
Color 'm-postt' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex:
#f26e9e80
executed 70S_colors.cxc
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colorstandard.cxc
> color 100,100,100,50
> color lsu silvert
> color /3 lightgrayt
> color /5 lightgrayt
> color ssu ssu-t
> color head head-t
> color efg efg-t
> color dt d-t
> color pt p-t
> color pep p-t
> color mrna m-t
executed 70S_colorstandard.cxc
> windowsize 1000 1000
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_helices.cxc
> color h18 h18-t
> color h23 h23-t
> color h24 h24-t
> color h28 h28-t
> color h29 h29-t
> color h30 h30-t
> color h31 h31-t
> color h34 h34-t
> color h35 h35-t
> color h36 h36-t
> color h44 h44-t
> color H69 hx69-t
executed 70S_color_helices.cxc
> color h30|h36|h35 head-t
> view dc3
> surface cap true
> color zone #12.1 near #12.3,5 distance 5
> color zone #13.1 near #13.3,5 distance 5
> color zone #14.1 near #14.3,5 distance 5
> color zone #30.1 near #30.3,5 distance 5
> color zone #31.1 near #31.3,5 distance 5
> color zone #32.1 near #32.3,5 distance 5
> color zone #33.1 near #33.3,5 distance 5
> color zone #34.1 near #34.3,5 distance 5
> color zone #30.9 near #30.3,5 distance 5
> color zone #31.9 near #31.3,5 distance 5
> color zone #32.9 near #32.3,5 distance 5
> color zone #33.9 near #33.3,5 distance 5
> color zone #34.9 near #34.3,5 distance 5
> color h30|h36|h35 head-c
> color h28 h28-c
> color h29 h29-c
> color h34 h34-c
> color h23 h23-c
> color h24 h24-c
> color h31 h31-c
> hide #!100
> hide #101 models
> cartoon style nucleic xsection oval width 1.3 thickness 1.3
> transparency #*.3 0 target abc
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_helices-s.cxc
> color h18 h18-c
> color h23 h23-c
> color h24 h24-c
> color h28 h28-c
> color h29 h29-c
> color h30 h30-c
> color h31 h31-c
> color h34 h34-c
> color h35 h35-c
> color h44 h44-c
> color H69 hx69-c
executed 70S_color_helices-s.cxc
> color /v d-c
> color /y p-c
> color /w m-c
executed gtpys_dc.cxc
> surface cap true
> lighting gentle
> lighting intensity .2
> size stickRadius 0.17
Changed 1744812 bond radii
> nucribthin
> style ringFill thin
Changed 122200 residue ring styles
> graphics silhouettes true color black
> ~select
Nothing selected
> ~select
Nothing selected
> ~ribbon
> ~display
> ribbon
> ~ribbon mrna
> display mrna
> display antiplus
> display /x:505-514,584
> display /6:1492,1493,530,532,1054,1400,1397
> display /3:1913
> display #*.3/L:44
> hide models
> show #31.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_ysH1b.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_ysH1b.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #32.3,5 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_ysH1c.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_ysH1c.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #12.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_H1apo.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_H1bapo.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #33.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_ysI1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_ysI1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #34.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_I1bys.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_I1bys.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #13.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_I1spc.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_I1spc.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #14.3,5 models
> ~display #14.3/w:38,49
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_I2fa.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_I2fa.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> graphics silhouettes true color 25,25,25,15
> style ringFill thick
Changed 122200 residue ring styles
> ~cartoon /6/3
> display /6/3
> ~cartoon trna
> display trna
> volume emmaps style surface step 1 level 3
> surface dust emmaps size 2
> volume emmaps surfaceSmoothing true
> view dc3
> hide models
> show #30 models
> select #30.3
60930 atoms, 65574 bonds, 3 pseudobonds, 4887 residues, 3 models selected
> hide #30.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_ysH1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #31 models
> select #31.3
60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected
> hide #31.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_ysH1b.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #32 models
> select #32.3
60097 atoms, 64722 bonds, 4 pseudobonds, 4779 residues, 3 models selected
> hide #32.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_ysH1c.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #12 models
> select #12.3
55765 atoms, 60298 bonds, 4230 residues, 1 model selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_H1apo.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #33 models
> select #33.3
61025 atoms, 65674 bonds, 2 pseudobonds, 4898 residues, 3 models selected
> hide #33.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_ysI1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #34 models
> select #34.3
61064 atoms, 65713 bonds, 3 pseudobonds, 4898 residues, 3 models selected
> hide #34.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_I1bys.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #13 models
> select #13.3
61103 atoms, 65762 bonds, 4902 residues, 1 model selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_I1spc.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #14 models
> ~display #14.3/w:38,49
> select #14.3
60702 atoms, 65388 bonds, 1 pseudobond, 4855 residues, 2 models selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_I2fa.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> volume emmaps style surface step 1 level 8
> surface dust emmaps size 2
> volume emmaps surfaceSmoothing true
> hide models
> show #30.3,5,9 models
> select #30.3
60930 atoms, 65574 bonds, 3 pseudobonds, 4887 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysH1a-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #31.3,5,9 models
> select #31.3
60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysH1b-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #32.3,5,9 models
> select #32.3
60097 atoms, 64722 bonds, 4 pseudobonds, 4779 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysH1c-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #33.3,5,9 models
> select #33.3
61025 atoms, 65674 bonds, 2 pseudobonds, 4898 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysI1a-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #34.3,5,9 models
> select #34.3
61064 atoms, 65713 bonds, 3 pseudobonds, 4898 residues, 3 models selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_I1bys-
> FR.tif format tiff width 1000 height 1000 supersample 20
> transparentBackground true
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
——— End of log from Thu Jul 20 18:51:54 2023 ———
opened ChimeraX session
> view dc2
> view dc1
> view dc3
> view dc2
> ui tool show "Side View"
> view name dc4
> hide models
> show #13 models
> view dc1
> display efg
> ui mousemode right pivot
> volume emmaps style surface step 1 level 3
> view name dc5
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
> color efg byhetero
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
——— End of log from Mon Jul 31 14:44:45 2023 ———
opened ChimeraX session
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_assign.cxc
> name atomods #*.3|#*.5
> name emmaps #*.1|#*.7|#*.8|#*.9
> name lsu #*.5
> name lsumap #*.8
> name ssu #*.3
> name ssumap #*.7
> name ligmap #*.9
> name rna /y,v,w,3,6,5
> name r23s /3
> name r16s /6
> name r5s /5
> name pt /y
> name dt /v
> name efg /x
> name pep /p
> name mrna /w
> name GSP :GSP
> name GDP :GDP
> name GTP :GTP
> name ntide :GTP|:GDP|:GSP
> name spc :SCM
> name fua :FUA
> name par :PAR
> name argb :LIG
> name drugs argb|par|fua|spc
> name D1 /x:start-293
> name D2 /x:294-410
> name D3 /x:411-489
> name D4 /x:490-612
> name D5 /x:613-end
> name sw1 /x:38-65
> name sw2 /x:89-108
> name pl /x:18-25
> name nkxd /x:142-146
> name mg /x:MG
> name trna /y,v
> name anticodon /y,v:34-36
> name antiplus /y,v:32-38
> name cca /y,v:74-76
> name astem /y,v:1-7,66-73
> name darm /y,v:8-25
> name aarm /y,v:26-43
> name varm /y,v:44-48
> name tarm /y,v:49-65
> name head #*.3/A/C/S/M/G/N/I/J/6:927-1390
> name arg-head #20.3/A/C/S/M/G/N/I/J/6:927-1390
> name post-head #15.3/A/C/S/M/G/N/I/J/6:927-1390
> name fa-head #14.3/A/C/S/M/G/N/I/J/6:927-1390
> name body #*.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name arg-body #20.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name post-body #15.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name fa-body #14.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name aploop /6:956-959
> name term16S /6:1503-end
> name aphelix /6:1228-1230
> name us2 #*.3/B
> name us3 #*.3/C
> name us4 #*.3/D
> name us5 #*.3/E
> name us6 #*.3/F
> name us7 #*.3/G
> name us8 #*.3/H
> name us9 #*.3/I
> name us10 #*.3/J
> name us11 #*.3/K
> name us12 #*.3/L
> name us13 #*.3/M
> name us14 #*.3/N
> name us15 #*.3/O
> name us16 #*.3/P
> name us17 #*.3/Q
> name us18 #*.3/R
> name us19 #*.3/S
> name us20 #*.3/T
> name us21 #*.3/U
> name us9-130 #*.3/I:130
> name l1stalk /3:2097-2191
> name srl /3:2652-2668
> name asf /3:863-910
> name l1stalk /3:2094-2195
> name ul1 #*.5/A
> name ul2 #*.5/B
> name ul3 #*.5/C
> name ul4 #*.5/D
> name ul5 #*.5/E
> name ul6 #*.5/F
> name ul7 #*.5/G
> name ul9 #*.5/I
> name ul10 #*.5/J
> name ul11 #*.5/K
> name ul13 #*.5/M
> name ul14 #*.5/N
> name ul15 #*.5/O
> name ul16 #*.5/P
> name ul17 #*.5/Q
> name ul18 #*.5/R
> name ul19 #*.5/S
> name ul20 #*.5/T
> name ul21 #*.5/U
> name ul22 #*.5/V
> name ul23 #*.5/W
> name ul24 #*.5/X
> name ul25 #*.5/Y
> name ul27 #*.5/a
> name ul28 #*.5/b
> name ul29 #*.5/c
> name ul30 #*.5/d
> name ul31 #*.5/e
> name ul32 #*.5/f
> name ul33 #*.5/g
> name ul34 #*.5/h
> name ul35 #*.5/i
> name ul36 #*.5/j
> name h1 #*.3/6:9-13|#*.3/6:21-25
> name h2 #*.3/6:17-19|#*.3/6:916-918
> name h3 #*.3/6:27-37|#*.3/6:547-556
> name h4 #*.3/6:39-46|#*.3/6:395-403
> name h5 #*.3/6:47-58|#*.3/6:354-360
> name h6 #*.3/6:61-106
> name h7 #*.3/6:122-142|#*.3/6:221-239
> name h8 #*.3/6:144-178
> name h9 #*.3/6:184-193
> name h10 #*.3/6:198-219
> name h11 #*.3/6:240-286
> name h12 #*.3/6:289-311
> name h13 #*.3/6:316-337
> name h14 #*.3/6:339-350
> name h15 #*.3/6:367-393
> name h16 #*.3/6:406-436
> name h17 #*.3/6:437-497
> name h18 #*.3/6:500-545
> name h19 #*.3/6:567-569|#*.3/6:881-88
> name h20 #*.3/6:577-586|#*.3/6:755-76
> name h21 #*.3/6:588-651
> name h22 #*.3/6:654-672|#*.3/6:734-75
> name h23 #*.3/6:673-733
> name h24 #*.3/6:769-810
> name h25 #*.3/6:821-827|#*.3/6:873-87
> name h26 #*.3/6:829-857
> name h26a #*.3/6:861-868
> name h27 #*.3/6:885-912
> name h28 #*.3/6:921-937|#*.3/6:1379-1400
> name h29 #*.3/6:938-943|#*.3/6:1337-1346
> name h30 #*.3/6:945-955|#*.3/6:1225-1236
> name h31 #*.3/6:956-975
> name h32 #*.3/6:984-991|#*.3/6:1212-1221
> name h33 #*.3/6:992-1045
> name h34 #*.3/6:1045-1065|#*.3/6:1188-1211
> name h35 #*.3/6:1066-1073|#*.3/6:1102-1110
> name h36 #*.3/6:1074-1083
> name h37 #*.3/6:1086-1099
> name h38 #*.3/6:1113-1117|#*.3/6:1183-1187
> name h39 #*.3/6:1118-1155
> name h40 #*.3/6:1161-1175
> name h41 #*.3/6:1241-1296
> name h42 #*.3/6:1303-1334
> name h43 #*.3/6:1350-1372
> name h44 #*.3/6:1401-1502
> name h45 #*.3/6:1506-1529
> name H1 #*.5/3:1-8|#*.5/3:2895-2904
> name H2 #*.5/3:15-24|#*.5/3:516-525
> name H3 #*.5/3:31-32|#*.5/3:473-474
> name H4 #*.5/3:35-45|#*.5/3:433-445
> name H5 #*.5/3:54-57|#*.5/3:114-117
> name H6 #*.5/3:58-69
> name H7 #*.5/3:75-110
> name H8 #*.5/3:121-130
> name H9 #*.5/3:131-148
> name H10 #*.5/3:150-176
> name H11 #*.5/3:183-213
> name H12 #*.5/3:224-231
> name H13 #*.5/3:235-262
> name H14 #*.5/3:265-268|#*.5/3:424-427
> name H16 #*.5/3:271-274|#*.5/3:363-366
> name H18 #*.5/3:281-297|#*.5/3:341-359
> name H19 #*.5/3:301-316
> name H20 #*.5/3:325-337
> name H21 #*.5/3:375-399
> name H22 #*.5/3:406-421
> name H23 #*.5/3:461-468
> name H24 #*.5/3:484-496
> name H25 #*.5/3:533-560
> name H26 #*.5/3:579-584|#*.5/3:1256-1261
> name H27 #*.5/3:589-601|#*.5/3:656-668
> name H28 #*.5/3:604-624
> name H29 #*.5/3:628-635
> name H31 #*.5/3:637-651
> name H32 #*.5/3:678-683|#*.5/3:794-799
> name H33 #*.5/3:687-698|#*.5/3:763-775
> name H34 #*.5/3:700-732
> name H35 #*.5/3:736-760
> name H35a #*.5/3:777-787
> name H36 #*.5/3:812-817|#*.5/3:1190-1195
> name H37 #*.5/3:822-835
> name H38 #*.5/3:838-940
> name H39 #*.5/3:946-971
> name H40 #*.5/3:976-987
> name H41 #*.5/3:991-1018|#*.5/3:1144-1163
> name H42 #*.5/3:1030-1055|#*.5/3:1104-1124
> name H43 #*.5/3:1057-1081
> name H44 #*.5/3:1087-1102
> name H45 #*.5/3:1164-1185
> name H46 #*.5/3:1198-1247
> name H47 #*.5/3:1276-1294
> name H48 #*.5/3:1295-1298|#*.5/3:1642-1646
> name H49 #*.5/3:1303-1306|#*.5/3:1622-1625
> name H50 #*.5/3:1314-1338
> name H51 #*.5/3:1345-1348|#*.5/3:1598-1601
> name H52 #*.5/3:1350-1381
> name H53 #*.5/3:1385-1402
> name H54 #*.5/3:1405-1417|#*.5/3:1581-1597
> name H55 #*.5/3:1420-1424|#*.5/3:1573-1578
> name H56 #*.5/3:1429-1444|#*.5/3:1547-1564
> name H57 #*.5/3:1445-1466
> name H58 #*.5/3:1467-1525
> name H59 #*.5/3:1527-1544
> name H60 #*.5/3:1627-1639
> name H61 #*.5/3:1647-1669|#*.5/3:1991-2009
> name H62 #*.5/3:1682-1706
> name H63 #*.5/3:1707-1751
> name H64 #*.5/3:1764-1772|#*.5/3:1979-1988
> name H65 #*.5/3:1775-1789
> name H66 #*.5/3:1792-1827
> name H67 #*.5/3:1830-1833|#*.5/3:1972-1975
> name H68 #*.5/3:1835-1905
> name H69 #*.5/3:1906-1924
> name H71 #*.5/3:1945-1960
> name H72 #*.5/3:2023-2040
> name H73 #*.5/3:2043-2057|#*.5/3:2611-2625
> name H74 #*.5/3:2064-2075|#*.5/3:2434-2446
> name H75 #*.5/3:2077-2090|#*.5/3:2229-2243
> name H76 #*.5/3:2093-2110|#*.5/3:2179-2196
> name H77 #*.5/3:2120-2124|#*.5/3:2174-2178
> name H78 #*.5/3:2127-2161
> name H79 #*.5/3:2200-2223
> name H80 #*.5/3:2246-2258
> name H81 #*.5/3:2259-2281
> name H82 #*.5/3:2284-2285|#*.5/3:2383-2384
> name H83 #*.5/3:2288-2295|#*.5/3:2337-2344
> name H84 #*.5/3:2296-2322
> name H85 #*.5/3:2323-2332
> name H86 #*.5/3:2347-2370
> name H87 #*.5/3:2372-2381
> name H88 #*.5/3:2395-2421
> name H89 #*.5/3:2453-2498
> name H90 #*.5/3:2507-2517|#*.5/3:2567-2582
> name H91 #*.5/3:2520-2545
> name H92 #*.5/3:2547-2561
> name H93 #*.5/3:2588-2606
> name H94 #*.5/3:2630-2643|#*.5/3:2771-2788
> name H95 #*.5/3:2646-2674
> name H96 #*.5/3:2675-2732
> name H97 #*.5/3:2735-2769
> name H98 #*.5/3:2791-2805
> name H99 #*.5/3:2811-2814|#*.5/3:2886-2889
> name H100 #*.5/3:2815-2831
executed 70S_assign.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_display.cxc
> alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6;
> alias nucribthin cartoon style nucleic xsect oval width 1.2 thick 1.2;
> alias cylinders cartoon style protein modeh tube rad 2 sides 24;
> alias licorice car style protein modeh default arrows f xsect oval width
1
> thick 1;
> dssp
> windowsize 1000 1000
> set bgColor white
> lighting full
> set silhouettes true
> set silhouetteWidth 1.7
> set silhouettes true
> set silhouetteDepthJump 0.02
> cartoon style width 2.5
> size atomRadius 2
Changed 1614330 atom radii
> nucleotides fill
> size ions atomRadius 1.6
Changed 31 atom radii
> size stickRadius 0.1
Changed 1744812 bond radii
> style stick ringFill thin
Changed 1614330 atom styles, 122200 residue ring styles
> show ribbons
> hide H
> hide :HOH
> hide target a
> show nucleic target a
> show drugs target a
> style drugs ball
Changed 106 atom styles
> graphics selection color black
> cartoon style protein xsection round width 2 thickness 0.6
> cartoon style modeHelix wrap
> cartoon style sides 24
> cartoon style strand xsection oval arrows false
> cartoon suppressBackboneDisplay true
> alias thinbois style ball;size ballscale 0.09; size stickradius 0.13;
> alias thickbois style stick;size stickradius 0.4;style stick ringFill
thick;
> volume emmaps style surface step 1 level 4
> surface dust emmaps size 3
> volume surfaceSmoothing true
> cartoon tether trna shape cone opacity 1
> dssp
> thickbois
Changed 1614330 atom styles
Changed 1744812 bond radii
Changed 1614330 atom styles, 122200 residue ring styles
executed 70S_display.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colors.cxc
> color name efg-t 100,0,0,50
Color 'efg-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
> color name sw1-t 100,92,0,50
Color 'sw1-t' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
> color name sw2-t 68,81,0,50
Color 'sw2-t' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
> color name pl-t 23,59,0,50
Color 'pl-t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
> color name d1-t 100,18,4,50
Color 'd1-t' is 50% transparent: rgba(100%, 18%, 4%, 50%) hex: #ff2e0a80
> color name d2-t 100,40,4,50
Color 'd2-t' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
> color name d3-t 100,27,36,50
Color 'd3-t' is 50% transparent: rgba(100%, 27%, 36%, 50%) hex: #ff455c80
> color name d4-t 80,0,23,50
Color 'd4-t' is 50% transparent: rgba(80%, 0%, 23%, 50%) hex: #cc003b80
> color name d5-t 100,60,4,50
Color 'd5-t' is 50% transparent: rgba(100%, 60%, 4%, 50%) hex: #ff990a80
> color name fa-t 100,90,4,50
Color 'fa-t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
> color name gtp-t 45,53,60,50
Color 'gtp-t' is 50% transparent: rgba(45%, 53%, 60%, 50%) hex: #73879980
> color name mg-t 1,39,16,50
Color 'mg-t' is 50% transparent: rgba(1%, 39%, 16%, 50%) hex: #03632980
> color name spc-t 100,0,0,50
Color 'spc-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
> color name argb-t 50,0,50,50
Color 'argb-t' is 50% transparent: rgba(50%, 0%, 50%, 50%) hex: #80008080
> color name g-1t 98,42,30,50
Color 'g-1t' is 50% transparent: rgba(98%, 42%, 30%, 50%) hex: #fa6b4d80
> color name g-2t 95,35,25,50
Color 'g-2t' is 50% transparent: rgba(95%, 35%, 25%, 50%) hex: #f2594080
> color name g-3t 92,28,20,50
Color 'g-3t' is 50% transparent: rgba(92%, 28%, 20%, 50%) hex: #eb473380
> color name g-4t 89,21,15,50
Color 'g-4t' is 50% transparent: rgba(89%, 21%, 15%, 50%) hex: #e3362680
> color name g-5t 86,14,10,50
Color 'g-5t' is 50% transparent: rgba(86%, 14%, 10%, 50%) hex: #db241a80
> color name g-6t 83,7,5,50
Color 'g-6t' is 50% transparent: rgba(83%, 7%, 5%, 50%) hex: #d4120d80
> color name g-7t 80,0,0,50
Color 'g-7t' is 50% transparent: rgba(80%, 0%, 0%, 50%) hex: #cc000080
> color name p-t 44,59,2,50
Color 'p-t' is 50% transparent: rgba(44%, 59%, 2%, 50%) hex: #70960580
> color name p-c 44,59,2,100
Color 'p-c' is opaque: rgb(44%, 59%, 2%) hex: #709605
> color name p-1t 4,34,1,50
Color 'p-1t' is 50% transparent: rgba(4%, 34%, 1%, 50%) hex: #0a570380
> color name p-2t 12,39,1,50
Color 'p-2t' is 50% transparent: rgba(12%, 39%, 1%, 50%) hex: #1f630380
> color name p-3t 20,44,1,50
Color 'p-3t' is 50% transparent: rgba(20%, 44%, 1%, 50%) hex: #33700380
> color name p-4t 28,49,1,50
Color 'p-4t' is 50% transparent: rgba(28%, 49%, 1%, 50%) hex: #477d0380
> color name p-5t 36,54,2,50
Color 'p-5t' is 50% transparent: rgba(36%, 54%, 2%, 50%) hex: #5c8a0580
> color name p-6t 44,59,2,50
Color 'p-6t' is 50% transparent: rgba(44%, 59%, 2%, 50%) hex: #70960580
> color name p-7t 52,64,2,50
Color 'p-7t' is 50% transparent: rgba(52%, 64%, 2%, 50%) hex: #85a30580
> color name p-8t 60,69,2,50
Color 'p-8t' is 50% transparent: rgba(60%, 69%, 2%, 50%) hex: #99b00580
> color name p-9t 68,74,3,50
Color 'p-9t' is 50% transparent: rgba(68%, 74%, 3%, 50%) hex: #adbd0880
> color name p-10t 76,79,3,50
Color 'p-10t' is 50% transparent: rgba(76%, 79%, 3%, 50%) hex: #c2c90880
> color name p-11t 84,84,3,50
Color 'p-11t' is 50% transparent: rgba(84%, 84%, 3%, 50%) hex: #d6d60880
> color name d-t 100,65,4,50
Color 'd-t' is 50% transparent: rgba(100%, 65%, 4%, 50%) hex: #ffa60a80
> color name d-c 100,65,4,100
Color 'd-c' is opaque: rgb(100%, 65%, 4%) hex: #ffa60a
> color name d-1t 100,100,4,50
Color 'd-1t' is 50% transparent: rgba(100%, 100%, 4%, 50%) hex: #ffff0a80
> color name d-2t 100,93,4,50
Color 'd-2t' is 50% transparent: rgba(100%, 93%, 4%, 50%) hex: #ffed0a80
> color name d-3t 100,86,4,50
Color 'd-3t' is 50% transparent: rgba(100%, 86%, 4%, 50%) hex: #ffdb0a80
> color name d-4t 100,79,4,50
Color 'd-4t' is 50% transparent: rgba(100%, 79%, 4%, 50%) hex: #ffc90a80
> color name d-5t 100,72,4,50
Color 'd-5t' is 50% transparent: rgba(100%, 72%, 4%, 50%) hex: #ffb80a80
> color name d-6t 100,65,4,50
Color 'd-6t' is 50% transparent: rgba(100%, 65%, 4%, 50%) hex: #ffa60a80
> color name d-7t 100,58,4,50
Color 'd-7t' is 50% transparent: rgba(100%, 58%, 4%, 50%) hex: #ff940a80
> color name d-8t 100,51,4,50
Color 'd-8t' is 50% transparent: rgba(100%, 51%, 4%, 50%) hex: #ff820a80
> color name d-9t 100,44,4,50
Color 'd-9t' is 50% transparent: rgba(100%, 44%, 4%, 50%) hex: #ff700a80
> color name d-10t 100,37,4,50
Color 'd-10t' is 50% transparent: rgba(100%, 37%, 4%, 50%) hex: #ff5e0a80
> color name d-11t 100,30,4,50
Color 'd-11t' is 50% transparent: rgba(100%, 30%, 4%, 50%) hex: #ff4d0a80
> color name m-t 95,43,62,50
Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
> color name m-c 95,43,62,100
Color 'm-c' is opaque: rgb(95%, 43%, 62%) hex: #f26e9e
> color name m-1t 100,80,90,50
Color 'm-1t' is 50% transparent: rgba(100%, 80%, 90%, 50%) hex: #ffcce680
> color name m-2t 98,76,87,50
Color 'm-2t' is 50% transparent: rgba(98%, 76%, 87%, 50%) hex: #fac2de80
> color name m-3t 96,72,84,50
Color 'm-3t' is 50% transparent: rgba(96%, 72%, 84%, 50%) hex: #f5b8d680
> color name m-4t 94,68,81,50
Color 'm-4t' is 50% transparent: rgba(94%, 68%, 81%, 50%) hex: #f0adcf80
> color name m-5t 92,64,78,50
Color 'm-5t' is 50% transparent: rgba(92%, 64%, 78%, 50%) hex: #eba3c780
> color name m-6t 90,60,75,50
Color 'm-6t' is 50% transparent: rgba(90%, 60%, 75%, 50%) hex: #e699bf80
> color name m-7t 88,56,72,50
Color 'm-7t' is 50% transparent: rgba(88%, 56%, 72%, 50%) hex: #e08fb880
> color name m-8t 86,52,69,50
Color 'm-8t' is 50% transparent: rgba(86%, 52%, 69%, 50%) hex: #db85b080
> color name m-9t 84,48,66,50
Color 'm-9t' is 50% transparent: rgba(84%, 48%, 66%, 50%) hex: #d67aa880
> color name m-10t 82,44,63,50
Color 'm-10t' is 50% transparent: rgba(82%, 44%, 63%, 50%) hex: #d170a180
> color name m-11t 80,40,60,50
Color 'm-11t' is 50% transparent: rgba(80%, 40%, 60%, 50%) hex: #cc669980
> color name head-t 82,74,84,50
Color 'head-t' is 50% transparent: rgba(82%, 74%, 84%, 50%) hex: #d1bdd680
> color name head-c 82,74,84,100
Color 'head-c' is opaque: rgb(82%, 74%, 84%) hex: #d1bdd6
> color name headfa-t 54,41,54,50
Color 'headfa-t' is 50% transparent: rgba(54%, 41%, 54%, 50%) hex:
#8a698a80
> color name headblue-t 59,78,94,50
Color 'headblue-t' is 50% transparent: rgba(59%, 78%, 94%, 50%) hex:
#96c7f080
> color name headh1-t 41,64,100,50
Color 'headh1-t' is 50% transparent: rgba(41%, 64%, 100%, 50%) hex:
#69a3ff80
> color name headh2-t 50,70,100,50
Color 'headh2-t' is 50% transparent: rgba(50%, 70%, 100%, 50%) hex:
#80b3ff80
> color name headgray-t 60,60,60,50
Color 'headgray-t' is 50% transparent: rgba(60%, 60%, 60%, 50%) hex:
#99999980
> color name darkhead-s 54,41,54,100
Color 'darkhead-s' is opaque: rgb(54%, 41%, 54%) hex: #8a698a
> color name bodywhite-t 90,90,90,50
Color 'bodywhite-t' is 50% transparent: rgba(90%, 90%, 90%, 50%) hex:
#e6e6e680
> color name rps-t 75,88,93,50
Color 'rps-t' is 50% transparent: rgba(75%, 88%, 93%, 50%) hex: #bfe0ed80
> color name ssu-t 69,79,82,50
Color 'ssu-t' is 50% transparent: rgba(69%, 79%, 82%, 50%) hex: #b0c9d180
> color name ssu-c 69,79,82,100
Color 'ssu-c' is opaque: rgb(69%, 79%, 82%) hex: #b0c9d1
> color name h16-t 79,85,89,50
Color 'h16-t' is 50% transparent: rgba(79%, 85%, 89%, 50%) hex: #c9d9e380
> color name h16-c 79,85,89,100
Color 'h16-c' is opaque: rgb(79%, 85%, 89%) hex: #c9d9e3
> color name h18-t 31,59,68,50
Color 'h18-t' is 50% transparent: rgba(31%, 59%, 68%, 50%) hex: #4f96ad80
> color name h18-dt 6,47,62,50
Color 'h18-dt' is 50% transparent: rgba(6%, 47%, 62%, 50%) hex: #0f789e80
> color name h18-dc 6,47,62,100
Color 'h18-dc' is opaque: rgb(6%, 47%, 62%) hex: #0f789e
> color name h18-c 31,59,68,100
Color 'h18-c' is opaque: rgb(31%, 59%, 68%) hex: #4f96ad
> color name h23-t 40,61,80,50
Color 'h23-t' is 50% transparent: rgba(40%, 61%, 80%, 50%) hex: #669ccc80
> color name h23-c 40,61,80,100
Color 'h23-c' is opaque: rgb(40%, 61%, 80%) hex: #669ccc
> color name h24-t 50,70,90,50
Color 'h24-t' is 50% transparent: rgba(50%, 70%, 90%, 50%) hex: #80b3e680
> color name h24-c 50,70,90,100
Color 'h24-c' is opaque: rgb(50%, 70%, 90%) hex: #80b3e6
> color name h28-t 21,27,56,50
Color 'h28-t' is 50% transparent: rgba(21%, 27%, 56%, 50%) hex: #36458f80
> color name h28-c 21,27,56,100
Color 'h28-c' is opaque: rgb(21%, 27%, 56%) hex: #36458f
> color name h29-t 80,69,92,50
Color 'h29-t' is 50% transparent: rgba(80%, 69%, 92%, 50%) hex: #ccb0eb80
> color name h29-c 80,69,92,100
Color 'h29-c' is opaque: rgb(80%, 69%, 92%) hex: #ccb0eb
> color name h30-t 40,40,59,50
Color 'h30-t' is 50% transparent: rgba(40%, 40%, 59%, 50%) hex: #66669680
> color name h30-c 40,40,59,100
Color 'h30-c' is opaque: rgb(40%, 40%, 59%) hex: #666696
> color name h31-t 45,35,55,50
Color 'h31-t' is 50% transparent: rgba(45%, 35%, 55%, 50%) hex: #73598c80
> color name h31-c 45,35,55,100
Color 'h31-c' is opaque: rgb(45%, 35%, 55%) hex: #73598c
> color name h32-t 75,62,79,50
Color 'h32-t' is 50% transparent: rgba(75%, 62%, 79%, 50%) hex: #bf9ec980
> color name h32-c 75,62,79,100
Color 'h32-c' is opaque: rgb(75%, 62%, 79%) hex: #bf9ec9
> color name h33-t 88,82,90,50
Color 'h33-t' is 50% transparent: rgba(88%, 82%, 90%, 50%) hex: #e0d1e680
> color name h33-c 88,82,90,100
Color 'h33-c' is opaque: rgb(88%, 82%, 90%) hex: #e0d1e6
> color name h34-t 59,35,59,50
Color 'h34-t' is 50% transparent: rgba(59%, 35%, 59%, 50%) hex: #96599680
> color name h34-c 59,35,59,100
Color 'h34-c' is opaque: rgb(59%, 35%, 59%) hex: #965996
> color name h35-t 50,22,45,50
Color 'h35-t' is 50% transparent: rgba(50%, 22%, 45%, 50%) hex: #80387380
> color name h35-c 50,22,45,100
Color 'h35-c' is opaque: rgb(50%, 22%, 45%) hex: #803873
> color name h44-t 32,54,70,50
Color 'h44-t' is 50% transparent: rgba(32%, 54%, 70%, 50%) hex: #528ab380
> color name h44-c 32,54,70,100
Color 'h44-c' is opaque: rgb(32%, 54%, 70%) hex: #528ab3
> color name aploop-t 27,0,50,50
Color 'aploop-t' is 50% transparent: rgba(27%, 0%, 50%, 50%) hex:
#45008080
> color name term16-t 40,64,64,50
Color 'term16-t' is 50% transparent: rgba(40%, 64%, 64%, 50%) hex:
#66a3a380
> color name uS3-t 48,44,57,50
Color 'uS3-t' is 50% transparent: rgba(48%, 44%, 57%, 50%) hex: #7a709180
> color name uS3-c 48,44,57,100
Color 'uS3-c' is opaque: rgb(48%, 44%, 57%) hex: #7a7091
> color name uS3-dt 40,37,57,50
Color 'uS3-dt' is 50% transparent: rgba(40%, 37%, 57%, 50%) hex: #665e9180
> color name uS3-dc 40,37,57,100
Color 'uS3-dc' is opaque: rgb(40%, 37%, 57%) hex: #665e91
> color name uS5-t 0,50,45,50
Color 'uS5-t' is 50% transparent: rgba(0%, 50%, 45%, 50%) hex: #00807380
> color name gray-t 70,70,70,50
Color 'gray-t' is 50% transparent: rgba(70%, 70%, 70%, 50%) hex: #b3b3b380
> color name hx84-t 50,50,50,50
Color 'hx84-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name hx84-c 50,50,50,100
Color 'hx84-c' is opaque: gray(50%) hex: #808080
> color name hx84-dt 30,30,30,50
Color 'hx84-dt' is 50% transparent: rgba(30%, 30%, 30%, 50%) hex:
#4d4d4d80
> color name hx84-dc 30,30,30,100
Color 'hx84-dc' is opaque: gray(30%) hex: #4d4d4d
> color name hx68-t 50,50,50,50
Color 'hx68-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name hx68-c 50,50,50,100
Color 'hx68-c' is opaque: gray(50%) hex: #808080
> color name hx69-t 40,40,40,50
Color 'hx69-t' is 50% transparent: rgba(40%, 40%, 40%, 50%) hex: #66666680
> color name hx69-c 40,40,40,100
Color 'hx69-c' is opaque: gray(40%) hex: #666666
> color name hx38-t 34,42,36,50
Color 'hx38-t' is 50% transparent: rgba(34%, 42%, 36%, 50%) hex: #576b5c80
> color name hx38-c 34,42,36,100
Color 'hx38-c' is opaque: rgb(34%, 42%, 36%) hex: #576b5c
> color name hx38-dt 34,42,36,50
Color 'hx38-dt' is 50% transparent: rgba(34%, 42%, 36%, 50%) hex:
#576b5c80
> color name hx38-dc 34,42,36,100
Color 'hx38-dc' is opaque: rgb(34%, 42%, 36%) hex: #576b5c
> color name ul5-t 55,62,67,50
Color 'ul5-t' is 50% transparent: rgba(55%, 62%, 67%, 50%) hex: #8c9eab80
> color name ul5-c 55,62,67,100
Color 'ul5-c' is opaque: rgb(55%, 62%, 67%) hex: #8c9eab
> color name ul5-dt 38,47,52,50
Color 'ul5-dt' is 50% transparent: rgba(38%, 47%, 52%, 50%) hex: #61788580
> color name ul5-dc 38,47,52,100
Color 'ul5-dc' is opaque: rgb(38%, 47%, 52%) hex: #617885
> color name ul16-t 70,70,70,50
Color 'ul16-t' is 50% transparent: rgba(70%, 70%, 70%, 50%) hex: #b3b3b380
> color name ul16-c 70,70,70,100
Color 'ul16-c' is opaque: gray(70%) hex: #b3b3b3
> color name srl-t 50,50,50,50
Color 'srl-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name srl-t 50,50,50,100
Color 'srl-t' is opaque: gray(50%) hex: #808080
> color name highlight-t 92,78,8,50
Color 'highlight-t' is 50% transparent: rgba(92%, 78%, 8%, 50%) hex:
#ebc71480
> color name highlight-c 92,78,8,100
Color 'highlight-c' is opaque: rgb(92%, 78%, 8%) hex: #ebc714
> color name tomato-t 100,39,28,50
Color 'tomato-t' is 50% transparent: rgba(100%, 39%, 28%, 50%) hex:
#ff634780
> color name tomato-c 100,39,28,100
Color 'tomato-c' is opaque: rgb(100%, 39%, 28%) hex: #ff6347
> color name lightgrayt 83,83,83,50
Color 'lightgrayt' is 50% transparent: rgba(83%, 83%, 83%, 50%) hex:
#d4d4d480
> color name silvert 75,75,75,50
Color 'silvert' is 50% transparent: rgba(75%, 75%, 75%, 50%) hex:
#bfbfbf80
> color name grayt 50,50,50,50
Color 'grayt' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name lightcyant 88,100,100,50
Color 'lightcyant' is 50% transparent: rgba(88%, 100%, 100%, 50%) hex:
#e0ffff80
> color name yellowt 100,90,0,50
Color 'yellowt' is 50% transparent: rgba(100%, 90%, 0%, 50%) hex:
#ffe60080
> color name deeppinkt 100,8,58,50
Color 'deeppinkt' is 50% transparent: rgba(100%, 8%, 58%, 50%) hex:
#ff149480
> color name oranget 100,65,0,50
Color 'oranget' is 50% transparent: rgba(100%, 65%, 0%, 50%) hex:
#ffa60080
> color name yellowgreent 60,80,20,50
Color 'yellowgreent' is 50% transparent: rgba(60%, 80%, 20%, 50%) hex:
#99cc3380
> color name darkmagentat 54,0,54,50
Color 'darkmagentat' is 50% transparent: rgba(54%, 0%, 54%, 50%) hex:
#8a008a80
> color name orchidt 86,44,84,50
Color 'orchidt' is 50% transparent: rgba(86%, 44%, 84%, 50%) hex:
#db70d680
> color name paleturquoiset 69,93,93,50
Color 'paleturquoiset' is 50% transparent: rgba(69%, 93%, 93%, 50%) hex:
#b0eded80
> color name pinkt 100,75,80,50
Color 'pinkt' is 50% transparent: rgba(100%, 75%, 80%, 50%) hex: #ffbfcc80
> color name darkgreent 0,39,0,50
Color 'darkgreent' is 50% transparent: rgba(0%, 39%, 0%, 50%) hex:
#00630080
> color name limegreent 20,80,20,50
Color 'limegreent' is 50% transparent: rgba(20%, 80%, 20%, 50%) hex:
#33cc3380
> color name turquoiset 25,88,82,50
Color 'turquoiset' is 50% transparent: rgba(25%, 88%, 82%, 50%) hex:
#40e0d180
> color name tealt 0,50,50,50
Color 'tealt' is 50% transparent: rgba(0%, 50%, 50%, 50%) hex: #00808080
> color name darkoranget 100,50,0,50
Color 'darkoranget' is 50% transparent: rgba(100%, 50%, 0%, 50%) hex:
#ff800080
> color name lightyellowt 100,100,50,50
Color 'lightyellowt' is 50% transparent: rgba(100%, 100%, 50%, 50%) hex:
#ffff8080
> color name goldt 100,75,0,50
Color 'goldt' is 50% transparent: rgba(100%, 75%, 0%, 50%) hex: #ffbf0080
> color name plumt 87,63,87,50
Color 'plumt' is 50% transparent: rgba(87%, 63%, 87%, 50%) hex: #dea1de80
> color name ssubluet 68,86,90,50
Color 'ssubluet' is 50% transparent: rgba(68%, 86%, 90%, 50%) hex:
#addbe680
> color name p-prect 10,41,0,50
Color 'p-prect' is 50% transparent: rgba(10%, 41%, 0%, 50%) hex: #1a690080
> color name p-h2t 23,59,0,50
Color 'p-h2t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
> color name p-h1t 40,73,0,50
Color 'p-h1t' is 50% transparent: rgba(40%, 73%, 0%, 50%) hex: #66ba0080
> color name p-h1c 40,73,0,100
Color 'p-h1c' is opaque: rgb(40%, 73%, 0%) hex: #66ba00
> color name p-spct 68,81,0,50
Color 'p-spct' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
> color name p-spcc 68,81,0,100
Color 'p-spcc' is opaque: rgb(68%, 81%, 0%) hex: #adcf00
> color name p-fat 82,92,0,50
Color 'p-fat' is 50% transparent: rgba(82%, 92%, 0%, 50%) hex: #d1eb0080
> color name p-postt 100,92,0,50
Color 'p-postt' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex:
#ffeb0080
> color name d-t 100,80,4,50
Color 'd-t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
> color name d-prect 95,100,50,50
Color 'd-prect' is 50% transparent: rgba(95%, 100%, 50%, 50%) hex:
#f2ff8080
> color name d-h2t 100,90,4,50
Color 'd-h2t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
> color name d-h1t 100,80,4,50
Color 'd-h1t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
> color name d-spct 100,70,4,50
Color 'd-spct' is 50% transparent: rgba(100%, 70%, 4%, 50%) hex: #ffb30a80
> color name d-fat 100,55,4,50
Color 'd-fat' is 50% transparent: rgba(100%, 55%, 4%, 50%) hex: #ff8c0a80
> color name d-fac 100,55,4,100
Color 'd-fac' is opaque: rgb(100%, 55%, 4%) hex: #ff8c0a
> color name d-postt 100,40,4,50
Color 'd-postt' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex:
#ff660a80
> color name m-t 95,43,62,50
Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
> color name m-prect 100,85,95,50
Color 'm-prect' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex:
#ffd9f280
> color name m-h2t 100,85,95,50
Color 'm-h2t' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex: #ffd9f280
> color name m-h1t 100,75,95,50
Color 'm-h1t' is 50% transparent: rgba(100%, 75%, 95%, 50%) hex: #ffbff280
> color name m-spct 89,63,75,50
Color 'm-spct' is 50% transparent: rgba(89%, 63%, 75%, 50%) hex: #e3a1bf80
> color name m-fat 95,51,75,50
Color 'm-fat' is 50% transparent: rgba(95%, 51%, 75%, 50%) hex: #f282bf80
> color name m-fac 95,51,75,100
Color 'm-fac' is opaque: rgb(95%, 51%, 75%) hex: #f282bf
> color name m-postt 95,43,62,50
Color 'm-postt' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex:
#f26e9e80
executed 70S_colors.cxc
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colorstandard.cxc
> color 100,100,100,50
> color lsu silvert
> color /3 lightgrayt
> color /5 lightgrayt
> color ssu ssu-t
> color head head-t
> color efg efg-t
> color dt d-t
> color pt p-t
> color pep p-t
> color mrna m-t
executed 70S_colorstandard.cxc
> windowsize 1000 1000
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_helices.cxc
> color h18 h18-t
> color h23 h23-t
> color h24 h24-t
> color h28 h28-t
> color h29 h29-t
> color h30 h30-t
> color h31 h31-t
> color h34 h34-t
> color h35 h35-t
> color h36 h36-t
> color h44 h44-t
> color H69 hx69-t
executed 70S_color_helices.cxc
> color h30|h36|h35 head-t
> view dc3
> surface cap true
> color zone #12.1 near #12.3,5 distance 5
> color zone #13.1 near #13.3,5 distance 5
> color zone #14.1 near #14.3,5 distance 5
> color zone #30.1 near #30.3,5 distance 5
> color zone #31.1 near #31.3,5 distance 5
> color zone #32.1 near #32.3,5 distance 5
> color zone #33.1 near #33.3,5 distance 5
> color zone #34.1 near #34.3,5 distance 5
> color zone #30.9 near #30.3,5 distance 5
> color zone #31.9 near #31.3,5 distance 5
> color zone #32.9 near #32.3,5 distance 5
> color zone #33.9 near #33.3,5 distance 5
> color zone #34.9 near #34.3,5 distance 5
> color h30|h36|h35 head-c
> color h28 h28-c
> color h29 h29-c
> color h34 h34-c
> color h23 h23-c
> color h24 h24-c
> color h31 h31-c
> hide #!100
> hide #101 models
> cartoon style nucleic xsection oval width 1.3 thickness 1.3
> transparency #*.3 0 target abc
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_helices-s.cxc
> color h18 h18-c
> color h23 h23-c
> color h24 h24-c
> color h28 h28-c
> color h29 h29-c
> color h30 h30-c
> color h31 h31-c
> color h34 h34-c
> color h35 h35-c
> color h44 h44-c
> color H69 hx69-c
executed 70S_color_helices-s.cxc
> color /v d-c
> color /y p-c
> color /w m-c
executed gtpys_dc.cxc
> surface cap true
> lighting gentle
> lighting intensity .2
> size stickRadius 0.17
Changed 1744812 bond radii
> nucribthin
> style ringFill thin
Changed 122200 residue ring styles
> graphics silhouettes true color black
> ~select
Nothing selected
> ~select
Nothing selected
> ~ribbon
> ~display
> ribbon
> ~ribbon mrna
> display mrna
> display antiplus
> display /x:504-514,584
> display /6:1492,1493,530,532,1054,1400,1397
> display /3:1913
> display #*.3/L:44
> color efg byhetero
> select efg
36728 atoms, 37417 bonds, 9 pseudobonds, 4797 residues, 16 models selected
> hide models
> show #30.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_ysH1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_ysH1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #31.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_ysH1b.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_ysH1b.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #32.3,5 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_ysH1c.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_ysH1c.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #12.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_H1apo.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_H1bapo.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #33.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_ysI1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_ysI1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #34.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_I1bys.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_I1bys.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #13.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_I1spc.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_I1spc.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #14.3,5 models
> ~display #14.3/w:38,49
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_I2fa.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_I2fa.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> graphics silhouettes true color 25,25,25,15
> style ringFill thick
Changed 122200 residue ring styles
> ~cartoon /6/3
> display /6/3
> ~cartoon trna
> display trna
> volume emmaps style surface step 1 level 3
> surface dust emmaps size 2
> volume emmaps surfaceSmoothing true
> view dc3
> hide models
> show #30 models
> select #30.3
60930 atoms, 65574 bonds, 3 pseudobonds, 4887 residues, 3 models selected
> hide #30.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_ysH1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #31 models
> select #31.3
60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected
> hide #31.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_ysH1b.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #32 models
> select #32.3
60097 atoms, 64722 bonds, 4 pseudobonds, 4779 residues, 3 models selected
> hide #32.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_ysH1c.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #12 models
> select #12.3
55765 atoms, 60298 bonds, 4230 residues, 1 model selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_H1apo.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #33 models
> select #33.3
61025 atoms, 65674 bonds, 2 pseudobonds, 4898 residues, 3 models selected
> hide #33.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_ysI1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #34 models
> select #34.3
61064 atoms, 65713 bonds, 3 pseudobonds, 4898 residues, 3 models selected
> hide #34.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_I1bys.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #13 models
> select #13.3
61103 atoms, 65762 bonds, 4902 residues, 1 model selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_I1spc.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #14 models
> ~display #14.3/w:38,49
> select #14.3
60702 atoms, 65388 bonds, 1 pseudobond, 4855 residues, 2 models selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_I2fa.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc4
> hide models
> show #30 models
> select #30.3
60930 atoms, 65574 bonds, 3 pseudobonds, 4887 residues, 3 models selected
> hide #30.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig3_ysH1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #31 models
> select #31.3
60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected
> hide #31.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig3_ysH1b.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #32 models
> select #32.3
60097 atoms, 64722 bonds, 4 pseudobonds, 4779 residues, 3 models selected
> hide #32.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig3_ysH1c.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #12 models
> select #12.3
55765 atoms, 60298 bonds, 4230 residues, 1 model selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig3_H1apo.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #33 models
> select #33.3
61025 atoms, 65674 bonds, 2 pseudobonds, 4898 residues, 3 models selected
> hide #33.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig3_ysI1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #34 models
> select #34.3
61064 atoms, 65713 bonds, 3 pseudobonds, 4898 residues, 3 models selected
> hide #34.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig3_I1bys.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #13 models
> select #13.3
61103 atoms, 65762 bonds, 4902 residues, 1 model selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig3_I1spc.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #14 models
> ~display #14.3/w:38,49
> select #14.3
60702 atoms, 65388 bonds, 1 pseudobond, 4855 residues, 2 models selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig3_I2fa.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc5
> hide models
> show #30 models
> select #30.3
60930 atoms, 65574 bonds, 3 pseudobonds, 4887 residues, 3 models selected
> hide #30.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig3_ysH1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #31 models
> select #31.3
60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected
> hide #31.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig3_ysH1b.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #32 models
> select #32.3
60097 atoms, 64722 bonds, 4 pseudobonds, 4779 residues, 3 models selected
> hide #32.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig3_ysH1c.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #12 models
> select #12.3
55765 atoms, 60298 bonds, 4230 residues, 1 model selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig3_H1apo.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #33 models
> select #33.3
61025 atoms, 65674 bonds, 2 pseudobonds, 4898 residues, 3 models selected
> hide #33.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig3_ysI1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #34 models
> select #34.3
61064 atoms, 65713 bonds, 3 pseudobonds, 4898 residues, 3 models selected
> hide #34.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig3_I1bys.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #13 models
> select #13.3
61103 atoms, 65762 bonds, 4902 residues, 1 model selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig3_I1spc.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #14 models
> ~display #14.3/w:38,49
> select #14.3
60702 atoms, 65388 bonds, 1 pseudobond, 4855 residues, 2 models selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig3_I2fa.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> volume emmaps style surface step 1 level 8
> surface dust emmaps size 2
> volume emmaps surfaceSmoothing true
> hide models
> show #30.3,5,9 models
> select #30.3
60930 atoms, 65574 bonds, 3 pseudobonds, 4887 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysH1a-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #31.3,5,9 models
> select #31.3
60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysH1b-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #32.3,5,9 models
> select #32.3
60097 atoms, 64722 bonds, 4 pseudobonds, 4779 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysH1c-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #33.3,5,9 models
> select #33.3
61025 atoms, 65674 bonds, 2 pseudobonds, 4898 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysI1a-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #34.3,5,9 models
> select #34.3
61064 atoms, 65713 bonds, 3 pseudobonds, 4898 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysI1b-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc4
> hide models
> show #30.3,5,9 models
> select #30.3
60930 atoms, 65574 bonds, 3 pseudobonds, 4887 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig8_ysH1a-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #31.3,5,9 models
> select #31.3
60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig8_ysH1b-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #32.3,5,9 models
> select #32.3
60097 atoms, 64722 bonds, 4 pseudobonds, 4779 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig8_ysH1c-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #33.3,5,9 models
> select #33.3
61025 atoms, 65674 bonds, 2 pseudobonds, 4898 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig8_ysI1a-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #34.3,5,9 models
> select #34.3
61064 atoms, 65713 bonds, 3 pseudobonds, 4898 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig8_ysI1b-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc4
> hide models
> show #30.3,5,9 models
> select #30.3
60930 atoms, 65574 bonds, 3 pseudobonds, 4887 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig8_ysH1a-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #31.3,5,9 models
> select #31.3
60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig8_ysH1b-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #32.3,5,9 models
> select #32.3
60097 atoms, 64722 bonds, 4 pseudobonds, 4779 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig8_ysH1c-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #33.3,5,9 models
> select #33.3
61025 atoms, 65674 bonds, 2 pseudobonds, 4898 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig8_ysI1a-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #34.3,5,9 models
> select #34.3
61064 atoms, 65713 bonds, 3 pseudobonds, 4898 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig8_ysI1b-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Unable to save 'nucleotides' ->
<chimerax.nucleotides._data.NucleotideState
object at 0x7f33faefe1c0>". Session might not restore properly.
——— End of log from Mon Jul 31 16:31:22 2023 ———
opened ChimeraX session
OpenGL version: 4.5 (Core Profile) Mesa 23.1.0
OpenGL renderer: llvmpipe (LLVM 15.0.7, 256 bits)
OpenGL vendor: Mesa
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb
XDG_SESSION_TYPE=
DESKTOP_SESSION=
XDG_SESSION_DESKTOP=
XDG_CURRENT_DESKTOP=
DISPLAY=localhost:10.0
Manufacturer: TYAN
Model: B7105F48TV4HR-2T-N
OS: CentOS Stream 8 n/a
Architecture: 64bit ELF
Virtual Machine: none
CPU: 72 Intel(R) Xeon(R) Gold 5220 CPU @ 2.20GHz
Cache Size: 25344 KB
Memory:
total used free shared
buff/cache available
Mem: 376Gi 22Gi 296Gi 327Mi
57Gi 351Gi
Swap: 9Gi 0B 9Gi
Graphics:
04:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc.
ASPEED Graphics Family [1a03:2000] (rev 41)
Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family
[1a03:2000]
Kernel driver in use: ast
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
}}}
--
Comment:
Can you send me the session file as an attachement? Either as a reply to
this ticket or directly to me at gregc@cgl.ucsf.edu. Thanks.
--
Ticket URL: <https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F9513%23comment%3A2&data=05%7C01%7CEmily.Rundlet%40StJude.org%7C14e62453835d4759427108db947306b8%7C22340fa892264871b677d3b3e377af72%7C0%7C0%7C638266994209197491%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=MpdCserTuuO16gCUmAGMwISlI4pWiDd1aSTktCRoKMo%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/9513#comment:2>>
ChimeraX <https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&data=05%7C01%7CEmily.Rundlet%40StJude.org%7C14e62453835d4759427108db947306b8%7C22340fa892264871b677d3b3e377af72%7C0%7C0%7C638266994209197491%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=9t%2BLolkpucq29KXQB9YpntqTMmNaDsDAowYlxTEw7wo%3D&reserved=0<https://www.rbvi.ucsf.edu/chimerax/>>
ChimeraX Issue Tracker
________________________________
Email Disclaimer: www.stjude.org/emaildisclaimer
Consultation Disclaimer: www.stjude.org/consultationdisclaimer
comment:4 by , 2 years ago
This is an example of a corrupted file.
https://www.dropbox.com/scl/fi/pc9k3gxashyjnf5z94egs/gtpys_elbow-corrupted.cxs?rlkey=a12qoeyfi7dfo6jtyftt3tqvy&dl=0
[https://www.dropbox.com/static/metaserver/static/images/opengraph/opengraph-content-icon-file-unknown-landscape.png]<https://www.dropbox.com/scl/fi/pc9k3gxashyjnf5z94egs/gtpys_elbow-corrupted.cxs?rlkey=a12qoeyfi7dfo6jtyftt3tqvy&dl=0>
gtpys_elbow-corrupted.cxs<https://www.dropbox.com/scl/fi/pc9k3gxashyjnf5z94egs/gtpys_elbow-corrupted.cxs?rlkey=a12qoeyfi7dfo6jtyftt3tqvy&dl=0>
Shared with Dropbox
www.dropbox.com
Please keep the contents of this session private as the data is unpublished.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, August 4, 2023 10:09 AM
To: Rundlet, Emily <Emily.Rundlet@STJUDE.ORG>; gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #9513: Nucleotide restore state is None
Caution: External Sender. Do not open unless you know the content is safe.
#9513: Nucleotide restore state is None
--------------------------------------+------------------------
Reporter: Emily.Rundlet@… | Owner: Greg Couch
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: Sessions | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------------+------------------------
Comment (by Emily.Rundlet@…):
{{{
The session is too large to send over email as an attachment, can we send
by dropbox?
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Thursday, August 3, 2023 at 5:43 PM
To: gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>, Rundlet, Emily
<Emily.Rundlet@STJUDE.ORG>
Subject: Re: [ChimeraX] #9513: Nucleotide restore state is None
Caution: External Sender. Do not open unless you know the content is safe.
#9513: Nucleotide restore state is None
--------------------------------------+------------------------
Reporter: Emily.Rundlet@… | Owner: Greg Couch
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: Sessions | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------------+------------------------
Changes (by Greg Couch):
* status: assigned => feedback
Old description:
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New description:
{{{
The following bug report has been submitted:
Platform: Linux-4.18.0-500.el8.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
}}}
The error occurs upon attempting to load a session file previously
written
by ChimeraX 1.6.1. Limited local debugging suggests that it is
associated
with loading "NucleotideState" data. The issue manifested after
upgrading
from ChimeraX 1.3. We can provide a session file with which we can
reliably reproduce the issue, but not via e-mail, on account of file
size.
In addition to a bug fix, we hope you can provide advice and / or
assistance with recovering the seemingly-corrupted session files.
{{{
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
format
> session
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step
1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at
level
8, step 1, values float32
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 734, in restore
obj = sm.restore_snapshot(self, data)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/nucleotides/_data.py", line 472, in restore_snapshot
if data['version'] != 1:
TypeError: 'NoneType' object is not subscriptable
Log from Mon Jul 31 16:31:22 2023UCSF ChimeraX version: 1.6.1
(2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at level
3,
step 1, values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at level
3,
step 1, values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at level 3, step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at level
3,
step 1, values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at level 3,
step
1, values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at
level
3,
step 1, values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at
level
3, step 1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at
level
3,
step 1, values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at
level
3, step 1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at
level
3,
step 1, values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at
level
3, step 1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at
level
3,
step 1, values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at
level
3, step 1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at
level
3,
step 1, values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at
level
3, step 1, values float32
Log from Mon Jul 31 14:44:45 2023UCSF ChimeraX version: 1.6.1
(2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step
1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at
level
8, step 1, values float32
Log from Thu Jul 20 18:51:54 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step
1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at
level
8, step 1, values float32
Log from Wed Jul 19 18:31:44 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step
1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at
level
8, step 1, values float32
Log from Tue Jul 18 13:01:32 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step
1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at
level
8, step 1, values float32
Log from Tue Jul 18 11:01:24 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step
1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at
level
8, step 1, values float32
Log from Thu Jun 15 17:34:19 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step
1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at
level
8, step 1, values float32
Log from Thu Jun 15 13:56:32 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step
1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at
level
8, step 1, values float32
Log from Mon Jun 12 17:35:46 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step
1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1a-FR as #30.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b-FR as #31.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c-FR as #32.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a-FR as #33.9, grid size 512,512,512, pixel 0.828, shown at
step
1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b-FR as #34.9, grid size 512,512,512, pixel 0.828, shown at
level
6, step 1, values float32
Log from Mon Jun 12 15:39:44 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at level 3, step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step
1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Log from Tue May 23 15:01:38 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at level 4, step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step
1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Log from Mon May 22 15:00:55 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at level 4, step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at step
1,
values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Log from Mon May 22 11:11:24 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at level
4,
step 1, values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at step 1,
values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at step
1,
values float32
Log from Tue May 16 16:53:33 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
> open gtpys/helix/gtpys_helix.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at level 0.000164, step 4, values float32
Opened post as #15.1, grid size 576,576,576, pixel 1.06, shown at level
4,
step 1, values float32
Opened prec as #10.1, grid size 576,576,576, pixel 1.06, shown at level
4,
step 1, values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at level 4, step 1, values float32
Opened i1spc as #13.1, grid size 576,576,576, pixel 1.06, shown at level
4,
step 1, values float32
Opened hy1 as #12.1, grid size 576,576,576, pixel 1.06, shown at level 4,
step
1, values float32
Opened ys-H1a as #30.1, grid size 512,512,512, pixel 0.826, shown at
level
4,
step 1, values float32
Opened ys-H1b as #31.1, grid size 512,512,512, pixel 0.826, shown at
level
4,
step 1, values float32
Opened ys-H1c as #32.1, grid size 512,512,512, pixel 0.826, shown at
level
4,
step 1, values float32
Opened ys-I1a as #33.1, grid size 512,512,512, pixel 0.826, shown at
level
4,
step 1, values float32
Opened ys-I1b as #34.1, grid size 512,512,512, pixel 0.826, shown at
level
4,
step 1, values float32
Log from Tue May 16 16:15:28 2023UCSF ChimeraX version: 1.3rc202111180839
(2021-11-18)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open gtpys/helix/argb_helix.cxs
Opened 4ybb_50Score_3A.mrc as #100, grid size 576,576,576, pixel 1.06,
shown
at step 4, values float32
Opened FA_j118_localres_filt_g0_n.mrc as #14.1, grid size 576,576,576,
pixel
1.06, shown at step 1, values float32
Opened arg_j152.mrc as #20.1, grid size 380,380,380, pixel 1.05, shown at
step
1, values float32
Opened arg-apo.mrc as #21.1, grid size 360,360,360, pixel 1.08, shown at
step
1, values float32
Opened POST_j93ct15_pplocal_g0_n.mrc as #15.1, grid size 576,576,576,
pixel
1.06, shown at step 1, values float32
Opened PREC_job225_ct14_pplocal_g0_n.mrc as #10.1, grid size 576,576,576,
pixel 1.06, shown at step 1, values float32
opened ChimeraX session
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_startup_gtpys.cxc
> close all
> open /data/EmilyRundlet/ChimeraX_70S/Maps/4ybb_50Score_3A.mrc
Opened 4ybb_50Score_3A.mrc as #1, grid size 576,576,576, pixel 1.06,
shown
at
level 0.000164, step 4, values float32
> rename #1 id #100
> open /data/EmilyRundlet/ChimeraX_70S/Models/prec_7n1p_50S.pdb
Chain information for prec_7n1p_50S.pdb #1
---
Chain | Description
3 | No description available
5 | No description available
P | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #101
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_post.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/post_50S.pdb
name
> post5
Chain information for post5 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #15.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/post_30S.pdb
name
> post3
Chain information for post3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
y | No description available
> rename #1 id #15.3
> open
>
/data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/POST_j93ct15_pplocal_g0_n.mrc
> name post
Opened post as #1, grid size 576,576,576, pixel 1.06, shown at level
1.16,
step 4, values float32
> rename #1 id #15.1
> rename #15 post
> matchmaker #15.5 to #101 matrix Nucleic bring #15.1#15.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with post5, chain 3 (#15.5),
sequence alignment score = 11580.3
RMSD between 2766 pruned atom pairs is 0.341 angstroms; (across all 2904
pairs: 2.745)
> fitmap #15.1 inMap #100
Fit map post in map 4ybb_50Score_3A.mrc using 29937 points
correlation = 0.7033, correlation about mean = 0.6059, overlap =
7.619e+04
steps = 48, shift = 0.0376, angle = 0.0465 degrees
Position of post (#15.1) relative to 4ybb_50Score_3A.mrc (#100)
coordinates:
Matrix rotation and translation
0.99999983 0.00051499 -0.00026539 -0.07015622
-0.00051501 0.99999986 -0.00009768 0.21094928
0.00026534 0.00009781 0.99999996 -0.12735627
Axis 0.16636276 -0.45165257 -0.87654628
Axis point 413.67366807 137.87803145 0.00000000
Rotation angle (degrees) 0.03366312
Shift along axis 0.00468650
> fitmap #15.5 inMap #15.1
Fit molecule post5 (#15.5) to map post (#15.1) using 90903 atoms
average map value = 15.29, steps = 40
shifted from previous position = 0.0173
rotated from previous position = 0.0481 degrees
atoms outside contour = 27101, contour level = 1.1571
Position of post5 (#15.5) relative to post (#15.1) coordinates:
Matrix rotation and translation
1.00000000 0.00007488 -0.00001293 -0.00984527
-0.00007488 1.00000000 0.00003964 0.01927617
0.00001293 -0.00003964 1.00000000 0.00608995
Axis -0.46249937 -0.15083335 -0.87369539
Axis point 250.02744189 154.19286933 0.00000000
Rotation angle (degrees) 0.00491036
Shift along axis -0.00367482
> fitmap #15.3 inMap #15.1
Fit molecule post3 (#15.3) to map post (#15.1) using 55643 atoms
average map value = 11.56, steps = 40
shifted from previous position = 0.0883
rotated from previous position = 0.0476 degrees
atoms outside contour = 13831, contour level = 1.1571
Position of post3 (#15.3) relative to post (#15.1) coordinates:
Matrix rotation and translation
1.00000000 -0.00005318 -0.00004310 0.02635100
0.00005318 1.00000000 -0.00000125 -0.02050708
0.00004310 0.00000124 1.00000000 -0.01832489
Axis 0.01818364 -0.62958007 0.77672279
Axis point 395.65049914 495.82230346 0.00000000
Rotation angle (degrees) 0.00392252
Shift along axis -0.00084336
executed 70S_open_post.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_prec.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/prec_50S.pdb
name
> prec5
Chain information for prec5 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #10.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/prec_30S.pdb
name
> prec3
Chain information for prec3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
y | No description available
> rename #1 id #10.3
> open
>
/data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/PREC*local*.mrc
> name prec
Opened prec as #1, grid size 576,576,576, pixel 1.06, shown at level
0.719,
step 4, values float32
> rename #1 id #10.1
> rename #10 prec
> matchmaker #10.5 to #101 matrix Nucleic bring #10.1#10.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with prec5, chain 3 (#10.5),
sequence alignment score = 11585.2
RMSD between 2904 pruned atom pairs is 0.000 angstroms; (across all 2904
pairs: 0.000)
> fitmap #10.1 inMap #100
Fit map prec in map 4ybb_50Score_3A.mrc using 29930 points
correlation = 0.705, correlation about mean = 0.6153, overlap = 7.403e+04
steps = 100, shift = 0.0276, angle = 0.0213 degrees
Position of prec (#10.1) relative to 4ybb_50Score_3A.mrc (#100)
coordinates:
Matrix rotation and translation
0.99999993 0.00023597 -0.00028739 0.01666834
-0.00023597 0.99999997 0.00000377 0.08653163
0.00028739 -0.00000370 0.99999996 -0.10871255
Axis -0.01003658 -0.77282074 -0.63454501
Axis point 373.98904576 -0.00000000 57.97612114
Rotation angle (degrees) 0.02130699
Shift along axis 0.00194228
> fitmap #10.5 inMap #10.1
Fit molecule prec5 (#10.5) to map prec (#10.1) using 93196 atoms
average map value = 15.31, steps = 40
shifted from previous position = 0.0241
rotated from previous position = 0.0378 degrees
atoms outside contour = 32220, contour level = 0.71858
Position of prec5 (#10.5) relative to prec (#10.1) coordinates:
Matrix rotation and translation
0.99999996 0.00028462 -0.00008450 -0.07054285
-0.00028461 0.99999995 0.00015462 0.06036830
0.00008454 -0.00015460 0.99999998 0.02731692
Axis -0.46188152 -0.25249170 -0.85024314
Axis point 206.84210925 257.43360450 0.00000000
Rotation angle (degrees) 0.01917937
Shift along axis -0.00588608
> fitmap #10.3 inMap #10.1
Fit molecule prec3 (#10.3) to map prec (#10.1) using 56259 atoms
average map value = 11.39, steps = 48
shifted from previous position = 0.0796
rotated from previous position = 0.0392 degrees
atoms outside contour = 16720, contour level = 0.71858
Position of prec3 (#10.3) relative to prec (#10.1) coordinates:
Matrix rotation and translation
0.99999994 0.00035395 -0.00002496 -0.09187678
-0.00035394 0.99999993 0.00014842 0.08455945
0.00002502 -0.00014841 0.99999999 0.04385687
Axis -0.38587760 -0.06497510 -0.92025905
Axis point 236.94211808 270.96015369 0.00000000
Rotation angle (degrees) 0.02203670
Shift along axis -0.01040075
executed 70S_open_prec.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_fa.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/fa_50S.pdb
name
> i2fa5
Chain information for i2fa5 #1
---
Chain | Description
3 | No description available
5 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
I | No description available
J | No description available
K | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #14.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/fa_30S.pdb
name
> i2fa3
Chain information for i2fa3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
x | No description available
y | No description available
> rename #1 id #14.3
> open
>
/data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/FA*local*.mrc
Opened FA_j118_localres_filt_g0_n.mrc as #1, grid size 576,576,576, pixel
1.06, shown at level 0.555, step 4, values float32
> rename #1 id #14.1
> matchmaker #14.5 to #101 matrix Nucleic bring #14.1#14.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with i2fa5, chain 3 (#14.5),
sequence alignment score = 11567.9
RMSD between 2675 pruned atom pairs is 0.458 angstroms; (across all 2903
pairs: 3.500)
> rename #14 fa
> fitmap #14.1 inMap #100
Fit map FA_j118_localres_filt_g0_n.mrc in map 4ybb_50Score_3A.mrc using
29876
points
correlation = 0.7652, correlation about mean = 0.6917, overlap =
8.026e+04
steps = 124, shift = 0.0674, angle = 0.0469 degrees
Position of FA_j118_localres_filt_g0_n.mrc (#14.1) relative to
4ybb_50Score_3A.mrc (#100) coordinates:
Matrix rotation and translation
0.99999951 0.00082837 -0.00054821 -0.07721517
-0.00082823 0.99999963 0.00024790 0.22483688
0.00054841 -0.00024745 0.99999982 -0.11895947
Axis -0.24193109 -0.53558675 -0.80908354
Axis point 267.87230737 94.97670830 0.00000000
Rotation angle (degrees) 0.05865666
Shift along axis -0.00549075
> fitmap #14.5 inMap #14.1
Fit molecule i2fa5 (#14.5) to map FA_j118_localres_filt_g0_n.mrc (#14.1)
using
94455 atoms
average map value = 14.71, steps = 44
shifted from previous position = 0.0492
rotated from previous position = 0.0489 degrees
atoms outside contour = 26009, contour level = 0.5555
Position of i2fa5 (#14.5) relative to FA_j118_localres_filt_g0_n.mrc
(#14.1)
coordinates:
Matrix rotation and translation
0.99999999 0.00013549 0.00005439 -0.05910674
-0.00013549 0.99999999 -0.00008462 0.07061428
-0.00005440 0.00008461 0.99999999 -0.01606966
Axis 0.50141948 0.32233497 -0.80291884
Axis point 506.79859217 458.57499403 0.00000000
Rotation angle (degrees) 0.00966859
Shift along axis 0.00602682
> fitmap #14.3 inMap #14.1
Fit molecule i2fa3 (#14.3) to map FA_j118_localres_filt_g0_n.mrc (#14.1)
using
60702 atoms
average map value = 7.538, steps = 40
shifted from previous position = 0.104
rotated from previous position = 0.0489 degrees
atoms outside contour = 11367, contour level = 0.5555
Position of i2fa3 (#14.3) relative to FA_j118_localres_filt_g0_n.mrc
(#14.1)
coordinates:
Matrix rotation and translation
0.99999996 0.00022144 0.00016174 -0.14067075
-0.00022141 0.99999996 -0.00017040 0.12305826
-0.00016178 0.00017037 0.99999997 -0.00200513
Axis 0.52777238 0.50104898 -0.68586167
Axis point 581.05763080 608.65192133 0.00000000
Rotation angle (degrees) 0.01849719
Shift along axis -0.01120868
executed 70S_open_fa.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_spc.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/spc_50S.pdb
name
> i1spc5
Chain information for i1spc5 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #13.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/spc_30S.pdb
name
> i1spc3
Chain information for i1spc3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
x | No description available
y | No description available
> rename #1 id #13.3
> open
>
/data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/INT1_spc*local*.mrc
> name i1spc
Opened i1spc as #1, grid size 576,576,576, pixel 1.06, shown at level
0.527,
step 4, values float32
> rename #1 id #13.1
> rename #13 i1spc
> matchmaker #13.5 to #101 matrix Nucleic bring #13.1#13.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with i1spc5, chain 3
(#13.5),
sequence alignment score = 11576.1
RMSD between 2613 pruned atom pairs is 0.440 angstroms; (across all 2904
pairs: 4.190)
> fitmap #13.1 inMap #100
Fit map i1spc in map 4ybb_50Score_3A.mrc using 29799 points
correlation = 0.7329, correlation about mean = 0.6398, overlap =
7.208e+04
steps = 104, shift = 0.0985, angle = 0.0628 degrees
Position of i1spc (#13.1) relative to 4ybb_50Score_3A.mrc (#100)
coordinates:
Matrix rotation and translation
0.99999127 -0.00305790 -0.00284733 1.91534327
0.00305942 0.99999518 0.00052889 -1.13631859
0.00284570 -0.00053760 0.99999581 -1.01117770
Axis -0.12659581 -0.67578369 0.72614730
Axis point 418.51647841 616.51914515 0.00000000
Rotation angle (degrees) 0.24134036
Shift along axis -0.20883282
> fitmap #13.5 inMap #13.1
Fit molecule i1spc5 (#13.5) to map i1spc (#13.1) using 93017 atoms
average map value = 14.57, steps = 48
shifted from previous position = 0.0733
rotated from previous position = 0.0651 degrees
atoms outside contour = 27434, contour level = 0.52653
Position of i1spc5 (#13.5) relative to i1spc (#13.1) coordinates:
Matrix rotation and translation
1.00000000 -0.00000053 -0.00005875 0.01737643
0.00000053 1.00000000 -0.00002655 0.00255801
0.00005875 0.00002655 1.00000000 -0.03456253
Axis 0.41177423 -0.91124934 0.00816220
Axis point 588.98331322 0.00000000 263.93669119
Rotation angle (degrees) 0.00369369
Shift along axis 0.00454208
> fitmap #13.3 inMap #13.1
Fit molecule i1spc3 (#13.3) to map i1spc (#13.1) using 61103 atoms
average map value = 9.699, steps = 60
shifted from previous position = 0.162
rotated from previous position = 0.0627 degrees
atoms outside contour = 14669, contour level = 0.52653
Position of i1spc3 (#13.3) relative to i1spc (#13.1) coordinates:
Matrix rotation and translation
0.99999999 0.00006855 -0.00007419 -0.00808096
-0.00006856 1.00000000 -0.00003421 0.02476248
0.00007419 0.00003421 1.00000000 -0.04490669
Axis 0.32075098 -0.69563238 -0.64281755
Axis point 526.89840240 0.00000000 -148.08272269
Rotation angle (degrees) 0.00611054
Shift along axis 0.00904925
executed 70S_open_spc.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_h1.cxc
> open
>
/data/EmilyRundlet/ChimeraX_70S/Maps/Published/Rundlet2021/apo_H1*local*.mrc
> name hy1
Opened hy1 as #1, grid size 576,576,576, pixel 1.06, shown at level
0.822,
step 4, values float32
> rename #1 id #12.1
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/h1_50S.pdb
name
> hy15
Chain information for hy15 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #12.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/h1_30S.pdb
name
> hy13
Chain information for hy13 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
y | No description available
> rename #1 id #12.3
> matchmaker #12.5 to #101 matrix Nucleic bring #12.1#12.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with hy15, chain 3 (#12.5),
sequence alignment score = 11572.3
RMSD between 2683 pruned atom pairs is 0.437 angstroms; (across all 2902
pairs: 4.227)
> fitmap #12.1 inMap #100
Fit map hy1 in map 4ybb_50Score_3A.mrc using 29865 points
correlation = 0.7182, correlation about mean = 0.6351, overlap = 7.48e+04
steps = 80, shift = 0.0539, angle = 0.0362 degrees
Position of hy1 (#12.1) relative to 4ybb_50Score_3A.mrc (#100)
coordinates:
Matrix rotation and translation
0.99999993 0.00033939 -0.00014651 -0.03967194
-0.00033939 0.99999994 0.00003379 0.08904027
0.00014652 -0.00003374 0.99999999 -0.04209798
Axis -0.09096206 -0.39471037 -0.91429187
Axis point 270.42268136 115.08181596 0.00000000
Rotation angle (degrees) 0.02126851
Shift along axis 0.00695336
> fitmap #12.5 inMap #12.1
Fit molecule hy15 (#12.5) to map hy1 (#12.1) using 91053 atoms
average map value = 15.92, steps = 40
shifted from previous position = 0.0355
rotated from previous position = 0.0365 degrees
atoms outside contour = 31662, contour level = 0.82202
Position of hy15 (#12.5) relative to hy1 (#12.1) coordinates:
Matrix rotation and translation
1.00000000 0.00001739 -0.00003452 0.00191493
-0.00001738 1.00000000 0.00005119 -0.00075625
0.00003452 -0.00005119 1.00000000 0.00373129
Axis -0.79805293 -0.53818813 -0.27104440
Axis point 0.00000000 61.60073087 37.19705100
Rotation angle (degrees) 0.00367501
Shift along axis -0.00213255
> fitmap #12.3 inMap #12.1
Fit molecule hy13 (#12.3) to map hy1 (#12.1) using 55765 atoms
average map value = 9.817, steps = 44
shifted from previous position = 0.0694
rotated from previous position = 0.0332 degrees
atoms outside contour = 14540, contour level = 0.82202
Position of hy13 (#12.3) relative to hy1 (#12.1) coordinates:
Matrix rotation and translation
1.00000000 -0.00000897 0.00000895 -0.00690250
0.00000897 0.99999999 0.00011154 -0.02727097
-0.00000895 -0.00011154 0.99999999 0.03999319
Axis -0.99361126 0.07969592 0.07990759
Axis point 0.00000000 352.90975575 250.15609103
Rotation angle (degrees) 0.00643159
Shift along axis 0.00788078
executed 70S_open_h1.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/open/70S_open_ys.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1a_50S.pdb
name
> ys-H1a5
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1a_50S.pdb
---
warnings | Ignored bad PDB record found on line 4
LINK ZN ZN Le0201 SG CY 04
Ignored bad PDB record found on line 5
LINK ZN ZN Le0201 SG CY 03
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 01
Ignored bad PDB record found on line 7
LINK ZN ZN Le0201 SG CY 01
Ignored bad PDB record found on line 8
LINK ZN ZN Lj0101 ND1 HI 03
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue ASP (2432820)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-H1a5 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #30.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1a_30S.pdb
name
> ys-H1a3
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1a_30S.pdb
---
warnings | Ignored bad PDB record found on line 4
LINK ZN ZN Le0201 SG CY 04
Ignored bad PDB record found on line 5
LINK ZN ZN Le0201 SG CY 03
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 01
Ignored bad PDB record found on line 7
LINK ZN ZN Le0201 SG CY 01
Ignored bad PDB record found on line 8
LINK ZN ZN Lj0101 ND1 HI 03
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue ASP (2432820)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-H1a3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
x | No description available
y | No description available
> rename #1 id #30.3
> open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/ys-H1a*.mrc name
ys-H1a
Opened ys-H1a as #1, grid size 512,512,512, pixel 0.826, shown at level
3.13,
step 2, values float32
> rename #1 id #30.1
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1b_50S.pdb
name
> ys-H1b5
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1b_50S.pdb
---
warnings | Ignored bad PDB record found on line 5
LINK ZN ZN Le0201 SG CY 04
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 03
Ignored bad PDB record found on line 7
LINK ZN ZN Le0201 SG CY 01
Ignored bad PDB record found on line 8
LINK ZN ZN Le0201 SG CY 01
Ignored bad PDB record found on line 9
LINK ZN ZN Lj0101 ND1 HI 03
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue LYS (2432823)
Cannot find LINK/SSBOND residue THR (2432824)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-H1b5 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #31.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1b_30S.pdb
name
> ys-H1b3
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1b_30S.pdb
---
warnings | Ignored bad PDB record found on line 5
LINK ZN ZN Le0201 SG CY 04
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 03
Ignored bad PDB record found on line 7
LINK ZN ZN Le0201 SG CY 01
Ignored bad PDB record found on line 8
LINK ZN ZN Le0201 SG CY 01
Ignored bad PDB record found on line 9
LINK ZN ZN Lj0101 ND1 HI 03
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue LYS (2432823)
Cannot find LINK/SSBOND residue THR (2432824)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-H1b3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
x | No description available
y | No description available
> rename #1 id #31.3
> open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/ys-H1b*.mrc name
ys-H1b
Opened ys-H1b as #1, grid size 512,512,512, pixel 0.826, shown at level
3.16,
step 2, values float32
> rename #1 id #31.1
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1c_50S.pdb
name
> ys-H1c5
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1c_50S.pdb
---
warnings | Ignored bad PDB record found on line 2
LINK ZN ZN Lj0101 ND1 HI 03
Ignored bad PDB record found on line 3
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 4
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 5
LINK ZN ZN Lj0101 SG CY 02
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 04
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-H1c5 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #32.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1c_30S.pdb
name
> ys-H1c3
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-H1c_30S.pdb
---
warnings | Ignored bad PDB record found on line 2
LINK ZN ZN Lj0101 ND1 HI 03
Ignored bad PDB record found on line 3
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 4
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 5
LINK ZN ZN Lj0101 SG CY 02
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 04
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-H1c3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
x | No description available
y | No description available
> rename #1 id #32.3
> open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/ys-H1c*.mrc name
ys-H1c
Opened ys-H1c as #1, grid size 512,512,512, pixel 0.826, shown at level
3.11,
step 2, values float32
> rename #1 id #32.1
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1a_50S.pdb
name
> ys-I1a5
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1a_50S.pdb
---
warnings | Ignored bad PDB record found on line 2
LINK ZN ZN Lj0101 ND1 HI 03
Ignored bad PDB record found on line 3
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 4
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 5
LINK ZN ZN Lj0101 SG CY 02
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 04
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-I1a5 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #33.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1a_30S.pdb
name
> ys-I1a3
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1a_30S.pdb
---
warnings | Ignored bad PDB record found on line 2
LINK ZN ZN Lj0101 ND1 HI 03
Ignored bad PDB record found on line 3
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 4
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 5
LINK ZN ZN Lj0101 SG CY 02
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 04
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-I1a3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
x | No description available
y | No description available
> rename #1 id #33.3
> open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/ys-I1a*.mrc name
ys-I1a
Opened ys-I1a as #1, grid size 512,512,512, pixel 0.826, shown at level
3.09,
step 2, values float32
> rename #1 id #33.1
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1b_50S.pdb
name
> ys-I1b5
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1b_50S.pdb
---
warnings | Ignored bad PDB record found on line 2
LINK ZN ZN Lj0101 ND1 HI 03
Ignored bad PDB record found on line 3
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 4
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 5
LINK ZN ZN Lj0101 SG CY 02
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 04
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-I1b5 #1
---
Chain | Description
3 | No description available
5 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> rename #1 id #34.5
> open /data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1b_30S.pdb
name
> ys-I1b3
Summary of feedback from opening
/data/EmilyRundlet/ChimeraX_70S/Models/For_ChimeraX/ys-I1b_30S.pdb
---
warnings | Ignored bad PDB record found on line 2
LINK ZN ZN Lj0101 ND1 HI 03
Ignored bad PDB record found on line 3
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 4
LINK ZN ZN Lj0101 SG CY 01
Ignored bad PDB record found on line 5
LINK ZN ZN Lj0101 SG CY 02
Ignored bad PDB record found on line 6
LINK ZN ZN Le0201 SG CY 04
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue THR (1033509)
Cannot find LINK/SSBOND residue ZN (567641)
Chain information for ys-I1b3 #1
---
Chain | Description
6 | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
p | No description available
v | No description available
w | No description available
x | No description available
y | No description available
> rename #1 id #34.3
> open /data/EmilyRundlet/ChimeraX_70S/Maps/Normalized/ys-I1b*.mrc name
ys-I1b
Opened ys-I1b as #1, grid size 512,512,512, pixel 0.826, shown at level
3.09,
step 2, values float32
> rename #1 id #34.1
> matchmaker #30.5 to #101 matrix Nucleic bring #30.1#30.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with ys-H1a5, chain 3
(#30.5),
sequence alignment score = 11576.1
RMSD between 2631 pruned atom pairs is 0.435 angstroms; (across all 2904
pairs: 4.260)
> matchmaker #31.5 to #101 matrix Nucleic bring #31.1#31.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with ys-H1b5, chain 3
(#31.5),
sequence alignment score = 11576.1
RMSD between 2629 pruned atom pairs is 0.438 angstroms; (across all 2904
pairs: 4.264)
> matchmaker #32.5 to #101 matrix Nucleic bring #32.1#32.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with ys-H1c5, chain 3
(#32.5),
sequence alignment score = 11576.1
RMSD between 2600 pruned atom pairs is 0.428 angstroms; (across all 2904
pairs: 4.256)
> matchmaker #33.5 to #101 matrix Nucleic bring #33.1#33.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with ys-I1a5, chain 3
(#33.5),
sequence alignment score = 11576.1
RMSD between 2595 pruned atom pairs is 0.428 angstroms; (across all 2904
pairs: 4.252)
> matchmaker #34.5 to #101 matrix Nucleic bring #34.1#34.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker prec_7n1p_50S.pdb, chain 3 (#101) with ys-I1b5, chain 3
(#34.5),
sequence alignment score = 11576.1
RMSD between 2617 pruned atom pairs is 0.432 angstroms; (across all 2904
pairs: 4.229)
> fitmap #30.1 inMap #100
Fit map ys-H1a in map 4ybb_50Score_3A.mrc using 167516 points
correlation = 0.7712, correlation about mean = 0.5068, overlap =
5.636e+05
steps = 116, shift = 0.0431, angle = 0.06 degrees
Position of ys-H1a (#30.1) relative to 4ybb_50Score_3A.mrc (#100)
coordinates:
Matrix rotation and translation
-0.16096874 0.07054784 0.98443490 117.93148350
-0.09736653 -0.99371151 0.05529186 532.16401993
0.98214501 -0.08695075 0.16682549 84.98416227
Axis -0.64633407 0.01040498 -0.76298362
Axis point 42.26680055 265.56440366 0.00000000
Rotation angle (degrees) 173.68249450
Shift along axis -135.52750571
> fitmap #30.5 inMap #30.1
Fit molecule ys-H1a5 (#30.5) to map ys-H1a (#30.1) using 92994 atoms
average map value = 7.904, steps = 44
shifted from previous position = 0.0158
rotated from previous position = 0.0583 degrees
atoms outside contour = 20674, contour level = 3.1252
Position of ys-H1a5 (#30.5) relative to ys-H1a (#30.1) coordinates:
Matrix rotation and translation
1.00000000 0.00007896 0.00002842 -0.01618923
-0.00007896 1.00000000 0.00000766 0.01408032
-0.00002842 -0.00000766 1.00000000 0.00064511
Axis -0.09088428 0.33726732 -0.93701163
Axis point 154.32943537 198.57692600 0.00000000
Rotation angle (degrees) 0.00482813
Shift along axis 0.00561570
> fitmap #30.3 inMap #30.1
Fit molecule ys-H1a3 (#30.3) to map ys-H1a (#30.1) using 60930 atoms
average map value = 5.423, steps = 44
shifted from previous position = 0.107
rotated from previous position = 0.0638 degrees
atoms outside contour = 21357, contour level = 3.1252
Position of ys-H1a3 (#30.3) relative to ys-H1a (#30.1) coordinates:
Matrix rotation and translation
1.00000000 -0.00007009 0.00004160 -0.00010326
0.00007009 1.00000000 -0.00003531 -0.00429301
-0.00004159 0.00003531 1.00000000 -0.00573932
Axis 0.39752790 0.46828522 0.78910108
Axis point 17.28659253 35.84690625 0.00000000
Rotation angle (degrees) 0.00508928
Shift along axis -0.00658030
> fitmap #31.1 inMap #100
Fit map ys-H1b in map 4ybb_50Score_3A.mrc using 167746 points
correlation = 0.7557, correlation about mean = 0.4732, overlap =
4.809e+05
steps = 104, shift = 0.0913, angle = 0.169 degrees
Position of ys-H1b (#31.1) relative to 4ybb_50Score_3A.mrc (#100)
coordinates:
Matrix rotation and translation
-0.16402794 0.07279267 0.98376626 117.06968879
-0.09958269 -0.99340097 0.05690170 531.99178964
0.98141639 -0.08863262 0.17019441 84.62198725
Axis -0.64507570 0.01041575 -0.76404768
Axis point 42.56283115 265.45365415 0.00000000
Rotation angle (degrees) 173.52301718
Shift along axis -134.63295191
> fitmap #31.5 inMap #31.1
Fit molecule ys-H1b5 (#31.5) to map ys-H1b (#31.1) using 92994 atoms
average map value = 6.419, steps = 48
shifted from previous position = 0.0121
rotated from previous position = 0.0631 degrees
atoms outside contour = 25942, contour level = 3.1558
Position of ys-H1b5 (#31.5) relative to ys-H1b (#31.1) coordinates:
Matrix rotation and translation
0.99999984 0.00056889 -0.00006451 -0.12124833
-0.00056878 0.99999829 0.00175780 -0.12851585
0.00006551 -0.00175777 0.99999845 0.36559707
Axis -0.95083394 -0.03516616 -0.30769816
Axis point 0.00000000 209.20515420 73.16839244
Rotation angle (degrees) 0.10592152
Shift along axis 0.00731289
> fitmap #31.3 inMap #31.1
Fit molecule ys-H1b3 (#31.3) to map ys-H1b (#31.1) using 60958 atoms
average map value = 4.602, steps = 44
shifted from previous position = 0.0971
rotated from previous position = 0.114 degrees
atoms outside contour = 25030, contour level = 3.1558
Position of ys-H1b3 (#31.3) relative to ys-H1b (#31.1) coordinates:
Matrix rotation and translation
0.99999972 -0.00035593 0.00066202 -0.06165935
0.00035492 0.99999877 0.00152816 -0.29466909
-0.00066256 -0.00152792 0.99999861 0.44538378
Axis -0.89731715 0.38891986 0.20871819
Axis point 0.00000000 286.71155040 201.62993409
Rotation angle (degrees) 0.09756906
Shift along axis 0.03368503
> fitmap #32.1 inMap #100
Fit map ys-H1c in map 4ybb_50Score_3A.mrc using 167598 points
correlation = 0.7687, correlation about mean = 0.5028, overlap =
5.462e+05
steps = 64, shift = 0.174, angle = 0.0444 degrees
Position of ys-H1c (#32.1) relative to 4ybb_50Score_3A.mrc (#100)
coordinates:
Matrix rotation and translation
-0.16402649 0.07085424 0.98390802 117.46660733
-0.09904792 -0.99355948 0.05503707 532.18633927
0.98147074 -0.08842650 0.16998804 84.56695102
Axis -0.64511751 0.01095977 -0.76400477
Axis point 42.50698240 265.58065026 0.00000000
Rotation angle (degrees) 173.61597695
Shift along axis -134.55667780
> fitmap #32.5 inMap #32.1
Fit molecule ys-H1c5 (#32.5) to map ys-H1c (#32.1) using 92992 atoms
average map value = 7.486, steps = 36
shifted from previous position = 0.0219
rotated from previous position = 0.0647 degrees
atoms outside contour = 22168, contour level = 3.1136
Position of ys-H1c5 (#32.5) relative to ys-H1c (#32.1) coordinates:
Matrix rotation and translation
0.99999983 -0.00057175 0.00006040 0.12367865
0.00057186 0.99999823 -0.00179030 0.13731617
-0.00005938 0.00179034 0.99999840 -0.36604473
Axis 0.95211000 0.03184871 0.30409245
Axis point 0.00000000 206.36170644 76.30401858
Rotation angle (degrees) 0.10773729
Shift along axis 0.01081758
> fitmap #32.3 inMap #32.1
Fit molecule ys-H1c3 (#32.3) to map ys-H1c (#32.1) using 60097 atoms
average map value = 5.192, steps = 48
shifted from previous position = 0.133
rotated from previous position = 0.0654 degrees
atoms outside contour = 21804, contour level = 3.1136
Position of ys-H1c3 (#32.3) relative to ys-H1c (#32.1) coordinates:
Matrix rotation and translation
0.99999975 0.00002916 -0.00070103 0.13056968
-0.00003034 0.99999858 -0.00168673 0.26834816
0.00070098 0.00168675 0.99999833 -0.48614194
Axis 0.92330390 -0.38372472 -0.01628638
Axis point 0.00000000 288.12835311 164.65187972
Rotation angle (degrees) 0.10467114
Shift along axis 0.02550116
> fitmap #33.1 inMap #100
Fit map ys-I1a in map 4ybb_50Score_3A.mrc using 167703 points
correlation = 0.7667, correlation about mean = 0.498, overlap = 5.302e+05
steps = 104, shift = 0.0538, angle = 0.0755 degrees
Position of ys-I1a (#33.1) relative to 4ybb_50Score_3A.mrc (#100)
coordinates:
Matrix rotation and translation
-0.16092884 0.07096607 0.98441136 117.88246252
-0.09669854 -0.99374659 0.05583104 532.06291528
0.98221754 -0.08620632 0.16678480 84.75523562
Axis -0.64635360 0.00998316 -0.76297271
Axis point 42.30362323 265.49282475 0.00000000
Rotation angle (degrees) 173.69183881
Shift along axis -135.54801612
> fitmap #33.5 inMap #33.1
Fit molecule ys-I1a5 (#33.5) to map ys-I1a (#33.1) using 92992 atoms
average map value = 7.334, steps = 36
shifted from previous position = 0.0203
rotated from previous position = 0.0746 degrees
atoms outside contour = 22072, contour level = 3.0948
Position of ys-I1a5 (#33.5) relative to ys-I1a (#33.1) coordinates:
Matrix rotation and translation
1.00000000 0.00006785 0.00002158 -0.01571402
-0.00006785 1.00000000 0.00000247 0.01394877
-0.00002158 -0.00000247 1.00000000 0.00028445
Axis -0.03462129 0.30294566 -0.95237875
Axis point 185.47857319 229.29962927 0.00000000
Rotation angle (degrees) 0.00408210
Shift along axis 0.00449885
> fitmap #33.3 inMap #33.1
Fit molecule ys-I1a3 (#33.3) to map ys-I1a (#33.1) using 61025 atoms
average map value = 5.134, steps = 60
shifted from previous position = 0.135
rotated from previous position = 0.08 degrees
atoms outside contour = 22330, contour level = 3.0948
Position of ys-I1a3 (#33.3) relative to ys-I1a (#33.1) coordinates:
Matrix rotation and translation
0.99999998 -0.00017787 0.00003522 0.02444707
0.00017787 0.99999998 -0.00002049 -0.02796573
-0.00003522 0.00002050 1.00000000 0.00287850
Axis 0.11232351 0.19300468 0.97474747
Axis point 157.40269238 137.32963987 0.00000000
Rotation angle (degrees) 0.01045538
Shift along axis 0.00015427
> fitmap #34.1 inMap #100
Fit map ys-I1b in map 4ybb_50Score_3A.mrc using 167622 points
correlation = 0.7694, correlation about mean = 0.5021, overlap =
5.244e+05
steps = 48, shift = 0.0515, angle = 0.0695 degrees
Position of ys-I1b (#34.1) relative to 4ybb_50Score_3A.mrc (#100)
coordinates:
Matrix rotation and translation
-0.15974764 0.06847542 0.98478008 118.03715648
-0.09853124 -0.99371554 0.05311334 533.28558991
0.98222822 -0.08854688 0.16549068 85.54764208
Axis -0.64682093 0.01165178 -0.76255290
Axis point 41.99640823 266.19892413 0.00000000
Rotation angle (degrees) 173.71321980
Shift along axis -135.36977768
> fitmap #34.5 inMap #34.1
Fit molecule ys-I1b5 (#34.5) to map ys-I1b (#34.1) using 92992 atoms
average map value = 7.158, steps = 44
shifted from previous position = 0.014
rotated from previous position = 0.0687 degrees
atoms outside contour = 22660, contour level = 3.0873
Position of ys-I1b5 (#34.5) relative to ys-I1b (#34.1) coordinates:
Matrix rotation and translation
1.00000000 -0.00003647 0.00000880 0.00851051
0.00003647 1.00000000 0.00003193 -0.01982466
-0.00000880 -0.00003193 1.00000000 0.00942241
Axis -0.64817747 0.17854187 0.74026263
Axis point 533.41299576 196.36486997 0.00000000
Rotation angle (degrees) 0.00282273
Shift along axis -0.00208080
> fitmap #34.3 inMap #34.1
Fit molecule ys-I1b3 (#34.3) to map ys-I1b (#34.1) using 61064 atoms
average map value = 4.951, steps = 48
shifted from previous position = 0.125
rotated from previous position = 0.0753 degrees
atoms outside contour = 23372, contour level = 3.0873
Position of ys-I1b3 (#34.3) relative to ys-I1b (#34.1) coordinates:
Matrix rotation and translation
0.99999999 -0.00013951 0.00000938 0.01771739
0.00013951 0.99999999 -0.00004705 -0.01825677
-0.00000937 0.00004706 1.00000000 -0.00740427
Axis 0.31895163 0.06356485 0.94563702
Axis point 129.73074307 132.73108386 0.00000000
Rotation angle (degrees) 0.00845277
Shift along axis -0.00251125
> rename #30 ys-H1a
> rename #31 ys-H1b
> rename #32 ys-H1c
> rename #33 ys-I1a
> rename #34 ys-I1b
executed 70S_open_ys.cxc
executed 70S_startup_gtpys.cxc
> open
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/helix/gtpys_helix.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_assign.cxc
> name atomods #*.3,5,7
> name emmaps #*.1
> name lsu #*.5
> name ssu #*.3
> name rna /y,v,w,3,6,5
> name r23s /3
> name r16s /6
> name r5s /5
> name pt /y
> name dt /v
> name efg /x
> name pep /p
> name mrna /w
> name GSP :GSP
> name GDP :GDP
> name GTP :GTP
> name ntide :GTP|:GDP|:GSP
> name spc :SCM
> name fua :FUA
> name par :PAR
> name argb :LIG | #20.7/b
> name drugs argb|par|fua|spc
> name D1 /x:start-293
> name D2 /x:294-410
> name D3 /x:411-489
> name D4 /x:490-612
> name D5 /x:613-end
> name sw1 /x:38-65
> name sw2 /x:89-108
> name pl /x:18-25
> name nkxd /x:142-146
> name kirby #20.7
> name mg /x:MG
> name trna /y,v
> name anticodon /y,v:34-36
> name antiplus /y,v:32-38
> name cca /y,v:74-76
> name astem /y,v:1-7,66-73
> name darm /y,v:8-25
> name aarm /y,v:26-43
> name varm /y,v:44-48
> name tarm /y,v:49-65
> name head #*.3/A/C/S/M/G/N/I/J/6:927-1390
> name arg-head #20.3/A/C/S/M/G/N/I/J/6:927-1390
> name post-head #15.3/A/C/S/M/G/N/I/J/6:927-1390
> name fa-head #14.3/A/C/S/M/G/N/I/J/6:927-1390
> name body #*.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name arg-body #20.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name post-body #15.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name fa-body #14.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name h8 /6:144-178
> name h14 /6:339-350
> name h18 /6:511-540
> name h23 /6:674-716
> name h24 /6:769-810
> name h27 /6:894-905
> name h28 /6:921-937,1379-1400
> name h29 /6:938-943,1337-1346
> name h30 /6:945-955,1225-1235
> name h31 /6:956-975
> name h32 /6:984-990,1215-1221
> name h34 /6:1045-1065,1188-1211
> name h35 /6:1066-1073,1102-1110
> name h36 /6:1074-1083
> name h44 /6:1401-1502
> name h45 /6:1506-1529
> name aploop /6:956-959
> name term16S /6:1503-end
> name aphelix /6:1228-1230
> name us3 #*.3/C
> name us5 #*.3/E
> name us7 #*.3/G
> name us9 #*.3/I
> name us11 #*.3/K
> name us12 #*.3/L
> name us13 #*.3/M
> name us14 #*.3/N
> name us15 #*.3/O
> name us9-130 #*.3/I:130
> name l1stalk /3:2097-2191
> name srl /3:2652-2668
> name H68 /3:1832-1906
> name H69 /3:1907-1924
> name H95 /3:2647-2673
> name ul2 #*.5/B
> name ul5 #*.5/E
> name ul14 #*.5/N
> name ul19 #*.5/S
> name ul31 #*.5/e
executed 70S_assign.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_display.cxc
> alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6;
> alias nucribthin cartoon style nucleic xsect oval width 1.2 thick 1.2;
> alias cylinders cartoon style protein modeh tube rad 2 sides 24;
> alias licorice car style protein modeh default arrows f xsect oval
width
1
> thick 1;
> dssp
> windowsize 1000 1000
> set bgColor white
> lighting full
> set silhouettes true
> set silhouetteWidth 1.7
> set silhouettes true
> set silhouetteDepthJump 0.02
> cartoon style width 2.5
> size atomRadius 2
Changed 1614330 atom radii
> nucleotides fill
> size ions atomRadius 1.6
Changed 31 atom radii
> size stickRadius 0.1
Changed 1744812 bond radii
> style stick ringFill thin
Changed 1614330 atom styles, 122200 residue ring styles
> show ribbons
> hide H
> hide :HOH
> hide target a
> show nucleic target a
> show drugs target a
> style drugs ball
Changed 106 atom styles
> nucrib
> graphics selection color black
> volume emmaps style surface step 1 level 4
> surface dust emmaps size 3
> volume surfaceSmoothing true
> cartoon tether trna shape cone opacity 1
> dssp
executed 70S_display.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colors.cxc
> color name efg-t 100,0,0,50
Color 'efg-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
> color name sw1-t 100,92,0,50
Color 'sw1-t' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
> color name sw2-t 68,81,0,50
Color 'sw2-t' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
> color name pl-t 23,59,0,50
Color 'pl-t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
> color name d1-t 100,18,4,50
Color 'd1-t' is 50% transparent: rgba(100%, 18%, 4%, 50%) hex: #ff2e0a80
> color name d2-t 100,40,4,50
Color 'd2-t' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
> color name d3-t 100,27,36,50
Color 'd3-t' is 50% transparent: rgba(100%, 27%, 36%, 50%) hex: #ff455c80
> color name d4-t 80,0,23,50
Color 'd4-t' is 50% transparent: rgba(80%, 0%, 23%, 50%) hex: #cc003b80
> color name d5-t 100,60,4,50
Color 'd5-t' is 50% transparent: rgba(100%, 60%, 4%, 50%) hex: #ff990a80
> color name fa-t 100,90,4,50
Color 'fa-t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
> color name gtp-t 45,53,60,50
Color 'gtp-t' is 50% transparent: rgba(45%, 53%, 60%, 50%) hex: #73879980
> color name mg-t 1,39,16,50
Color 'mg-t' is 50% transparent: rgba(1%, 39%, 16%, 50%) hex: #03632980
> color name spc-t 100,0,0,50
Color 'spc-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
> color name argb-t 50,0,50,50
Color 'argb-t' is 50% transparent: rgba(50%, 0%, 50%, 50%) hex: #80008080
> color name g-1t 98,42,30,50
Color 'g-1t' is 50% transparent: rgba(98%, 42%, 30%, 50%) hex: #fa6b4d80
> color name g-2t 95,35,25,50
Color 'g-2t' is 50% transparent: rgba(95%, 35%, 25%, 50%) hex: #f2594080
> color name g-3t 92,28,20,50
Color 'g-3t' is 50% transparent: rgba(92%, 28%, 20%, 50%) hex: #eb473380
> color name g-4t 89,21,15,50
Color 'g-4t' is 50% transparent: rgba(89%, 21%, 15%, 50%) hex: #e3362680
> color name g-5t 86,14,10,50
Color 'g-5t' is 50% transparent: rgba(86%, 14%, 10%, 50%) hex: #db241a80
> color name g-6t 83,7,5,50
Color 'g-6t' is 50% transparent: rgba(83%, 7%, 5%, 50%) hex: #d4120d80
> color name g-7t 80,0,0,50
Color 'g-7t' is 50% transparent: rgba(80%, 0%, 0%, 50%) hex: #cc000080
> color name p-t 40,60,2,50
Color 'p-t' is 50% transparent: rgba(40%, 60%, 2%, 50%) hex: #66990580
> color name p-1t 4,34,1,50
Color 'p-1t' is 50% transparent: rgba(4%, 34%, 1%, 50%) hex: #0a570380
> color name p-2t 12,39,1,50
Color 'p-2t' is 50% transparent: rgba(12%, 39%, 1%, 50%) hex: #1f630380
> color name p-3t 20,44,1,50
Color 'p-3t' is 50% transparent: rgba(20%, 44%, 1%, 50%) hex: #33700380
> color name p-4t 28,49,1,50
Color 'p-4t' is 50% transparent: rgba(28%, 49%, 1%, 50%) hex: #477d0380
> color name p-5t 36,54,2,50
Color 'p-5t' is 50% transparent: rgba(36%, 54%, 2%, 50%) hex: #5c8a0580
> color name p-6t 44,59,2,50
Color 'p-6t' is 50% transparent: rgba(44%, 59%, 2%, 50%) hex: #70960580
> color name p-7t 52,64,2,50
Color 'p-7t' is 50% transparent: rgba(52%, 64%, 2%, 50%) hex: #85a30580
> color name p-8t 60,69,2,50
Color 'p-8t' is 50% transparent: rgba(60%, 69%, 2%, 50%) hex: #99b00580
> color name p-9t 68,74,3,50
Color 'p-9t' is 50% transparent: rgba(68%, 74%, 3%, 50%) hex: #adbd0880
> color name p-10t 76,79,3,50
Color 'p-10t' is 50% transparent: rgba(76%, 79%, 3%, 50%) hex: #c2c90880
> color name p-11t 84,84,3,50
Color 'p-11t' is 50% transparent: rgba(84%, 84%, 3%, 50%) hex: #d6d60880
> color name d-t 100,75,4,50
Color 'd-t' is 50% transparent: rgba(100%, 75%, 4%, 50%) hex: #ffbf0a80
> color name d-1t 100,100,4,50
Color 'd-1t' is 50% transparent: rgba(100%, 100%, 4%, 50%) hex: #ffff0a80
> color name d-2t 100,93,4,50
Color 'd-2t' is 50% transparent: rgba(100%, 93%, 4%, 50%) hex: #ffed0a80
> color name d-3t 100,86,4,50
Color 'd-3t' is 50% transparent: rgba(100%, 86%, 4%, 50%) hex: #ffdb0a80
> color name d-4t 100,79,4,50
Color 'd-4t' is 50% transparent: rgba(100%, 79%, 4%, 50%) hex: #ffc90a80
> color name d-5t 100,72,4,50
Color 'd-5t' is 50% transparent: rgba(100%, 72%, 4%, 50%) hex: #ffb80a80
> color name d-6t 100,65,4,50
Color 'd-6t' is 50% transparent: rgba(100%, 65%, 4%, 50%) hex: #ffa60a80
> color name d-7t 100,58,4,50
Color 'd-7t' is 50% transparent: rgba(100%, 58%, 4%, 50%) hex: #ff940a80
> color name d-8t 100,51,4,50
Color 'd-8t' is 50% transparent: rgba(100%, 51%, 4%, 50%) hex: #ff820a80
> color name d-9t 100,44,4,50
Color 'd-9t' is 50% transparent: rgba(100%, 44%, 4%, 50%) hex: #ff700a80
> color name d-10t 100,37,4,50
Color 'd-10t' is 50% transparent: rgba(100%, 37%, 4%, 50%) hex: #ff5e0a80
> color name d-11t 100,30,4,50
Color 'd-11t' is 50% transparent: rgba(100%, 30%, 4%, 50%) hex: #ff4d0a80
> color name m-t 95,43,62,50
Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
> color name m-1t 100,80,90,50
Color 'm-1t' is 50% transparent: rgba(100%, 80%, 90%, 50%) hex: #ffcce680
> color name m-2t 98,76,87,50
Color 'm-2t' is 50% transparent: rgba(98%, 76%, 87%, 50%) hex: #fac2de80
> color name m-3t 96,72,84,50
Color 'm-3t' is 50% transparent: rgba(96%, 72%, 84%, 50%) hex: #f5b8d680
> color name m-4t 94,68,81,50
Color 'm-4t' is 50% transparent: rgba(94%, 68%, 81%, 50%) hex: #f0adcf80
> color name m-5t 92,64,78,50
Color 'm-5t' is 50% transparent: rgba(92%, 64%, 78%, 50%) hex: #eba3c780
> color name m-6t 90,60,75,50
Color 'm-6t' is 50% transparent: rgba(90%, 60%, 75%, 50%) hex: #e699bf80
> color name m-7t 88,56,72,50
Color 'm-7t' is 50% transparent: rgba(88%, 56%, 72%, 50%) hex: #e08fb880
> color name m-8t 86,52,69,50
Color 'm-8t' is 50% transparent: rgba(86%, 52%, 69%, 50%) hex: #db85b080
> color name m-9t 84,48,66,50
Color 'm-9t' is 50% transparent: rgba(84%, 48%, 66%, 50%) hex: #d67aa880
> color name m-10t 82,44,63,50
Color 'm-10t' is 50% transparent: rgba(82%, 44%, 63%, 50%) hex: #d170a180
> color name m-11t 80,40,60,50
Color 'm-11t' is 50% transparent: rgba(80%, 40%, 60%, 50%) hex: #cc669980
> color name head-t 71,51,66,50
Color 'head-t' is 50% transparent: rgba(71%, 51%, 66%, 50%) hex:
#b582a880
> color name head-c 89,89,100,100
Color 'head-c' is opaque: rgb(89%, 89%, 100%) hex: #e3e3ff
> color name headfa-t 80,79,100,50
Color 'headfa-t' is 50% transparent: rgba(80%, 79%, 100%, 50%) hex:
#ccc9ff80
> color name headblue-t 59,78,94,50
Color 'headblue-t' is 50% transparent: rgba(59%, 78%, 94%, 50%) hex:
#96c7f080
> color name headh1-t 41,64,100,50
Color 'headh1-t' is 50% transparent: rgba(41%, 64%, 100%, 50%) hex:
#69a3ff80
> color name headh2-t 50,70,100,50
Color 'headh2-t' is 50% transparent: rgba(50%, 70%, 100%, 50%) hex:
#80b3ff80
> color name headgray-t 60,60,60,50
Color 'headgray-t' is 50% transparent: rgba(60%, 60%, 60%, 50%) hex:
#99999980
> color name darkhead-s 58,34,52,100
Color 'darkhead-s' is opaque: rgb(58%, 34%, 52%) hex: #945785
> color name bodywhite-t 90,90,90,50
Color 'bodywhite-t' is 50% transparent: rgba(90%, 90%, 90%, 50%) hex:
#e6e6e680
> color name rps-t 75,88,93,50
Color 'rps-t' is 50% transparent: rgba(75%, 88%, 93%, 50%) hex: #bfe0ed80
> color name ssu-t 57,71,75,50
Color 'ssu-t' is 50% transparent: rgba(57%, 71%, 75%, 50%) hex: #91b5bf80
> color name h18-t 31,59,68,50
Color 'h18-t' is 50% transparent: rgba(31%, 59%, 68%, 50%) hex: #4f96ad80
> color name h23-t 18,36,100,50
Color 'h23-t' is 50% transparent: rgba(18%, 36%, 100%, 50%) hex:
#2e5cff80
> color name h23-c 18,36,100,100
Color 'h23-c' is opaque: rgb(18%, 36%, 100%) hex: #2e5cff
> color name h24-t 50,70,90,50
Color 'h24-t' is 50% transparent: rgba(50%, 70%, 90%, 50%) hex: #80b3e680
> color name h24-c 50,70,90,100
Color 'h24-c' is opaque: rgb(50%, 70%, 90%) hex: #80b3e6
> color name h28-t 0,24,57,50
Color 'h28-t' is 50% transparent: rgba(0%, 24%, 57%, 50%) hex: #003d9180
> color name h28-c 0,24,57,100
Color 'h28-c' is opaque: rgb(0%, 24%, 57%) hex: #003d91
> color name h29-t 80,69,92,50
Color 'h29-t' is 50% transparent: rgba(80%, 69%, 92%, 50%) hex: #ccb0eb80
> color name h29-c 80,69,92,100
Color 'h29-c' is opaque: rgb(80%, 69%, 92%) hex: #ccb0eb
> color name h30-t 40,40,59,50
Color 'h30-t' is 50% transparent: rgba(40%, 40%, 59%, 50%) hex: #66669680
> color name h31-t 45,18,59,50
Color 'h31-t' is 50% transparent: rgba(45%, 18%, 59%, 50%) hex: #732e9680
> color name h31-c 45,18,59,100
Color 'h31-c' is opaque: rgb(45%, 18%, 59%) hex: #732e96
> color name h34-t 59,18,59,50
Color 'h34-t' is 50% transparent: rgba(59%, 18%, 59%, 50%) hex: #962e9680
> color name h34-c 59,18,59,100
Color 'h34-c' is opaque: rgb(59%, 18%, 59%) hex: #962e96
> color name h35-t 50,22,45,50
Color 'h35-t' is 50% transparent: rgba(50%, 22%, 45%, 50%) hex: #80387380
> color name h44-t 27,50,80,50
Color 'h44-t' is 50% transparent: rgba(27%, 50%, 80%, 50%) hex: #4580cc80
> color name aploop-t 27,0,50,50
Color 'aploop-t' is 50% transparent: rgba(27%, 0%, 50%, 50%) hex:
#45008080
> color name term16-t 40,64,64,50
Color 'term16-t' is 50% transparent: rgba(40%, 64%, 64%, 50%) hex:
#66a3a380
> color name uS3-t 64,41,82,50
Color 'uS3-t' is 50% transparent: rgba(64%, 41%, 82%, 50%) hex: #a369d180
> color name uS5-t 0,50,45,50
Color 'uS5-t' is 50% transparent: rgba(0%, 50%, 45%, 50%) hex: #00807380
> color name gray-t 70,70,70,50
Color 'gray-t' is 50% transparent: rgba(70%, 70%, 70%, 50%) hex:
#b3b3b380
> color name hx68-t 50,50,50,50
Color 'hx68-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex:
#80808080
> color name hx69-t 30,30,30,50
Color 'hx69-t' is 50% transparent: rgba(30%, 30%, 30%, 50%) hex:
#4d4d4d80
> color name srl-t 50,50,50,50
Color 'srl-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name lightgrayt 83,83,83,50
Color 'lightgrayt' is 50% transparent: rgba(83%, 83%, 83%, 50%) hex:
#d4d4d480
> color name silvert 75,75,75,50
Color 'silvert' is 50% transparent: rgba(75%, 75%, 75%, 50%) hex:
#bfbfbf80
> color name grayt 50,50,50,50
Color 'grayt' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name lightcyant 88,100,100,50
Color 'lightcyant' is 50% transparent: rgba(88%, 100%, 100%, 50%) hex:
#e0ffff80
> color name yellowt 100,90,0,50
Color 'yellowt' is 50% transparent: rgba(100%, 90%, 0%, 50%) hex:
#ffe60080
> color name deeppinkt 100,8,58,50
Color 'deeppinkt' is 50% transparent: rgba(100%, 8%, 58%, 50%) hex:
#ff149480
> color name oranget 100,65,0,50
Color 'oranget' is 50% transparent: rgba(100%, 65%, 0%, 50%) hex:
#ffa60080
> color name yellowgreent 60,80,20,50
Color 'yellowgreent' is 50% transparent: rgba(60%, 80%, 20%, 50%) hex:
#99cc3380
> color name darkmagentat 54,0,54,50
Color 'darkmagentat' is 50% transparent: rgba(54%, 0%, 54%, 50%) hex:
#8a008a80
> color name orchidt 86,44,84,50
Color 'orchidt' is 50% transparent: rgba(86%, 44%, 84%, 50%) hex:
#db70d680
> color name paleturquoiset 69,93,93,50
Color 'paleturquoiset' is 50% transparent: rgba(69%, 93%, 93%, 50%) hex:
#b0eded80
> color name pinkt 100,75,80,50
Color 'pinkt' is 50% transparent: rgba(100%, 75%, 80%, 50%) hex:
#ffbfcc80
> color name darkgreent 0,39,0,50
Color 'darkgreent' is 50% transparent: rgba(0%, 39%, 0%, 50%) hex:
#00630080
> color name limegreent 20,80,20,50
Color 'limegreent' is 50% transparent: rgba(20%, 80%, 20%, 50%) hex:
#33cc3380
> color name turquoiset 25,88,82,50
Color 'turquoiset' is 50% transparent: rgba(25%, 88%, 82%, 50%) hex:
#40e0d180
> color name tealt 0,50,50,50
Color 'tealt' is 50% transparent: rgba(0%, 50%, 50%, 50%) hex: #00808080
> color name darkoranget 100,50,0,50
Color 'darkoranget' is 50% transparent: rgba(100%, 50%, 0%, 50%) hex:
#ff800080
> color name lightyellowt 100,100,50,50
Color 'lightyellowt' is 50% transparent: rgba(100%, 100%, 50%, 50%) hex:
#ffff8080
> color name goldt 100,75,0,50
Color 'goldt' is 50% transparent: rgba(100%, 75%, 0%, 50%) hex: #ffbf0080
> color name plumt 87,63,87,50
Color 'plumt' is 50% transparent: rgba(87%, 63%, 87%, 50%) hex: #dea1de80
> color name ssubluet 68,86,90,50
Color 'ssubluet' is 50% transparent: rgba(68%, 86%, 90%, 50%) hex:
#addbe680
> color name p-prect 10,41,0,50
Color 'p-prect' is 50% transparent: rgba(10%, 41%, 0%, 50%) hex:
#1a690080
> color name p-h2t 23,59,0,50
Color 'p-h2t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
> color name p-h1t 40,73,0,50
Color 'p-h1t' is 50% transparent: rgba(40%, 73%, 0%, 50%) hex: #66ba0080
> color name p-h1c 40,73,0,100
Color 'p-h1c' is opaque: rgb(40%, 73%, 0%) hex: #66ba00
> color name p-spct 68,81,0,50
Color 'p-spct' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
> color name p-spcc 68,81,0,100
Color 'p-spcc' is opaque: rgb(68%, 81%, 0%) hex: #adcf00
> color name p-fat 82,92,0,50
Color 'p-fat' is 50% transparent: rgba(82%, 92%, 0%, 50%) hex: #d1eb0080
> color name p-postt 100,92,0,50
Color 'p-postt' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex:
#ffeb0080
> color name d-t 100,80,4,50
Color 'd-t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
> color name d-prect 95,100,50,50
Color 'd-prect' is 50% transparent: rgba(95%, 100%, 50%, 50%) hex:
#f2ff8080
> color name d-h2t 100,90,4,50
Color 'd-h2t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
> color name d-h1t 100,80,4,50
Color 'd-h1t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
> color name d-spct 100,70,4,50
Color 'd-spct' is 50% transparent: rgba(100%, 70%, 4%, 50%) hex:
#ffb30a80
> color name d-fat 100,55,4,50
Color 'd-fat' is 50% transparent: rgba(100%, 55%, 4%, 50%) hex: #ff8c0a80
> color name d-fac 100,55,4,100
Color 'd-fac' is opaque: rgb(100%, 55%, 4%) hex: #ff8c0a
> color name d-postt 100,40,4,50
Color 'd-postt' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex:
#ff660a80
> color name m-t 95,43,62,50
Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
> color name m-prect 100,85,95,50
Color 'm-prect' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex:
#ffd9f280
> color name m-h2t 100,85,95,50
Color 'm-h2t' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex:
#ffd9f280
> color name m-h1t 100,75,95,50
Color 'm-h1t' is 50% transparent: rgba(100%, 75%, 95%, 50%) hex:
#ffbff280
> color name m-spct 89,63,75,50
Color 'm-spct' is 50% transparent: rgba(89%, 63%, 75%, 50%) hex:
#e3a1bf80
> color name m-fat 95,51,75,50
Color 'm-fat' is 50% transparent: rgba(95%, 51%, 75%, 50%) hex: #f282bf80
> color name m-fac 95,51,75,100
Color 'm-fac' is opaque: rgb(95%, 51%, 75%) hex: #f282bf
> color name m-postt 95,43,62,50
Color 'm-postt' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex:
#f26e9e80
executed 70S_colors.cxc
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colorstandard.cxc
> color 100,100,100,50
> color lsu silvert
> color /3 lightgrayt
> color /5 lightgrayt
> color ssu ssu-t
> color head head-t
> color efg efg-t
> color dt d-t
> color pt p-t
> color pep p-t
> color mrna m-t
executed 70S_colorstandard.cxc
> windowsize 1000 1000
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_helices.cxc
> color h18 h18-t
> color h23 h23-t
> color h24 h24-t
> color h28 h28-t
> color h29 h29-t
> color h30 h30-t
> color h31 h31-t
> color h34 h34-t
> color h35 h35-t
> color h36 h36-t
> color h44 h44-t
executed 70S_color_helices.cxc
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_helices.cxc
> color h18 h18-t
> color h23 h23-t
> color h24 h24-t
> color h28 h28-t
> color h29 h29-t
> color h30 h30-t
> color h31 h31-t
> color h34 h34-t
> color h35 h35-t
> color h36 h36-t
> color h44 h44-t
executed 70S_color_helices.cxc
> color h30|h36|h35 head-t
> color zone #12.1 near #12.3,5 distance 5
> color zone #13.1 near #13.3,5 distance 5
> color zone #14.1 near #14.3,5 distance 5
> color zone #30.1 near #30.3,5 distance 5
> color zone #31.1 near #31.3,5 distance 5
> color zone #32.1 near #32.3,5 distance 5
> color zone #33.1 near #33.3,5 distance 5
> color zone #34.1 near #34.3,5 distance 5
> color h30|h36|h35 head-c
> color h28 h28-c
> color h29 h29-c
> color h34 h34-c
> color h23 h23-c
> color h24 h24-c
> color h31 h31-c
> hide #!100
> hide #101 models
> cartoon style nucleic xsection oval width 1.3 thickness 1.3
> transparency #*.3 0 target abc
executed gtpys_helix.cxc
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/helix/gtpys_helix.cxs
——— End of log from Tue May 16 16:15:28 2023 ———
opened ChimeraX session
> hide models
> show #13.3,5 models
> ui mousemode right pivot
> color h69 hx69-t
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or
'random'
or a keyword
> color H69 hx69-t
> ui tool show "Side View"
> view name dc1
> view name dc2
[Repeated 1 time(s)]
> show #13.1 models
> view name dc3
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
——— End of log from Tue May 16 16:53:33 2023 ———
opened ChimeraX session
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_assign.cxc
> name atomods #*.3,5,7
> name emmaps #*.1
> name lsu #*.5
> name ssu #*.3
> name rna /y,v,w,3,6,5
> name r23s /3
> name r16s /6
> name r5s /5
> name pt /y
> name dt /v
> name efg /x
> name pep /p
> name mrna /w
> name GSP :GSP
> name GDP :GDP
> name GTP :GTP
> name ntide :GTP|:GDP|:GSP
> name spc :SCM
> name fua :FUA
> name par :PAR
> name argb :LIG | #20.7/b
> name drugs argb|par|fua|spc
> name D1 /x:start-293
> name D2 /x:294-410
> name D3 /x:411-489
> name D4 /x:490-612
> name D5 /x:613-end
> name sw1 /x:38-65
> name sw2 /x:89-108
> name pl /x:18-25
> name nkxd /x:142-146
> name kirby #20.7
> name mg /x:MG
> name trna /y,v
> name anticodon /y,v:34-36
> name antiplus /y,v:32-38
> name cca /y,v:74-76
> name astem /y,v:1-7,66-73
> name darm /y,v:8-25
> name aarm /y,v:26-43
> name varm /y,v:44-48
> name tarm /y,v:49-65
> name head #*.3/A/C/S/M/G/N/I/J/6:927-1390
> name arg-head #20.3/A/C/S/M/G/N/I/J/6:927-1390
> name post-head #15.3/A/C/S/M/G/N/I/J/6:927-1390
> name fa-head #14.3/A/C/S/M/G/N/I/J/6:927-1390
> name body #*.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name arg-body #20.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name post-body #15.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name fa-body #14.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name h8 /6:144-178
> name h14 /6:339-350
> name h18 /6:511-540
> name h23 /6:674-716
> name h24 /6:769-810
> name h27 /6:894-905
> name h28 /6:921-937,1379-1400
> name h29 /6:938-943,1337-1346
> name h30 /6:945-955,1225-1235
> name h31 /6:956-975
> name h32 /6:984-990,1215-1221
> name h34 /6:1045-1065,1188-1211
> name h35 /6:1066-1073,1102-1110
> name h36 /6:1074-1083
> name h44 /6:1401-1502
> name h45 /6:1506-1529
> name aploop /6:956-959
> name term16S /6:1503-end
> name aphelix /6:1228-1230
> name us3 #*.3/C
> name us5 #*.3/E
> name us7 #*.3/G
> name us9 #*.3/I
> name us11 #*.3/K
> name us12 #*.3/L
> name us13 #*.3/M
> name us14 #*.3/N
> name us15 #*.3/O
> name us9-130 #*.3/I:130
> name l1stalk /3:2097-2191
> name srl /3:2652-2668
> name H68 /3:1832-1906
> name H69 /3:1907-1924
> name H95 /3:2647-2673
> name ul2 #*.5/B
> name ul5 #*.5/E
> name ul14 #*.5/N
> name ul19 #*.5/S
> name ul31 #*.5/e
executed 70S_assign.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_display.cxc
> alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6;
> alias nucribthin cartoon style nucleic xsect oval width 1.2 thick 1.2;
> alias cylinders cartoon style protein modeh tube rad 2 sides 24;
> alias licorice car style protein modeh default arrows f xsect oval
width
1
> thick 1;
> dssp
> windowsize 1000 1000
> set bgColor white
> lighting full
> set silhouettes true
> set silhouetteWidth 1.7
> set silhouettes true
> set silhouetteDepthJump 0.02
> cartoon style width 2.5
> size atomRadius 2
Changed 1614330 atom radii
> nucleotides fill
> size ions atomRadius 1.6
Changed 31 atom radii
> size stickRadius 0.1
Changed 1744812 bond radii
> style stick ringFill thin
Changed 1614330 atom styles, 122200 residue ring styles
> show ribbons
> hide H
> hide :HOH
> hide target a
> show nucleic target a
> show drugs target a
> style drugs ball
Changed 106 atom styles
> nucrib
> graphics selection color black
> volume emmaps style surface step 1 level 4
> surface dust emmaps size 3
> volume surfaceSmoothing true
> cartoon tether trna shape cone opacity 1
> dssp
executed 70S_display.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colors.cxc
> color name efg-t 100,0,0,50
Color 'efg-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
> color name sw1-t 100,92,0,50
Color 'sw1-t' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
> color name sw2-t 68,81,0,50
Color 'sw2-t' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
> color name pl-t 23,59,0,50
Color 'pl-t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
> color name d1-t 100,18,4,50
Color 'd1-t' is 50% transparent: rgba(100%, 18%, 4%, 50%) hex: #ff2e0a80
> color name d2-t 100,40,4,50
Color 'd2-t' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
> color name d3-t 100,27,36,50
Color 'd3-t' is 50% transparent: rgba(100%, 27%, 36%, 50%) hex: #ff455c80
> color name d4-t 80,0,23,50
Color 'd4-t' is 50% transparent: rgba(80%, 0%, 23%, 50%) hex: #cc003b80
> color name d5-t 100,60,4,50
Color 'd5-t' is 50% transparent: rgba(100%, 60%, 4%, 50%) hex: #ff990a80
> color name fa-t 100,90,4,50
Color 'fa-t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
> color name gtp-t 45,53,60,50
Color 'gtp-t' is 50% transparent: rgba(45%, 53%, 60%, 50%) hex: #73879980
> color name mg-t 1,39,16,50
Color 'mg-t' is 50% transparent: rgba(1%, 39%, 16%, 50%) hex: #03632980
> color name spc-t 100,0,0,50
Color 'spc-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
> color name argb-t 50,0,50,50
Color 'argb-t' is 50% transparent: rgba(50%, 0%, 50%, 50%) hex: #80008080
> color name g-1t 98,42,30,50
Color 'g-1t' is 50% transparent: rgba(98%, 42%, 30%, 50%) hex: #fa6b4d80
> color name g-2t 95,35,25,50
Color 'g-2t' is 50% transparent: rgba(95%, 35%, 25%, 50%) hex: #f2594080
> color name g-3t 92,28,20,50
Color 'g-3t' is 50% transparent: rgba(92%, 28%, 20%, 50%) hex: #eb473380
> color name g-4t 89,21,15,50
Color 'g-4t' is 50% transparent: rgba(89%, 21%, 15%, 50%) hex: #e3362680
> color name g-5t 86,14,10,50
Color 'g-5t' is 50% transparent: rgba(86%, 14%, 10%, 50%) hex: #db241a80
> color name g-6t 83,7,5,50
Color 'g-6t' is 50% transparent: rgba(83%, 7%, 5%, 50%) hex: #d4120d80
> color name g-7t 80,0,0,50
Color 'g-7t' is 50% transparent: rgba(80%, 0%, 0%, 50%) hex: #cc000080
> color name p-t 40,60,2,50
Color 'p-t' is 50% transparent: rgba(40%, 60%, 2%, 50%) hex: #66990580
> color name p-c 40,60,2,100
Color 'p-c' is opaque: rgb(40%, 60%, 2%) hex: #669905
> color name p-1t 4,34,1,50
Color 'p-1t' is 50% transparent: rgba(4%, 34%, 1%, 50%) hex: #0a570380
> color name p-2t 12,39,1,50
Color 'p-2t' is 50% transparent: rgba(12%, 39%, 1%, 50%) hex: #1f630380
> color name p-3t 20,44,1,50
Color 'p-3t' is 50% transparent: rgba(20%, 44%, 1%, 50%) hex: #33700380
> color name p-4t 28,49,1,50
Color 'p-4t' is 50% transparent: rgba(28%, 49%, 1%, 50%) hex: #477d0380
> color name p-5t 36,54,2,50
Color 'p-5t' is 50% transparent: rgba(36%, 54%, 2%, 50%) hex: #5c8a0580
> color name p-6t 44,59,2,50
Color 'p-6t' is 50% transparent: rgba(44%, 59%, 2%, 50%) hex: #70960580
> color name p-7t 52,64,2,50
Color 'p-7t' is 50% transparent: rgba(52%, 64%, 2%, 50%) hex: #85a30580
> color name p-8t 60,69,2,50
Color 'p-8t' is 50% transparent: rgba(60%, 69%, 2%, 50%) hex: #99b00580
> color name p-9t 68,74,3,50
Color 'p-9t' is 50% transparent: rgba(68%, 74%, 3%, 50%) hex: #adbd0880
> color name p-10t 76,79,3,50
Color 'p-10t' is 50% transparent: rgba(76%, 79%, 3%, 50%) hex: #c2c90880
> color name p-11t 84,84,3,50
Color 'p-11t' is 50% transparent: rgba(84%, 84%, 3%, 50%) hex: #d6d60880
> color name d-t 100,75,4,50
Color 'd-t' is 50% transparent: rgba(100%, 75%, 4%, 50%) hex: #ffbf0a80
> color name d-c 100,75,4,100
Color 'd-c' is opaque: rgb(100%, 75%, 4%) hex: #ffbf0a
> color name d-1t 100,100,4,50
Color 'd-1t' is 50% transparent: rgba(100%, 100%, 4%, 50%) hex: #ffff0a80
> color name d-2t 100,93,4,50
Color 'd-2t' is 50% transparent: rgba(100%, 93%, 4%, 50%) hex: #ffed0a80
> color name d-3t 100,86,4,50
Color 'd-3t' is 50% transparent: rgba(100%, 86%, 4%, 50%) hex: #ffdb0a80
> color name d-4t 100,79,4,50
Color 'd-4t' is 50% transparent: rgba(100%, 79%, 4%, 50%) hex: #ffc90a80
> color name d-5t 100,72,4,50
Color 'd-5t' is 50% transparent: rgba(100%, 72%, 4%, 50%) hex: #ffb80a80
> color name d-6t 100,65,4,50
Color 'd-6t' is 50% transparent: rgba(100%, 65%, 4%, 50%) hex: #ffa60a80
> color name d-7t 100,58,4,50
Color 'd-7t' is 50% transparent: rgba(100%, 58%, 4%, 50%) hex: #ff940a80
> color name d-8t 100,51,4,50
Color 'd-8t' is 50% transparent: rgba(100%, 51%, 4%, 50%) hex: #ff820a80
> color name d-9t 100,44,4,50
Color 'd-9t' is 50% transparent: rgba(100%, 44%, 4%, 50%) hex: #ff700a80
> color name d-10t 100,37,4,50
Color 'd-10t' is 50% transparent: rgba(100%, 37%, 4%, 50%) hex: #ff5e0a80
> color name d-11t 100,30,4,50
Color 'd-11t' is 50% transparent: rgba(100%, 30%, 4%, 50%) hex: #ff4d0a80
> color name m-t 95,43,62,50
Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
> color name m-c 95,43,62,100
Color 'm-c' is opaque: rgb(95%, 43%, 62%) hex: #f26e9e
> color name m-1t 100,80,90,50
Color 'm-1t' is 50% transparent: rgba(100%, 80%, 90%, 50%) hex: #ffcce680
> color name m-2t 98,76,87,50
Color 'm-2t' is 50% transparent: rgba(98%, 76%, 87%, 50%) hex: #fac2de80
> color name m-3t 96,72,84,50
Color 'm-3t' is 50% transparent: rgba(96%, 72%, 84%, 50%) hex: #f5b8d680
> color name m-4t 94,68,81,50
Color 'm-4t' is 50% transparent: rgba(94%, 68%, 81%, 50%) hex: #f0adcf80
> color name m-5t 92,64,78,50
Color 'm-5t' is 50% transparent: rgba(92%, 64%, 78%, 50%) hex: #eba3c780
> color name m-6t 90,60,75,50
Color 'm-6t' is 50% transparent: rgba(90%, 60%, 75%, 50%) hex: #e699bf80
> color name m-7t 88,56,72,50
Color 'm-7t' is 50% transparent: rgba(88%, 56%, 72%, 50%) hex: #e08fb880
> color name m-8t 86,52,69,50
Color 'm-8t' is 50% transparent: rgba(86%, 52%, 69%, 50%) hex: #db85b080
> color name m-9t 84,48,66,50
Color 'm-9t' is 50% transparent: rgba(84%, 48%, 66%, 50%) hex: #d67aa880
> color name m-10t 82,44,63,50
Color 'm-10t' is 50% transparent: rgba(82%, 44%, 63%, 50%) hex: #d170a180
> color name m-11t 80,40,60,50
Color 'm-11t' is 50% transparent: rgba(80%, 40%, 60%, 50%) hex: #cc669980
> color name head-t 71,51,66,50
Color 'head-t' is 50% transparent: rgba(71%, 51%, 66%, 50%) hex:
#b582a880
> color name head-c 89,89,100,100
Color 'head-c' is opaque: rgb(89%, 89%, 100%) hex: #e3e3ff
> color name headfa-t 80,79,100,50
Color 'headfa-t' is 50% transparent: rgba(80%, 79%, 100%, 50%) hex:
#ccc9ff80
> color name headblue-t 59,78,94,50
Color 'headblue-t' is 50% transparent: rgba(59%, 78%, 94%, 50%) hex:
#96c7f080
> color name headh1-t 41,64,100,50
Color 'headh1-t' is 50% transparent: rgba(41%, 64%, 100%, 50%) hex:
#69a3ff80
> color name headh2-t 50,70,100,50
Color 'headh2-t' is 50% transparent: rgba(50%, 70%, 100%, 50%) hex:
#80b3ff80
> color name headgray-t 60,60,60,50
Color 'headgray-t' is 50% transparent: rgba(60%, 60%, 60%, 50%) hex:
#99999980
> color name darkhead-s 58,34,52,100
Color 'darkhead-s' is opaque: rgb(58%, 34%, 52%) hex: #945785
> color name bodywhite-t 90,90,90,50
Color 'bodywhite-t' is 50% transparent: rgba(90%, 90%, 90%, 50%) hex:
#e6e6e680
> color name rps-t 75,88,93,50
Color 'rps-t' is 50% transparent: rgba(75%, 88%, 93%, 50%) hex: #bfe0ed80
> color name ssu-t 57,71,75,50
Color 'ssu-t' is 50% transparent: rgba(57%, 71%, 75%, 50%) hex: #91b5bf80
> color name h18-t 31,59,68,50
Color 'h18-t' is 50% transparent: rgba(31%, 59%, 68%, 50%) hex: #4f96ad80
> color name h18-c 31,59,68,100
Color 'h18-c' is opaque: rgb(31%, 59%, 68%) hex: #4f96ad
> color name h23-t 18,36,100,50
Color 'h23-t' is 50% transparent: rgba(18%, 36%, 100%, 50%) hex:
#2e5cff80
> color name h23-c 18,36,100,100
Color 'h23-c' is opaque: rgb(18%, 36%, 100%) hex: #2e5cff
> color name h24-t 50,70,90,50
Color 'h24-t' is 50% transparent: rgba(50%, 70%, 90%, 50%) hex: #80b3e680
> color name h24-c 50,70,90,100
Color 'h24-c' is opaque: rgb(50%, 70%, 90%) hex: #80b3e6
> color name h28-t 0,24,57,50
Color 'h28-t' is 50% transparent: rgba(0%, 24%, 57%, 50%) hex: #003d9180
> color name h28-c 0,24,57,100
Color 'h28-c' is opaque: rgb(0%, 24%, 57%) hex: #003d91
> color name h29-t 80,69,92,50
Color 'h29-t' is 50% transparent: rgba(80%, 69%, 92%, 50%) hex: #ccb0eb80
> color name h29-c 80,69,92,100
Color 'h29-c' is opaque: rgb(80%, 69%, 92%) hex: #ccb0eb
> color name h30-t 40,40,59,50
Color 'h30-t' is 50% transparent: rgba(40%, 40%, 59%, 50%) hex: #66669680
> color name h30-c 40,40,59,100
Color 'h30-c' is opaque: rgb(40%, 40%, 59%) hex: #666696
> color name h31-t 45,18,59,50
Color 'h31-t' is 50% transparent: rgba(45%, 18%, 59%, 50%) hex: #732e9680
> color name h31-c 45,18,59,100
Color 'h31-c' is opaque: rgb(45%, 18%, 59%) hex: #732e96
> color name h34-t 59,18,59,50
Color 'h34-t' is 50% transparent: rgba(59%, 18%, 59%, 50%) hex: #962e9680
> color name h34-c 59,18,59,100
Color 'h34-c' is opaque: rgb(59%, 18%, 59%) hex: #962e96
> color name h35-t 50,22,45,50
Color 'h35-t' is 50% transparent: rgba(50%, 22%, 45%, 50%) hex: #80387380
> color name h35-c 50,22,45,100
Color 'h35-c' is opaque: rgb(50%, 22%, 45%) hex: #803873
> color name h44-t 27,50,80,50
Color 'h44-t' is 50% transparent: rgba(27%, 50%, 80%, 50%) hex: #4580cc80
> color name h44-c 27,50,80,100
Color 'h44-c' is opaque: rgb(27%, 50%, 80%) hex: #4580cc
> color name aploop-t 27,0,50,50
Color 'aploop-t' is 50% transparent: rgba(27%, 0%, 50%, 50%) hex:
#45008080
> color name term16-t 40,64,64,50
Color 'term16-t' is 50% transparent: rgba(40%, 64%, 64%, 50%) hex:
#66a3a380
> color name uS3-t 64,41,82,50
Color 'uS3-t' is 50% transparent: rgba(64%, 41%, 82%, 50%) hex: #a369d180
> color name uS5-t 0,50,45,50
Color 'uS5-t' is 50% transparent: rgba(0%, 50%, 45%, 50%) hex: #00807380
> color name gray-t 70,70,70,50
Color 'gray-t' is 50% transparent: rgba(70%, 70%, 70%, 50%) hex:
#b3b3b380
> color name hx68-t 50,50,50,50
Color 'hx68-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex:
#80808080
> color name hx68-c 50,50,50,100
Color 'hx68-c' is opaque: gray(50%) hex: #808080
> color name hx69-t 40,40,40,50
Color 'hx69-t' is 50% transparent: rgba(40%, 40%, 40%, 50%) hex:
#66666680
> color name hx69-c 40,40,40,100
Color 'hx69-c' is opaque: gray(40%) hex: #666666
> color name srl-t 50,50,50,50
Color 'srl-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name srl-t 50,50,50,100
Color 'srl-t' is opaque: gray(50%) hex: #808080
> color name lightgrayt 83,83,83,50
Color 'lightgrayt' is 50% transparent: rgba(83%, 83%, 83%, 50%) hex:
#d4d4d480
> color name silvert 75,75,75,50
Color 'silvert' is 50% transparent: rgba(75%, 75%, 75%, 50%) hex:
#bfbfbf80
> color name grayt 50,50,50,50
Color 'grayt' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name lightcyant 88,100,100,50
Color 'lightcyant' is 50% transparent: rgba(88%, 100%, 100%, 50%) hex:
#e0ffff80
> color name yellowt 100,90,0,50
Color 'yellowt' is 50% transparent: rgba(100%, 90%, 0%, 50%) hex:
#ffe60080
> color name deeppinkt 100,8,58,50
Color 'deeppinkt' is 50% transparent: rgba(100%, 8%, 58%, 50%) hex:
#ff149480
> color name oranget 100,65,0,50
Color 'oranget' is 50% transparent: rgba(100%, 65%, 0%, 50%) hex:
#ffa60080
> color name yellowgreent 60,80,20,50
Color 'yellowgreent' is 50% transparent: rgba(60%, 80%, 20%, 50%) hex:
#99cc3380
> color name darkmagentat 54,0,54,50
Color 'darkmagentat' is 50% transparent: rgba(54%, 0%, 54%, 50%) hex:
#8a008a80
> color name orchidt 86,44,84,50
Color 'orchidt' is 50% transparent: rgba(86%, 44%, 84%, 50%) hex:
#db70d680
> color name paleturquoiset 69,93,93,50
Color 'paleturquoiset' is 50% transparent: rgba(69%, 93%, 93%, 50%) hex:
#b0eded80
> color name pinkt 100,75,80,50
Color 'pinkt' is 50% transparent: rgba(100%, 75%, 80%, 50%) hex:
#ffbfcc80
> color name darkgreent 0,39,0,50
Color 'darkgreent' is 50% transparent: rgba(0%, 39%, 0%, 50%) hex:
#00630080
> color name limegreent 20,80,20,50
Color 'limegreent' is 50% transparent: rgba(20%, 80%, 20%, 50%) hex:
#33cc3380
> color name turquoiset 25,88,82,50
Color 'turquoiset' is 50% transparent: rgba(25%, 88%, 82%, 50%) hex:
#40e0d180
> color name tealt 0,50,50,50
Color 'tealt' is 50% transparent: rgba(0%, 50%, 50%, 50%) hex: #00808080
> color name darkoranget 100,50,0,50
Color 'darkoranget' is 50% transparent: rgba(100%, 50%, 0%, 50%) hex:
#ff800080
> color name lightyellowt 100,100,50,50
Color 'lightyellowt' is 50% transparent: rgba(100%, 100%, 50%, 50%) hex:
#ffff8080
> color name goldt 100,75,0,50
Color 'goldt' is 50% transparent: rgba(100%, 75%, 0%, 50%) hex: #ffbf0080
> color name plumt 87,63,87,50
Color 'plumt' is 50% transparent: rgba(87%, 63%, 87%, 50%) hex: #dea1de80
> color name ssubluet 68,86,90,50
Color 'ssubluet' is 50% transparent: rgba(68%, 86%, 90%, 50%) hex:
#addbe680
> color name p-prect 10,41,0,50
Color 'p-prect' is 50% transparent: rgba(10%, 41%, 0%, 50%) hex:
#1a690080
> color name p-h2t 23,59,0,50
Color 'p-h2t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
> color name p-h1t 40,73,0,50
Color 'p-h1t' is 50% transparent: rgba(40%, 73%, 0%, 50%) hex: #66ba0080
> color name p-h1c 40,73,0,100
Color 'p-h1c' is opaque: rgb(40%, 73%, 0%) hex: #66ba00
> color name p-spct 68,81,0,50
Color 'p-spct' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
> color name p-spcc 68,81,0,100
Color 'p-spcc' is opaque: rgb(68%, 81%, 0%) hex: #adcf00
> color name p-fat 82,92,0,50
Color 'p-fat' is 50% transparent: rgba(82%, 92%, 0%, 50%) hex: #d1eb0080
> color name p-postt 100,92,0,50
Color 'p-postt' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex:
#ffeb0080
> color name d-t 100,80,4,50
Color 'd-t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
> color name d-prect 95,100,50,50
Color 'd-prect' is 50% transparent: rgba(95%, 100%, 50%, 50%) hex:
#f2ff8080
> color name d-h2t 100,90,4,50
Color 'd-h2t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
> color name d-h1t 100,80,4,50
Color 'd-h1t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
> color name d-spct 100,70,4,50
Color 'd-spct' is 50% transparent: rgba(100%, 70%, 4%, 50%) hex:
#ffb30a80
> color name d-fat 100,55,4,50
Color 'd-fat' is 50% transparent: rgba(100%, 55%, 4%, 50%) hex: #ff8c0a80
> color name d-fac 100,55,4,100
Color 'd-fac' is opaque: rgb(100%, 55%, 4%) hex: #ff8c0a
> color name d-postt 100,40,4,50
Color 'd-postt' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex:
#ff660a80
> color name m-t 95,43,62,50
Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
> color name m-prect 100,85,95,50
Color 'm-prect' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex:
#ffd9f280
> color name m-h2t 100,85,95,50
Color 'm-h2t' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex:
#ffd9f280
> color name m-h1t 100,75,95,50
Color 'm-h1t' is 50% transparent: rgba(100%, 75%, 95%, 50%) hex:
#ffbff280
> color name m-spct 89,63,75,50
Color 'm-spct' is 50% transparent: rgba(89%, 63%, 75%, 50%) hex:
#e3a1bf80
> color name m-fat 95,51,75,50
Color 'm-fat' is 50% transparent: rgba(95%, 51%, 75%, 50%) hex: #f282bf80
> color name m-fac 95,51,75,100
Color 'm-fac' is opaque: rgb(95%, 51%, 75%) hex: #f282bf
> color name m-postt 95,43,62,50
Color 'm-postt' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex:
#f26e9e80
executed 70S_colors.cxc
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colorstandard.cxc
> color 100,100,100,50
> color lsu silvert
> color /3 lightgrayt
> color /5 lightgrayt
> color ssu ssu-t
> color head head-t
> color efg efg-t
> color dt d-t
> color pt p-t
> color pep p-t
> color mrna m-t
executed 70S_colorstandard.cxc
> windowsize 1000 1000
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_helices.cxc
> color h18 h18-t
> color h23 h23-t
> color h24 h24-t
> color h28 h28-t
> color h29 h29-t
> color h30 h30-t
> color h31 h31-t
> color h34 h34-t
> color h35 h35-t
> color h36 h36-t
> color h44 h44-t
> color H69 hx69-t
executed 70S_color_helices.cxc
> color h30|h36|h35 head-t
> view dc3
> surface cap true
> color zone #12.1 near #12.3,5 distance 5
> color zone #13.1 near #13.3,5 distance 5
> color zone #14.1 near #14.3,5 distance 5
> color zone #30.1 near #30.3,5 distance 5
> color zone #31.1 near #31.3,5 distance 5
> color zone #32.1 near #32.3,5 distance 5
> color zone #33.1 near #33.3,5 distance 5
> color zone #34.1 near #34.3,5 distance 5
> color h30|h36|h35 head-c
> color h28 h28-c
> color h29 h29-c
> color h34 h34-c
> color h23 h23-c
> color h24 h24-c
> color h31 h31-c
> hide #!100
> hide #101 models
> cartoon style nucleic xsection oval width 1.3 thickness 1.3
> transparency #*.3 0 target abc
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_helices-s.cxc
> color h18 h18-c
> color h23 h23-c
> color h24 h24-c
[had to delete some of the log to fit within ticket length limits]
> name H79 #*.5/3:2200-2223
> name H80 #*.5/3:2246-2258
> name H81 #*.5/3:2259-2281
> name H82 #*.5/3:2284-2285|#*.5/3:2383-2384
> name H83 #*.5/3:2288-2295|#*.5/3:2337-2344
> name H84 #*.5/3:2296-2322
> name H85 #*.5/3:2323-2332
> name H86 #*.5/3:2347-2370
> name H87 #*.5/3:2372-2381
> name H88 #*.5/3:2395-2421
> name H89 #*.5/3:2453-2498
> name H90 #*.5/3:2507-2517|#*.5/3:2567-2582
> name H91 #*.5/3:2520-2545
> name H92 #*.5/3:2547-2561
> name H93 #*.5/3:2588-2606
> name H94 #*.5/3:2630-2643|#*.5/3:2771-2788
> name H95 #*.5/3:2646-2674
> name H96 #*.5/3:2675-2732
> name H97 #*.5/3:2735-2769
> name H98 #*.5/3:2791-2805
> name H99 #*.5/3:2811-2814|#*.5/3:2886-2889
> name H100 #*.5/3:2815-2831
executed 70S_assign.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_display.cxc
> alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6;
> alias nucribthin cartoon style nucleic xsect oval width 1.2 thick 1.2;
> alias cylinders cartoon style protein modeh tube rad 2 sides 24;
> alias licorice car style protein modeh default arrows f xsect oval
width
1
> thick 1;
> dssp
> windowsize 1000 1000
> set bgColor white
> lighting full
> set silhouettes true
> set silhouetteWidth 1.7
> set silhouettes true
> set silhouetteDepthJump 0.02
> cartoon style width 2.5
> size atomRadius 2
Changed 1614330 atom radii
> nucleotides fill
> size ions atomRadius 1.6
Changed 31 atom radii
> size stickRadius 0.1
Changed 1744812 bond radii
> style stick ringFill thin
Changed 1614330 atom styles, 122200 residue ring styles
> show ribbons
> hide H
> hide :HOH
> hide target a
> show nucleic target a
> show drugs target a
> style drugs ball
Changed 106 atom styles
> graphics selection color black
> cartoon style protein xsection round width 2 thickness 0.6
> cartoon style modeHelix wrap
> cartoon style sides 24
> cartoon style strand xsection oval arrows false
> cartoon suppressBackboneDisplay true
> alias thinbois style ball;size ballscale 0.09; size stickradius 0.13;
> alias thickbois style stick;size stickradius 0.4;style stick ringFill
thick;
> volume emmaps style surface step 1 level 4
> surface dust emmaps size 3
> volume surfaceSmoothing true
> cartoon tether trna shape cone opacity 1
> dssp
> thickbois
Changed 1614330 atom styles
Changed 1744812 bond radii
Changed 1614330 atom styles, 122200 residue ring styles
executed 70S_display.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colors.cxc
> color name efg-t 100,0,0,50
Color 'efg-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
> color name sw1-t 100,92,0,50
Color 'sw1-t' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
> color name sw2-t 68,81,0,50
Color 'sw2-t' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
> color name pl-t 23,59,0,50
Color 'pl-t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
> color name d1-t 100,18,4,50
Color 'd1-t' is 50% transparent: rgba(100%, 18%, 4%, 50%) hex: #ff2e0a80
> color name d2-t 100,40,4,50
Color 'd2-t' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
> color name d3-t 100,27,36,50
Color 'd3-t' is 50% transparent: rgba(100%, 27%, 36%, 50%) hex: #ff455c80
> color name d4-t 80,0,23,50
Color 'd4-t' is 50% transparent: rgba(80%, 0%, 23%, 50%) hex: #cc003b80
> color name d5-t 100,60,4,50
Color 'd5-t' is 50% transparent: rgba(100%, 60%, 4%, 50%) hex: #ff990a80
> color name fa-t 100,90,4,50
Color 'fa-t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
> color name gtp-t 45,53,60,50
Color 'gtp-t' is 50% transparent: rgba(45%, 53%, 60%, 50%) hex: #73879980
> color name mg-t 1,39,16,50
Color 'mg-t' is 50% transparent: rgba(1%, 39%, 16%, 50%) hex: #03632980
> color name spc-t 100,0,0,50
Color 'spc-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
> color name argb-t 50,0,50,50
Color 'argb-t' is 50% transparent: rgba(50%, 0%, 50%, 50%) hex: #80008080
> color name g-1t 98,42,30,50
Color 'g-1t' is 50% transparent: rgba(98%, 42%, 30%, 50%) hex: #fa6b4d80
> color name g-2t 95,35,25,50
Color 'g-2t' is 50% transparent: rgba(95%, 35%, 25%, 50%) hex: #f2594080
> color name g-3t 92,28,20,50
Color 'g-3t' is 50% transparent: rgba(92%, 28%, 20%, 50%) hex: #eb473380
> color name g-4t 89,21,15,50
Color 'g-4t' is 50% transparent: rgba(89%, 21%, 15%, 50%) hex: #e3362680
> color name g-5t 86,14,10,50
Color 'g-5t' is 50% transparent: rgba(86%, 14%, 10%, 50%) hex: #db241a80
> color name g-6t 83,7,5,50
Color 'g-6t' is 50% transparent: rgba(83%, 7%, 5%, 50%) hex: #d4120d80
> color name g-7t 80,0,0,50
Color 'g-7t' is 50% transparent: rgba(80%, 0%, 0%, 50%) hex: #cc000080
> color name p-t 44,59,2,50
Color 'p-t' is 50% transparent: rgba(44%, 59%, 2%, 50%) hex: #70960580
> color name p-c 44,59,2,100
Color 'p-c' is opaque: rgb(44%, 59%, 2%) hex: #709605
> color name p-1t 4,34,1,50
Color 'p-1t' is 50% transparent: rgba(4%, 34%, 1%, 50%) hex: #0a570380
> color name p-2t 12,39,1,50
Color 'p-2t' is 50% transparent: rgba(12%, 39%, 1%, 50%) hex: #1f630380
> color name p-3t 20,44,1,50
Color 'p-3t' is 50% transparent: rgba(20%, 44%, 1%, 50%) hex: #33700380
> color name p-4t 28,49,1,50
Color 'p-4t' is 50% transparent: rgba(28%, 49%, 1%, 50%) hex: #477d0380
> color name p-5t 36,54,2,50
Color 'p-5t' is 50% transparent: rgba(36%, 54%, 2%, 50%) hex: #5c8a0580
> color name p-6t 44,59,2,50
Color 'p-6t' is 50% transparent: rgba(44%, 59%, 2%, 50%) hex: #70960580
> color name p-7t 52,64,2,50
Color 'p-7t' is 50% transparent: rgba(52%, 64%, 2%, 50%) hex: #85a30580
> color name p-8t 60,69,2,50
Color 'p-8t' is 50% transparent: rgba(60%, 69%, 2%, 50%) hex: #99b00580
> color name p-9t 68,74,3,50
Color 'p-9t' is 50% transparent: rgba(68%, 74%, 3%, 50%) hex: #adbd0880
> color name p-10t 76,79,3,50
Color 'p-10t' is 50% transparent: rgba(76%, 79%, 3%, 50%) hex: #c2c90880
> color name p-11t 84,84,3,50
Color 'p-11t' is 50% transparent: rgba(84%, 84%, 3%, 50%) hex: #d6d60880
> color name d-t 100,65,4,50
Color 'd-t' is 50% transparent: rgba(100%, 65%, 4%, 50%) hex: #ffa60a80
> color name d-c 100,65,4,100
Color 'd-c' is opaque: rgb(100%, 65%, 4%) hex: #ffa60a
> color name d-1t 100,100,4,50
Color 'd-1t' is 50% transparent: rgba(100%, 100%, 4%, 50%) hex: #ffff0a80
> color name d-2t 100,93,4,50
Color 'd-2t' is 50% transparent: rgba(100%, 93%, 4%, 50%) hex: #ffed0a80
> color name d-3t 100,86,4,50
Color 'd-3t' is 50% transparent: rgba(100%, 86%, 4%, 50%) hex: #ffdb0a80
> color name d-4t 100,79,4,50
Color 'd-4t' is 50% transparent: rgba(100%, 79%, 4%, 50%) hex: #ffc90a80
> color name d-5t 100,72,4,50
Color 'd-5t' is 50% transparent: rgba(100%, 72%, 4%, 50%) hex: #ffb80a80
> color name d-6t 100,65,4,50
Color 'd-6t' is 50% transparent: rgba(100%, 65%, 4%, 50%) hex: #ffa60a80
> color name d-7t 100,58,4,50
Color 'd-7t' is 50% transparent: rgba(100%, 58%, 4%, 50%) hex: #ff940a80
> color name d-8t 100,51,4,50
Color 'd-8t' is 50% transparent: rgba(100%, 51%, 4%, 50%) hex: #ff820a80
> color name d-9t 100,44,4,50
Color 'd-9t' is 50% transparent: rgba(100%, 44%, 4%, 50%) hex: #ff700a80
> color name d-10t 100,37,4,50
Color 'd-10t' is 50% transparent: rgba(100%, 37%, 4%, 50%) hex: #ff5e0a80
> color name d-11t 100,30,4,50
Color 'd-11t' is 50% transparent: rgba(100%, 30%, 4%, 50%) hex: #ff4d0a80
> color name m-t 95,43,62,50
Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
> color name m-c 95,43,62,100
Color 'm-c' is opaque: rgb(95%, 43%, 62%) hex: #f26e9e
> color name m-1t 100,80,90,50
Color 'm-1t' is 50% transparent: rgba(100%, 80%, 90%, 50%) hex: #ffcce680
> color name m-2t 98,76,87,50
Color 'm-2t' is 50% transparent: rgba(98%, 76%, 87%, 50%) hex: #fac2de80
> color name m-3t 96,72,84,50
Color 'm-3t' is 50% transparent: rgba(96%, 72%, 84%, 50%) hex: #f5b8d680
> color name m-4t 94,68,81,50
Color 'm-4t' is 50% transparent: rgba(94%, 68%, 81%, 50%) hex: #f0adcf80
> color name m-5t 92,64,78,50
Color 'm-5t' is 50% transparent: rgba(92%, 64%, 78%, 50%) hex: #eba3c780
> color name m-6t 90,60,75,50
Color 'm-6t' is 50% transparent: rgba(90%, 60%, 75%, 50%) hex: #e699bf80
> color name m-7t 88,56,72,50
Color 'm-7t' is 50% transparent: rgba(88%, 56%, 72%, 50%) hex: #e08fb880
> color name m-8t 86,52,69,50
Color 'm-8t' is 50% transparent: rgba(86%, 52%, 69%, 50%) hex: #db85b080
> color name m-9t 84,48,66,50
Color 'm-9t' is 50% transparent: rgba(84%, 48%, 66%, 50%) hex: #d67aa880
> color name m-10t 82,44,63,50
Color 'm-10t' is 50% transparent: rgba(82%, 44%, 63%, 50%) hex: #d170a180
> color name m-11t 80,40,60,50
Color 'm-11t' is 50% transparent: rgba(80%, 40%, 60%, 50%) hex: #cc669980
> color name head-t 82,74,84,50
Color 'head-t' is 50% transparent: rgba(82%, 74%, 84%, 50%) hex:
#d1bdd680
> color name head-c 82,74,84,100
Color 'head-c' is opaque: rgb(82%, 74%, 84%) hex: #d1bdd6
> color name headfa-t 54,41,54,50
Color 'headfa-t' is 50% transparent: rgba(54%, 41%, 54%, 50%) hex:
#8a698a80
> color name headblue-t 59,78,94,50
Color 'headblue-t' is 50% transparent: rgba(59%, 78%, 94%, 50%) hex:
#96c7f080
> color name headh1-t 41,64,100,50
Color 'headh1-t' is 50% transparent: rgba(41%, 64%, 100%, 50%) hex:
#69a3ff80
> color name headh2-t 50,70,100,50
Color 'headh2-t' is 50% transparent: rgba(50%, 70%, 100%, 50%) hex:
#80b3ff80
> color name headgray-t 60,60,60,50
Color 'headgray-t' is 50% transparent: rgba(60%, 60%, 60%, 50%) hex:
#99999980
> color name darkhead-s 54,41,54,100
Color 'darkhead-s' is opaque: rgb(54%, 41%, 54%) hex: #8a698a
> color name bodywhite-t 90,90,90,50
Color 'bodywhite-t' is 50% transparent: rgba(90%, 90%, 90%, 50%) hex:
#e6e6e680
> color name rps-t 75,88,93,50
Color 'rps-t' is 50% transparent: rgba(75%, 88%, 93%, 50%) hex: #bfe0ed80
> color name ssu-t 69,79,82,50
Color 'ssu-t' is 50% transparent: rgba(69%, 79%, 82%, 50%) hex: #b0c9d180
> color name ssu-c 69,79,82,100
Color 'ssu-c' is opaque: rgb(69%, 79%, 82%) hex: #b0c9d1
> color name h16-t 79,85,89,50
Color 'h16-t' is 50% transparent: rgba(79%, 85%, 89%, 50%) hex: #c9d9e380
> color name h16-c 79,85,89,100
Color 'h16-c' is opaque: rgb(79%, 85%, 89%) hex: #c9d9e3
> color name h18-t 31,59,68,50
Color 'h18-t' is 50% transparent: rgba(31%, 59%, 68%, 50%) hex: #4f96ad80
> color name h18-dt 6,47,62,50
Color 'h18-dt' is 50% transparent: rgba(6%, 47%, 62%, 50%) hex: #0f789e80
> color name h18-dc 6,47,62,100
Color 'h18-dc' is opaque: rgb(6%, 47%, 62%) hex: #0f789e
> color name h18-c 31,59,68,100
Color 'h18-c' is opaque: rgb(31%, 59%, 68%) hex: #4f96ad
> color name h23-t 40,61,80,50
Color 'h23-t' is 50% transparent: rgba(40%, 61%, 80%, 50%) hex: #669ccc80
> color name h23-c 40,61,80,100
Color 'h23-c' is opaque: rgb(40%, 61%, 80%) hex: #669ccc
> color name h24-t 50,70,90,50
Color 'h24-t' is 50% transparent: rgba(50%, 70%, 90%, 50%) hex: #80b3e680
> color name h24-c 50,70,90,100
Color 'h24-c' is opaque: rgb(50%, 70%, 90%) hex: #80b3e6
> color name h28-t 21,27,56,50
Color 'h28-t' is 50% transparent: rgba(21%, 27%, 56%, 50%) hex: #36458f80
> color name h28-c 21,27,56,100
Color 'h28-c' is opaque: rgb(21%, 27%, 56%) hex: #36458f
> color name h29-t 80,69,92,50
Color 'h29-t' is 50% transparent: rgba(80%, 69%, 92%, 50%) hex: #ccb0eb80
> color name h29-c 80,69,92,100
Color 'h29-c' is opaque: rgb(80%, 69%, 92%) hex: #ccb0eb
> color name h30-t 40,40,59,50
Color 'h30-t' is 50% transparent: rgba(40%, 40%, 59%, 50%) hex: #66669680
> color name h30-c 40,40,59,100
Color 'h30-c' is opaque: rgb(40%, 40%, 59%) hex: #666696
> color name h31-t 45,35,55,50
Color 'h31-t' is 50% transparent: rgba(45%, 35%, 55%, 50%) hex: #73598c80
> color name h31-c 45,35,55,100
Color 'h31-c' is opaque: rgb(45%, 35%, 55%) hex: #73598c
> color name h32-t 75,62,79,50
Color 'h32-t' is 50% transparent: rgba(75%, 62%, 79%, 50%) hex: #bf9ec980
> color name h32-c 75,62,79,100
Color 'h32-c' is opaque: rgb(75%, 62%, 79%) hex: #bf9ec9
> color name h33-t 88,82,90,50
Color 'h33-t' is 50% transparent: rgba(88%, 82%, 90%, 50%) hex: #e0d1e680
> color name h33-c 88,82,90,100
Color 'h33-c' is opaque: rgb(88%, 82%, 90%) hex: #e0d1e6
> color name h34-t 59,35,59,50
Color 'h34-t' is 50% transparent: rgba(59%, 35%, 59%, 50%) hex: #96599680
> color name h34-c 59,35,59,100
Color 'h34-c' is opaque: rgb(59%, 35%, 59%) hex: #965996
> color name h35-t 50,22,45,50
Color 'h35-t' is 50% transparent: rgba(50%, 22%, 45%, 50%) hex: #80387380
> color name h35-c 50,22,45,100
Color 'h35-c' is opaque: rgb(50%, 22%, 45%) hex: #803873
> color name h44-t 32,54,70,50
Color 'h44-t' is 50% transparent: rgba(32%, 54%, 70%, 50%) hex: #528ab380
> color name h44-c 32,54,70,100
Color 'h44-c' is opaque: rgb(32%, 54%, 70%) hex: #528ab3
> color name aploop-t 27,0,50,50
Color 'aploop-t' is 50% transparent: rgba(27%, 0%, 50%, 50%) hex:
#45008080
> color name term16-t 40,64,64,50
Color 'term16-t' is 50% transparent: rgba(40%, 64%, 64%, 50%) hex:
#66a3a380
> color name uS3-t 48,44,57,50
Color 'uS3-t' is 50% transparent: rgba(48%, 44%, 57%, 50%) hex: #7a709180
> color name uS3-c 48,44,57,100
Color 'uS3-c' is opaque: rgb(48%, 44%, 57%) hex: #7a7091
> color name uS3-dt 40,37,57,50
Color 'uS3-dt' is 50% transparent: rgba(40%, 37%, 57%, 50%) hex:
#665e9180
> color name uS3-dc 40,37,57,100
Color 'uS3-dc' is opaque: rgb(40%, 37%, 57%) hex: #665e91
> color name uS5-t 0,50,45,50
Color 'uS5-t' is 50% transparent: rgba(0%, 50%, 45%, 50%) hex: #00807380
> color name gray-t 70,70,70,50
Color 'gray-t' is 50% transparent: rgba(70%, 70%, 70%, 50%) hex:
#b3b3b380
> color name hx84-t 50,50,50,50
Color 'hx84-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex:
#80808080
> color name hx84-c 50,50,50,100
Color 'hx84-c' is opaque: gray(50%) hex: #808080
> color name hx84-dt 30,30,30,50
Color 'hx84-dt' is 50% transparent: rgba(30%, 30%, 30%, 50%) hex:
#4d4d4d80
> color name hx84-dc 30,30,30,100
Color 'hx84-dc' is opaque: gray(30%) hex: #4d4d4d
> color name hx68-t 50,50,50,50
Color 'hx68-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex:
#80808080
> color name hx68-c 50,50,50,100
Color 'hx68-c' is opaque: gray(50%) hex: #808080
> color name hx69-t 40,40,40,50
Color 'hx69-t' is 50% transparent: rgba(40%, 40%, 40%, 50%) hex:
#66666680
> color name hx69-c 40,40,40,100
Color 'hx69-c' is opaque: gray(40%) hex: #666666
> color name hx38-t 34,42,36,50
Color 'hx38-t' is 50% transparent: rgba(34%, 42%, 36%, 50%) hex:
#576b5c80
> color name hx38-c 34,42,36,100
Color 'hx38-c' is opaque: rgb(34%, 42%, 36%) hex: #576b5c
> color name hx38-dt 34,42,36,50
Color 'hx38-dt' is 50% transparent: rgba(34%, 42%, 36%, 50%) hex:
#576b5c80
> color name hx38-dc 34,42,36,100
Color 'hx38-dc' is opaque: rgb(34%, 42%, 36%) hex: #576b5c
> color name ul5-t 55,62,67,50
Color 'ul5-t' is 50% transparent: rgba(55%, 62%, 67%, 50%) hex: #8c9eab80
> color name ul5-c 55,62,67,100
Color 'ul5-c' is opaque: rgb(55%, 62%, 67%) hex: #8c9eab
> color name ul5-dt 38,47,52,50
Color 'ul5-dt' is 50% transparent: rgba(38%, 47%, 52%, 50%) hex:
#61788580
> color name ul5-dc 38,47,52,100
Color 'ul5-dc' is opaque: rgb(38%, 47%, 52%) hex: #617885
> color name ul16-t 70,70,70,50
Color 'ul16-t' is 50% transparent: rgba(70%, 70%, 70%, 50%) hex:
#b3b3b380
> color name ul16-c 70,70,70,100
Color 'ul16-c' is opaque: gray(70%) hex: #b3b3b3
> color name srl-t 50,50,50,50
Color 'srl-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name srl-t 50,50,50,100
Color 'srl-t' is opaque: gray(50%) hex: #808080
> color name highlight-t 92,78,8,50
Color 'highlight-t' is 50% transparent: rgba(92%, 78%, 8%, 50%) hex:
#ebc71480
> color name highlight-c 92,78,8,100
Color 'highlight-c' is opaque: rgb(92%, 78%, 8%) hex: #ebc714
> color name tomato-t 100,39,28,50
Color 'tomato-t' is 50% transparent: rgba(100%, 39%, 28%, 50%) hex:
#ff634780
> color name tomato-c 100,39,28,100
Color 'tomato-c' is opaque: rgb(100%, 39%, 28%) hex: #ff6347
> color name lightgrayt 83,83,83,50
Color 'lightgrayt' is 50% transparent: rgba(83%, 83%, 83%, 50%) hex:
#d4d4d480
> color name silvert 75,75,75,50
Color 'silvert' is 50% transparent: rgba(75%, 75%, 75%, 50%) hex:
#bfbfbf80
> color name grayt 50,50,50,50
Color 'grayt' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name lightcyant 88,100,100,50
Color 'lightcyant' is 50% transparent: rgba(88%, 100%, 100%, 50%) hex:
#e0ffff80
> color name yellowt 100,90,0,50
Color 'yellowt' is 50% transparent: rgba(100%, 90%, 0%, 50%) hex:
#ffe60080
> color name deeppinkt 100,8,58,50
Color 'deeppinkt' is 50% transparent: rgba(100%, 8%, 58%, 50%) hex:
#ff149480
> color name oranget 100,65,0,50
Color 'oranget' is 50% transparent: rgba(100%, 65%, 0%, 50%) hex:
#ffa60080
> color name yellowgreent 60,80,20,50
Color 'yellowgreent' is 50% transparent: rgba(60%, 80%, 20%, 50%) hex:
#99cc3380
> color name darkmagentat 54,0,54,50
Color 'darkmagentat' is 50% transparent: rgba(54%, 0%, 54%, 50%) hex:
#8a008a80
> color name orchidt 86,44,84,50
Color 'orchidt' is 50% transparent: rgba(86%, 44%, 84%, 50%) hex:
#db70d680
> color name paleturquoiset 69,93,93,50
Color 'paleturquoiset' is 50% transparent: rgba(69%, 93%, 93%, 50%) hex:
#b0eded80
> color name pinkt 100,75,80,50
Color 'pinkt' is 50% transparent: rgba(100%, 75%, 80%, 50%) hex:
#ffbfcc80
> color name darkgreent 0,39,0,50
Color 'darkgreent' is 50% transparent: rgba(0%, 39%, 0%, 50%) hex:
#00630080
> color name limegreent 20,80,20,50
Color 'limegreent' is 50% transparent: rgba(20%, 80%, 20%, 50%) hex:
#33cc3380
> color name turquoiset 25,88,82,50
Color 'turquoiset' is 50% transparent: rgba(25%, 88%, 82%, 50%) hex:
#40e0d180
> color name tealt 0,50,50,50
Color 'tealt' is 50% transparent: rgba(0%, 50%, 50%, 50%) hex: #00808080
> color name darkoranget 100,50,0,50
Color 'darkoranget' is 50% transparent: rgba(100%, 50%, 0%, 50%) hex:
#ff800080
> color name lightyellowt 100,100,50,50
Color 'lightyellowt' is 50% transparent: rgba(100%, 100%, 50%, 50%) hex:
#ffff8080
> color name goldt 100,75,0,50
Color 'goldt' is 50% transparent: rgba(100%, 75%, 0%, 50%) hex: #ffbf0080
> color name plumt 87,63,87,50
Color 'plumt' is 50% transparent: rgba(87%, 63%, 87%, 50%) hex: #dea1de80
> color name ssubluet 68,86,90,50
Color 'ssubluet' is 50% transparent: rgba(68%, 86%, 90%, 50%) hex:
#addbe680
> color name p-prect 10,41,0,50
Color 'p-prect' is 50% transparent: rgba(10%, 41%, 0%, 50%) hex:
#1a690080
> color name p-h2t 23,59,0,50
Color 'p-h2t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
> color name p-h1t 40,73,0,50
Color 'p-h1t' is 50% transparent: rgba(40%, 73%, 0%, 50%) hex: #66ba0080
> color name p-h1c 40,73,0,100
Color 'p-h1c' is opaque: rgb(40%, 73%, 0%) hex: #66ba00
> color name p-spct 68,81,0,50
Color 'p-spct' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
> color name p-spcc 68,81,0,100
Color 'p-spcc' is opaque: rgb(68%, 81%, 0%) hex: #adcf00
> color name p-fat 82,92,0,50
Color 'p-fat' is 50% transparent: rgba(82%, 92%, 0%, 50%) hex: #d1eb0080
> color name p-postt 100,92,0,50
Color 'p-postt' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex:
#ffeb0080
> color name d-t 100,80,4,50
Color 'd-t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
> color name d-prect 95,100,50,50
Color 'd-prect' is 50% transparent: rgba(95%, 100%, 50%, 50%) hex:
#f2ff8080
> color name d-h2t 100,90,4,50
Color 'd-h2t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
> color name d-h1t 100,80,4,50
Color 'd-h1t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
> color name d-spct 100,70,4,50
Color 'd-spct' is 50% transparent: rgba(100%, 70%, 4%, 50%) hex:
#ffb30a80
> color name d-fat 100,55,4,50
Color 'd-fat' is 50% transparent: rgba(100%, 55%, 4%, 50%) hex: #ff8c0a80
> color name d-fac 100,55,4,100
Color 'd-fac' is opaque: rgb(100%, 55%, 4%) hex: #ff8c0a
> color name d-postt 100,40,4,50
Color 'd-postt' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex:
#ff660a80
> color name m-t 95,43,62,50
Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
> color name m-prect 100,85,95,50
Color 'm-prect' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex:
#ffd9f280
> color name m-h2t 100,85,95,50
Color 'm-h2t' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex:
#ffd9f280
> color name m-h1t 100,75,95,50
Color 'm-h1t' is 50% transparent: rgba(100%, 75%, 95%, 50%) hex:
#ffbff280
> color name m-spct 89,63,75,50
Color 'm-spct' is 50% transparent: rgba(89%, 63%, 75%, 50%) hex:
#e3a1bf80
> color name m-fat 95,51,75,50
Color 'm-fat' is 50% transparent: rgba(95%, 51%, 75%, 50%) hex: #f282bf80
> color name m-fac 95,51,75,100
Color 'm-fac' is opaque: rgb(95%, 51%, 75%) hex: #f282bf
> color name m-postt 95,43,62,50
Color 'm-postt' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex:
#f26e9e80
executed 70S_colors.cxc
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colorstandard.cxc
> color 100,100,100,50
> color lsu silvert
> color /3 lightgrayt
> color /5 lightgrayt
> color ssu ssu-t
> color head head-t
> color efg efg-t
> color dt d-t
> color pt p-t
> color pep p-t
> color mrna m-t
executed 70S_colorstandard.cxc
> windowsize 1000 1000
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_helices.cxc
> color h18 h18-t
> color h23 h23-t
> color h24 h24-t
> color h28 h28-t
> color h29 h29-t
> color h30 h30-t
> color h31 h31-t
> color h34 h34-t
> color h35 h35-t
> color h36 h36-t
> color h44 h44-t
> color H69 hx69-t
executed 70S_color_helices.cxc
> color h30|h36|h35 head-t
> view dc3
> surface cap true
> color zone #12.1 near #12.3,5 distance 5
> color zone #13.1 near #13.3,5 distance 5
> color zone #14.1 near #14.3,5 distance 5
> color zone #30.1 near #30.3,5 distance 5
> color zone #31.1 near #31.3,5 distance 5
> color zone #32.1 near #32.3,5 distance 5
> color zone #33.1 near #33.3,5 distance 5
> color zone #34.1 near #34.3,5 distance 5
> color zone #30.9 near #30.3,5 distance 5
> color zone #31.9 near #31.3,5 distance 5
> color zone #32.9 near #32.3,5 distance 5
> color zone #33.9 near #33.3,5 distance 5
> color zone #34.9 near #34.3,5 distance 5
> color h30|h36|h35 head-c
> color h28 h28-c
> color h29 h29-c
> color h34 h34-c
> color h23 h23-c
> color h24 h24-c
> color h31 h31-c
> hide #!100
> hide #101 models
> cartoon style nucleic xsection oval width 1.3 thickness 1.3
> transparency #*.3 0 target abc
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_helices-s.cxc
> color h18 h18-c
> color h23 h23-c
> color h24 h24-c
> color h28 h28-c
> color h29 h29-c
> color h30 h30-c
> color h31 h31-c
> color h34 h34-c
> color h35 h35-c
> color h44 h44-c
> color H69 hx69-c
executed 70S_color_helices-s.cxc
> color /v d-c
> color /y p-c
> color /w m-c
executed gtpys_dc.cxc
> surface cap true
> lighting gentle
> lighting intensity .2
> size stickRadius 0.17
Changed 1744812 bond radii
> nucribthin
> style ringFill thin
Changed 122200 residue ring styles
> graphics silhouettes true color black
> ~select
Nothing selected
> ~select
Nothing selected
> ~ribbon
> ~display
> ribbon
> ~ribbon mrna
> display mrna
> display antiplus
> display /x:505-514,584
> display /6:1492,1493,530,532,1054,1400,1397
> display /3:1913
> display #*.3/L:44
> hide models
> show #31.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_ysH1b.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_ysH1b.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #32.3,5 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_ysH1c.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_ysH1c.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #12.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_H1apo.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_H1bapo.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #33.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_ysI1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_ysI1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #34.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_I1bys.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_I1bys.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #13.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_I1spc.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_I1spc.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #14.3,5 models
> ~display #14.3/w:38,49
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_I2fa.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_I2fa.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> graphics silhouettes true color 25,25,25,15
> style ringFill thick
Changed 122200 residue ring styles
> ~cartoon /6/3
> display /6/3
> ~cartoon trna
> display trna
> volume emmaps style surface step 1 level 3
> surface dust emmaps size 2
> volume emmaps surfaceSmoothing true
> view dc3
> hide models
> show #30 models
> select #30.3
60930 atoms, 65574 bonds, 3 pseudobonds, 4887 residues, 3 models selected
> hide #30.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_ysH1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #31 models
> select #31.3
60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected
> hide #31.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_ysH1b.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #32 models
> select #32.3
60097 atoms, 64722 bonds, 4 pseudobonds, 4779 residues, 3 models selected
> hide #32.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_ysH1c.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #12 models
> select #12.3
55765 atoms, 60298 bonds, 4230 residues, 1 model selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_H1apo.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #33 models
> select #33.3
61025 atoms, 65674 bonds, 2 pseudobonds, 4898 residues, 3 models selected
> hide #33.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_ysI1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #34 models
> select #34.3
61064 atoms, 65713 bonds, 3 pseudobonds, 4898 residues, 3 models selected
> hide #34.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_I1bys.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #13 models
> select #13.3
61103 atoms, 65762 bonds, 4902 residues, 1 model selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_I1spc.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #14 models
> ~display #14.3/w:38,49
> select #14.3
60702 atoms, 65388 bonds, 1 pseudobond, 4855 residues, 2 models selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_I2fa.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> volume emmaps style surface step 1 level 8
> surface dust emmaps size 2
> volume emmaps surfaceSmoothing true
> hide models
> show #30.3,5,9 models
> select #30.3
60930 atoms, 65574 bonds, 3 pseudobonds, 4887 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysH1a-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #31.3,5,9 models
> select #31.3
60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysH1b-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #32.3,5,9 models
> select #32.3
60097 atoms, 64722 bonds, 4 pseudobonds, 4779 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysH1c-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #33.3,5,9 models
> select #33.3
61025 atoms, 65674 bonds, 2 pseudobonds, 4898 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysI1a-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #34.3,5,9 models
> select #34.3
61064 atoms, 65713 bonds, 3 pseudobonds, 4898 residues, 3 models selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_I1bys-
> FR.tif format tiff width 1000 height 1000 supersample 20
> transparentBackground true
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
——— End of log from Thu Jul 20 18:51:54 2023 ———
opened ChimeraX session
> view dc2
> view dc1
> view dc3
> view dc2
> ui tool show "Side View"
> view name dc4
> hide models
> show #13 models
> view dc1
> display efg
> ui mousemode right pivot
> volume emmaps style surface step 1 level 3
> view name dc5
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
> color efg byhetero
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
——— End of log from Mon Jul 31 14:44:45 2023 ———
opened ChimeraX session
> open /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_assign.cxc
> name atomods #*.3|#*.5
> name emmaps #*.1|#*.7|#*.8|#*.9
> name lsu #*.5
> name lsumap #*.8
> name ssu #*.3
> name ssumap #*.7
> name ligmap #*.9
> name rna /y,v,w,3,6,5
> name r23s /3
> name r16s /6
> name r5s /5
> name pt /y
> name dt /v
> name efg /x
> name pep /p
> name mrna /w
> name GSP :GSP
> name GDP :GDP
> name GTP :GTP
> name ntide :GTP|:GDP|:GSP
> name spc :SCM
> name fua :FUA
> name par :PAR
> name argb :LIG
> name drugs argb|par|fua|spc
> name D1 /x:start-293
> name D2 /x:294-410
> name D3 /x:411-489
> name D4 /x:490-612
> name D5 /x:613-end
> name sw1 /x:38-65
> name sw2 /x:89-108
> name pl /x:18-25
> name nkxd /x:142-146
> name mg /x:MG
> name trna /y,v
> name anticodon /y,v:34-36
> name antiplus /y,v:32-38
> name cca /y,v:74-76
> name astem /y,v:1-7,66-73
> name darm /y,v:8-25
> name aarm /y,v:26-43
> name varm /y,v:44-48
> name tarm /y,v:49-65
> name head #*.3/A/C/S/M/G/N/I/J/6:927-1390
> name arg-head #20.3/A/C/S/M/G/N/I/J/6:927-1390
> name post-head #15.3/A/C/S/M/G/N/I/J/6:927-1390
> name fa-head #14.3/A/C/S/M/G/N/I/J/6:927-1390
> name body #*.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name arg-body #20.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name post-body #15.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name fa-body #14.3/B/D/E/L/O/T/P/H/U/K/Q/R/F/6:start-926,1391-end
> name aploop /6:956-959
> name term16S /6:1503-end
> name aphelix /6:1228-1230
> name us2 #*.3/B
> name us3 #*.3/C
> name us4 #*.3/D
> name us5 #*.3/E
> name us6 #*.3/F
> name us7 #*.3/G
> name us8 #*.3/H
> name us9 #*.3/I
> name us10 #*.3/J
> name us11 #*.3/K
> name us12 #*.3/L
> name us13 #*.3/M
> name us14 #*.3/N
> name us15 #*.3/O
> name us16 #*.3/P
> name us17 #*.3/Q
> name us18 #*.3/R
> name us19 #*.3/S
> name us20 #*.3/T
> name us21 #*.3/U
> name us9-130 #*.3/I:130
> name l1stalk /3:2097-2191
> name srl /3:2652-2668
> name asf /3:863-910
> name l1stalk /3:2094-2195
> name ul1 #*.5/A
> name ul2 #*.5/B
> name ul3 #*.5/C
> name ul4 #*.5/D
> name ul5 #*.5/E
> name ul6 #*.5/F
> name ul7 #*.5/G
> name ul9 #*.5/I
> name ul10 #*.5/J
> name ul11 #*.5/K
> name ul13 #*.5/M
> name ul14 #*.5/N
> name ul15 #*.5/O
> name ul16 #*.5/P
> name ul17 #*.5/Q
> name ul18 #*.5/R
> name ul19 #*.5/S
> name ul20 #*.5/T
> name ul21 #*.5/U
> name ul22 #*.5/V
> name ul23 #*.5/W
> name ul24 #*.5/X
> name ul25 #*.5/Y
> name ul27 #*.5/a
> name ul28 #*.5/b
> name ul29 #*.5/c
> name ul30 #*.5/d
> name ul31 #*.5/e
> name ul32 #*.5/f
> name ul33 #*.5/g
> name ul34 #*.5/h
> name ul35 #*.5/i
> name ul36 #*.5/j
> name h1 #*.3/6:9-13|#*.3/6:21-25
> name h2 #*.3/6:17-19|#*.3/6:916-918
> name h3 #*.3/6:27-37|#*.3/6:547-556
> name h4 #*.3/6:39-46|#*.3/6:395-403
> name h5 #*.3/6:47-58|#*.3/6:354-360
> name h6 #*.3/6:61-106
> name h7 #*.3/6:122-142|#*.3/6:221-239
> name h8 #*.3/6:144-178
> name h9 #*.3/6:184-193
> name h10 #*.3/6:198-219
> name h11 #*.3/6:240-286
> name h12 #*.3/6:289-311
> name h13 #*.3/6:316-337
> name h14 #*.3/6:339-350
> name h15 #*.3/6:367-393
> name h16 #*.3/6:406-436
> name h17 #*.3/6:437-497
> name h18 #*.3/6:500-545
> name h19 #*.3/6:567-569|#*.3/6:881-88
> name h20 #*.3/6:577-586|#*.3/6:755-76
> name h21 #*.3/6:588-651
> name h22 #*.3/6:654-672|#*.3/6:734-75
> name h23 #*.3/6:673-733
> name h24 #*.3/6:769-810
> name h25 #*.3/6:821-827|#*.3/6:873-87
> name h26 #*.3/6:829-857
> name h26a #*.3/6:861-868
> name h27 #*.3/6:885-912
> name h28 #*.3/6:921-937|#*.3/6:1379-1400
> name h29 #*.3/6:938-943|#*.3/6:1337-1346
> name h30 #*.3/6:945-955|#*.3/6:1225-1236
> name h31 #*.3/6:956-975
> name h32 #*.3/6:984-991|#*.3/6:1212-1221
> name h33 #*.3/6:992-1045
> name h34 #*.3/6:1045-1065|#*.3/6:1188-1211
> name h35 #*.3/6:1066-1073|#*.3/6:1102-1110
> name h36 #*.3/6:1074-1083
> name h37 #*.3/6:1086-1099
> name h38 #*.3/6:1113-1117|#*.3/6:1183-1187
> name h39 #*.3/6:1118-1155
> name h40 #*.3/6:1161-1175
> name h41 #*.3/6:1241-1296
> name h42 #*.3/6:1303-1334
> name h43 #*.3/6:1350-1372
> name h44 #*.3/6:1401-1502
> name h45 #*.3/6:1506-1529
> name H1 #*.5/3:1-8|#*.5/3:2895-2904
> name H2 #*.5/3:15-24|#*.5/3:516-525
> name H3 #*.5/3:31-32|#*.5/3:473-474
> name H4 #*.5/3:35-45|#*.5/3:433-445
> name H5 #*.5/3:54-57|#*.5/3:114-117
> name H6 #*.5/3:58-69
> name H7 #*.5/3:75-110
> name H8 #*.5/3:121-130
> name H9 #*.5/3:131-148
> name H10 #*.5/3:150-176
> name H11 #*.5/3:183-213
> name H12 #*.5/3:224-231
> name H13 #*.5/3:235-262
> name H14 #*.5/3:265-268|#*.5/3:424-427
> name H16 #*.5/3:271-274|#*.5/3:363-366
> name H18 #*.5/3:281-297|#*.5/3:341-359
> name H19 #*.5/3:301-316
> name H20 #*.5/3:325-337
> name H21 #*.5/3:375-399
> name H22 #*.5/3:406-421
> name H23 #*.5/3:461-468
> name H24 #*.5/3:484-496
> name H25 #*.5/3:533-560
> name H26 #*.5/3:579-584|#*.5/3:1256-1261
> name H27 #*.5/3:589-601|#*.5/3:656-668
> name H28 #*.5/3:604-624
> name H29 #*.5/3:628-635
> name H31 #*.5/3:637-651
> name H32 #*.5/3:678-683|#*.5/3:794-799
> name H33 #*.5/3:687-698|#*.5/3:763-775
> name H34 #*.5/3:700-732
> name H35 #*.5/3:736-760
> name H35a #*.5/3:777-787
> name H36 #*.5/3:812-817|#*.5/3:1190-1195
> name H37 #*.5/3:822-835
> name H38 #*.5/3:838-940
> name H39 #*.5/3:946-971
> name H40 #*.5/3:976-987
> name H41 #*.5/3:991-1018|#*.5/3:1144-1163
> name H42 #*.5/3:1030-1055|#*.5/3:1104-1124
> name H43 #*.5/3:1057-1081
> name H44 #*.5/3:1087-1102
> name H45 #*.5/3:1164-1185
> name H46 #*.5/3:1198-1247
> name H47 #*.5/3:1276-1294
> name H48 #*.5/3:1295-1298|#*.5/3:1642-1646
> name H49 #*.5/3:1303-1306|#*.5/3:1622-1625
> name H50 #*.5/3:1314-1338
> name H51 #*.5/3:1345-1348|#*.5/3:1598-1601
> name H52 #*.5/3:1350-1381
> name H53 #*.5/3:1385-1402
> name H54 #*.5/3:1405-1417|#*.5/3:1581-1597
> name H55 #*.5/3:1420-1424|#*.5/3:1573-1578
> name H56 #*.5/3:1429-1444|#*.5/3:1547-1564
> name H57 #*.5/3:1445-1466
> name H58 #*.5/3:1467-1525
> name H59 #*.5/3:1527-1544
> name H60 #*.5/3:1627-1639
> name H61 #*.5/3:1647-1669|#*.5/3:1991-2009
> name H62 #*.5/3:1682-1706
> name H63 #*.5/3:1707-1751
> name H64 #*.5/3:1764-1772|#*.5/3:1979-1988
> name H65 #*.5/3:1775-1789
> name H66 #*.5/3:1792-1827
> name H67 #*.5/3:1830-1833|#*.5/3:1972-1975
> name H68 #*.5/3:1835-1905
> name H69 #*.5/3:1906-1924
> name H71 #*.5/3:1945-1960
> name H72 #*.5/3:2023-2040
> name H73 #*.5/3:2043-2057|#*.5/3:2611-2625
> name H74 #*.5/3:2064-2075|#*.5/3:2434-2446
> name H75 #*.5/3:2077-2090|#*.5/3:2229-2243
> name H76 #*.5/3:2093-2110|#*.5/3:2179-2196
> name H77 #*.5/3:2120-2124|#*.5/3:2174-2178
> name H78 #*.5/3:2127-2161
> name H79 #*.5/3:2200-2223
> name H80 #*.5/3:2246-2258
> name H81 #*.5/3:2259-2281
> name H82 #*.5/3:2284-2285|#*.5/3:2383-2384
> name H83 #*.5/3:2288-2295|#*.5/3:2337-2344
> name H84 #*.5/3:2296-2322
> name H85 #*.5/3:2323-2332
> name H86 #*.5/3:2347-2370
> name H87 #*.5/3:2372-2381
> name H88 #*.5/3:2395-2421
> name H89 #*.5/3:2453-2498
> name H90 #*.5/3:2507-2517|#*.5/3:2567-2582
> name H91 #*.5/3:2520-2545
> name H92 #*.5/3:2547-2561
> name H93 #*.5/3:2588-2606
> name H94 #*.5/3:2630-2643|#*.5/3:2771-2788
> name H95 #*.5/3:2646-2674
> name H96 #*.5/3:2675-2732
> name H97 #*.5/3:2735-2769
> name H98 #*.5/3:2791-2805
> name H99 #*.5/3:2811-2814|#*.5/3:2886-2889
> name H100 #*.5/3:2815-2831
executed 70S_assign.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/startup/70S_display.cxc
> alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6;
> alias nucribthin cartoon style nucleic xsect oval width 1.2 thick 1.2;
> alias cylinders cartoon style protein modeh tube rad 2 sides 24;
> alias licorice car style protein modeh default arrows f xsect oval
width
1
> thick 1;
> dssp
> windowsize 1000 1000
> set bgColor white
> lighting full
> set silhouettes true
> set silhouetteWidth 1.7
> set silhouettes true
> set silhouetteDepthJump 0.02
> cartoon style width 2.5
> size atomRadius 2
Changed 1614330 atom radii
> nucleotides fill
> size ions atomRadius 1.6
Changed 31 atom radii
> size stickRadius 0.1
Changed 1744812 bond radii
> style stick ringFill thin
Changed 1614330 atom styles, 122200 residue ring styles
> show ribbons
> hide H
> hide :HOH
> hide target a
> show nucleic target a
> show drugs target a
> style drugs ball
Changed 106 atom styles
> graphics selection color black
> cartoon style protein xsection round width 2 thickness 0.6
> cartoon style modeHelix wrap
> cartoon style sides 24
> cartoon style strand xsection oval arrows false
> cartoon suppressBackboneDisplay true
> alias thinbois style ball;size ballscale 0.09; size stickradius 0.13;
> alias thickbois style stick;size stickradius 0.4;style stick ringFill
thick;
> volume emmaps style surface step 1 level 4
> surface dust emmaps size 3
> volume surfaceSmoothing true
> cartoon tether trna shape cone opacity 1
> dssp
> thickbois
Changed 1614330 atom styles
Changed 1744812 bond radii
Changed 1614330 atom styles, 122200 residue ring styles
executed 70S_display.cxc
> open /data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colors.cxc
> color name efg-t 100,0,0,50
Color 'efg-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
> color name sw1-t 100,92,0,50
Color 'sw1-t' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex: #ffeb0080
> color name sw2-t 68,81,0,50
Color 'sw2-t' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
> color name pl-t 23,59,0,50
Color 'pl-t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
> color name d1-t 100,18,4,50
Color 'd1-t' is 50% transparent: rgba(100%, 18%, 4%, 50%) hex: #ff2e0a80
> color name d2-t 100,40,4,50
Color 'd2-t' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex: #ff660a80
> color name d3-t 100,27,36,50
Color 'd3-t' is 50% transparent: rgba(100%, 27%, 36%, 50%) hex: #ff455c80
> color name d4-t 80,0,23,50
Color 'd4-t' is 50% transparent: rgba(80%, 0%, 23%, 50%) hex: #cc003b80
> color name d5-t 100,60,4,50
Color 'd5-t' is 50% transparent: rgba(100%, 60%, 4%, 50%) hex: #ff990a80
> color name fa-t 100,90,4,50
Color 'fa-t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
> color name gtp-t 45,53,60,50
Color 'gtp-t' is 50% transparent: rgba(45%, 53%, 60%, 50%) hex: #73879980
> color name mg-t 1,39,16,50
Color 'mg-t' is 50% transparent: rgba(1%, 39%, 16%, 50%) hex: #03632980
> color name spc-t 100,0,0,50
Color 'spc-t' is 50% transparent: rgba(100%, 0%, 0%, 50%) hex: #ff000080
> color name argb-t 50,0,50,50
Color 'argb-t' is 50% transparent: rgba(50%, 0%, 50%, 50%) hex: #80008080
> color name g-1t 98,42,30,50
Color 'g-1t' is 50% transparent: rgba(98%, 42%, 30%, 50%) hex: #fa6b4d80
> color name g-2t 95,35,25,50
Color 'g-2t' is 50% transparent: rgba(95%, 35%, 25%, 50%) hex: #f2594080
> color name g-3t 92,28,20,50
Color 'g-3t' is 50% transparent: rgba(92%, 28%, 20%, 50%) hex: #eb473380
> color name g-4t 89,21,15,50
Color 'g-4t' is 50% transparent: rgba(89%, 21%, 15%, 50%) hex: #e3362680
> color name g-5t 86,14,10,50
Color 'g-5t' is 50% transparent: rgba(86%, 14%, 10%, 50%) hex: #db241a80
> color name g-6t 83,7,5,50
Color 'g-6t' is 50% transparent: rgba(83%, 7%, 5%, 50%) hex: #d4120d80
> color name g-7t 80,0,0,50
Color 'g-7t' is 50% transparent: rgba(80%, 0%, 0%, 50%) hex: #cc000080
> color name p-t 44,59,2,50
Color 'p-t' is 50% transparent: rgba(44%, 59%, 2%, 50%) hex: #70960580
> color name p-c 44,59,2,100
Color 'p-c' is opaque: rgb(44%, 59%, 2%) hex: #709605
> color name p-1t 4,34,1,50
Color 'p-1t' is 50% transparent: rgba(4%, 34%, 1%, 50%) hex: #0a570380
> color name p-2t 12,39,1,50
Color 'p-2t' is 50% transparent: rgba(12%, 39%, 1%, 50%) hex: #1f630380
> color name p-3t 20,44,1,50
Color 'p-3t' is 50% transparent: rgba(20%, 44%, 1%, 50%) hex: #33700380
> color name p-4t 28,49,1,50
Color 'p-4t' is 50% transparent: rgba(28%, 49%, 1%, 50%) hex: #477d0380
> color name p-5t 36,54,2,50
Color 'p-5t' is 50% transparent: rgba(36%, 54%, 2%, 50%) hex: #5c8a0580
> color name p-6t 44,59,2,50
Color 'p-6t' is 50% transparent: rgba(44%, 59%, 2%, 50%) hex: #70960580
> color name p-7t 52,64,2,50
Color 'p-7t' is 50% transparent: rgba(52%, 64%, 2%, 50%) hex: #85a30580
> color name p-8t 60,69,2,50
Color 'p-8t' is 50% transparent: rgba(60%, 69%, 2%, 50%) hex: #99b00580
> color name p-9t 68,74,3,50
Color 'p-9t' is 50% transparent: rgba(68%, 74%, 3%, 50%) hex: #adbd0880
> color name p-10t 76,79,3,50
Color 'p-10t' is 50% transparent: rgba(76%, 79%, 3%, 50%) hex: #c2c90880
> color name p-11t 84,84,3,50
Color 'p-11t' is 50% transparent: rgba(84%, 84%, 3%, 50%) hex: #d6d60880
> color name d-t 100,65,4,50
Color 'd-t' is 50% transparent: rgba(100%, 65%, 4%, 50%) hex: #ffa60a80
> color name d-c 100,65,4,100
Color 'd-c' is opaque: rgb(100%, 65%, 4%) hex: #ffa60a
> color name d-1t 100,100,4,50
Color 'd-1t' is 50% transparent: rgba(100%, 100%, 4%, 50%) hex: #ffff0a80
> color name d-2t 100,93,4,50
Color 'd-2t' is 50% transparent: rgba(100%, 93%, 4%, 50%) hex: #ffed0a80
> color name d-3t 100,86,4,50
Color 'd-3t' is 50% transparent: rgba(100%, 86%, 4%, 50%) hex: #ffdb0a80
> color name d-4t 100,79,4,50
Color 'd-4t' is 50% transparent: rgba(100%, 79%, 4%, 50%) hex: #ffc90a80
> color name d-5t 100,72,4,50
Color 'd-5t' is 50% transparent: rgba(100%, 72%, 4%, 50%) hex: #ffb80a80
> color name d-6t 100,65,4,50
Color 'd-6t' is 50% transparent: rgba(100%, 65%, 4%, 50%) hex: #ffa60a80
> color name d-7t 100,58,4,50
Color 'd-7t' is 50% transparent: rgba(100%, 58%, 4%, 50%) hex: #ff940a80
> color name d-8t 100,51,4,50
Color 'd-8t' is 50% transparent: rgba(100%, 51%, 4%, 50%) hex: #ff820a80
> color name d-9t 100,44,4,50
Color 'd-9t' is 50% transparent: rgba(100%, 44%, 4%, 50%) hex: #ff700a80
> color name d-10t 100,37,4,50
Color 'd-10t' is 50% transparent: rgba(100%, 37%, 4%, 50%) hex: #ff5e0a80
> color name d-11t 100,30,4,50
Color 'd-11t' is 50% transparent: rgba(100%, 30%, 4%, 50%) hex: #ff4d0a80
> color name m-t 95,43,62,50
Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
> color name m-c 95,43,62,100
Color 'm-c' is opaque: rgb(95%, 43%, 62%) hex: #f26e9e
> color name m-1t 100,80,90,50
Color 'm-1t' is 50% transparent: rgba(100%, 80%, 90%, 50%) hex: #ffcce680
> color name m-2t 98,76,87,50
Color 'm-2t' is 50% transparent: rgba(98%, 76%, 87%, 50%) hex: #fac2de80
> color name m-3t 96,72,84,50
Color 'm-3t' is 50% transparent: rgba(96%, 72%, 84%, 50%) hex: #f5b8d680
> color name m-4t 94,68,81,50
Color 'm-4t' is 50% transparent: rgba(94%, 68%, 81%, 50%) hex: #f0adcf80
> color name m-5t 92,64,78,50
Color 'm-5t' is 50% transparent: rgba(92%, 64%, 78%, 50%) hex: #eba3c780
> color name m-6t 90,60,75,50
Color 'm-6t' is 50% transparent: rgba(90%, 60%, 75%, 50%) hex: #e699bf80
> color name m-7t 88,56,72,50
Color 'm-7t' is 50% transparent: rgba(88%, 56%, 72%, 50%) hex: #e08fb880
> color name m-8t 86,52,69,50
Color 'm-8t' is 50% transparent: rgba(86%, 52%, 69%, 50%) hex: #db85b080
> color name m-9t 84,48,66,50
Color 'm-9t' is 50% transparent: rgba(84%, 48%, 66%, 50%) hex: #d67aa880
> color name m-10t 82,44,63,50
Color 'm-10t' is 50% transparent: rgba(82%, 44%, 63%, 50%) hex: #d170a180
> color name m-11t 80,40,60,50
Color 'm-11t' is 50% transparent: rgba(80%, 40%, 60%, 50%) hex: #cc669980
> color name head-t 82,74,84,50
Color 'head-t' is 50% transparent: rgba(82%, 74%, 84%, 50%) hex:
#d1bdd680
> color name head-c 82,74,84,100
Color 'head-c' is opaque: rgb(82%, 74%, 84%) hex: #d1bdd6
> color name headfa-t 54,41,54,50
Color 'headfa-t' is 50% transparent: rgba(54%, 41%, 54%, 50%) hex:
#8a698a80
> color name headblue-t 59,78,94,50
Color 'headblue-t' is 50% transparent: rgba(59%, 78%, 94%, 50%) hex:
#96c7f080
> color name headh1-t 41,64,100,50
Color 'headh1-t' is 50% transparent: rgba(41%, 64%, 100%, 50%) hex:
#69a3ff80
> color name headh2-t 50,70,100,50
Color 'headh2-t' is 50% transparent: rgba(50%, 70%, 100%, 50%) hex:
#80b3ff80
> color name headgray-t 60,60,60,50
Color 'headgray-t' is 50% transparent: rgba(60%, 60%, 60%, 50%) hex:
#99999980
> color name darkhead-s 54,41,54,100
Color 'darkhead-s' is opaque: rgb(54%, 41%, 54%) hex: #8a698a
> color name bodywhite-t 90,90,90,50
Color 'bodywhite-t' is 50% transparent: rgba(90%, 90%, 90%, 50%) hex:
#e6e6e680
> color name rps-t 75,88,93,50
Color 'rps-t' is 50% transparent: rgba(75%, 88%, 93%, 50%) hex: #bfe0ed80
> color name ssu-t 69,79,82,50
Color 'ssu-t' is 50% transparent: rgba(69%, 79%, 82%, 50%) hex: #b0c9d180
> color name ssu-c 69,79,82,100
Color 'ssu-c' is opaque: rgb(69%, 79%, 82%) hex: #b0c9d1
> color name h16-t 79,85,89,50
Color 'h16-t' is 50% transparent: rgba(79%, 85%, 89%, 50%) hex: #c9d9e380
> color name h16-c 79,85,89,100
Color 'h16-c' is opaque: rgb(79%, 85%, 89%) hex: #c9d9e3
> color name h18-t 31,59,68,50
Color 'h18-t' is 50% transparent: rgba(31%, 59%, 68%, 50%) hex: #4f96ad80
> color name h18-dt 6,47,62,50
Color 'h18-dt' is 50% transparent: rgba(6%, 47%, 62%, 50%) hex: #0f789e80
> color name h18-dc 6,47,62,100
Color 'h18-dc' is opaque: rgb(6%, 47%, 62%) hex: #0f789e
> color name h18-c 31,59,68,100
Color 'h18-c' is opaque: rgb(31%, 59%, 68%) hex: #4f96ad
> color name h23-t 40,61,80,50
Color 'h23-t' is 50% transparent: rgba(40%, 61%, 80%, 50%) hex: #669ccc80
> color name h23-c 40,61,80,100
Color 'h23-c' is opaque: rgb(40%, 61%, 80%) hex: #669ccc
> color name h24-t 50,70,90,50
Color 'h24-t' is 50% transparent: rgba(50%, 70%, 90%, 50%) hex: #80b3e680
> color name h24-c 50,70,90,100
Color 'h24-c' is opaque: rgb(50%, 70%, 90%) hex: #80b3e6
> color name h28-t 21,27,56,50
Color 'h28-t' is 50% transparent: rgba(21%, 27%, 56%, 50%) hex: #36458f80
> color name h28-c 21,27,56,100
Color 'h28-c' is opaque: rgb(21%, 27%, 56%) hex: #36458f
> color name h29-t 80,69,92,50
Color 'h29-t' is 50% transparent: rgba(80%, 69%, 92%, 50%) hex: #ccb0eb80
> color name h29-c 80,69,92,100
Color 'h29-c' is opaque: rgb(80%, 69%, 92%) hex: #ccb0eb
> color name h30-t 40,40,59,50
Color 'h30-t' is 50% transparent: rgba(40%, 40%, 59%, 50%) hex: #66669680
> color name h30-c 40,40,59,100
Color 'h30-c' is opaque: rgb(40%, 40%, 59%) hex: #666696
> color name h31-t 45,35,55,50
Color 'h31-t' is 50% transparent: rgba(45%, 35%, 55%, 50%) hex: #73598c80
> color name h31-c 45,35,55,100
Color 'h31-c' is opaque: rgb(45%, 35%, 55%) hex: #73598c
> color name h32-t 75,62,79,50
Color 'h32-t' is 50% transparent: rgba(75%, 62%, 79%, 50%) hex: #bf9ec980
> color name h32-c 75,62,79,100
Color 'h32-c' is opaque: rgb(75%, 62%, 79%) hex: #bf9ec9
> color name h33-t 88,82,90,50
Color 'h33-t' is 50% transparent: rgba(88%, 82%, 90%, 50%) hex: #e0d1e680
> color name h33-c 88,82,90,100
Color 'h33-c' is opaque: rgb(88%, 82%, 90%) hex: #e0d1e6
> color name h34-t 59,35,59,50
Color 'h34-t' is 50% transparent: rgba(59%, 35%, 59%, 50%) hex: #96599680
> color name h34-c 59,35,59,100
Color 'h34-c' is opaque: rgb(59%, 35%, 59%) hex: #965996
> color name h35-t 50,22,45,50
Color 'h35-t' is 50% transparent: rgba(50%, 22%, 45%, 50%) hex: #80387380
> color name h35-c 50,22,45,100
Color 'h35-c' is opaque: rgb(50%, 22%, 45%) hex: #803873
> color name h44-t 32,54,70,50
Color 'h44-t' is 50% transparent: rgba(32%, 54%, 70%, 50%) hex: #528ab380
> color name h44-c 32,54,70,100
Color 'h44-c' is opaque: rgb(32%, 54%, 70%) hex: #528ab3
> color name aploop-t 27,0,50,50
Color 'aploop-t' is 50% transparent: rgba(27%, 0%, 50%, 50%) hex:
#45008080
> color name term16-t 40,64,64,50
Color 'term16-t' is 50% transparent: rgba(40%, 64%, 64%, 50%) hex:
#66a3a380
> color name uS3-t 48,44,57,50
Color 'uS3-t' is 50% transparent: rgba(48%, 44%, 57%, 50%) hex: #7a709180
> color name uS3-c 48,44,57,100
Color 'uS3-c' is opaque: rgb(48%, 44%, 57%) hex: #7a7091
> color name uS3-dt 40,37,57,50
Color 'uS3-dt' is 50% transparent: rgba(40%, 37%, 57%, 50%) hex:
#665e9180
> color name uS3-dc 40,37,57,100
Color 'uS3-dc' is opaque: rgb(40%, 37%, 57%) hex: #665e91
> color name uS5-t 0,50,45,50
Color 'uS5-t' is 50% transparent: rgba(0%, 50%, 45%, 50%) hex: #00807380
> color name gray-t 70,70,70,50
Color 'gray-t' is 50% transparent: rgba(70%, 70%, 70%, 50%) hex:
#b3b3b380
> color name hx84-t 50,50,50,50
Color 'hx84-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex:
#80808080
> color name hx84-c 50,50,50,100
Color 'hx84-c' is opaque: gray(50%) hex: #808080
> color name hx84-dt 30,30,30,50
Color 'hx84-dt' is 50% transparent: rgba(30%, 30%, 30%, 50%) hex:
#4d4d4d80
> color name hx84-dc 30,30,30,100
Color 'hx84-dc' is opaque: gray(30%) hex: #4d4d4d
> color name hx68-t 50,50,50,50
Color 'hx68-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex:
#80808080
> color name hx68-c 50,50,50,100
Color 'hx68-c' is opaque: gray(50%) hex: #808080
> color name hx69-t 40,40,40,50
Color 'hx69-t' is 50% transparent: rgba(40%, 40%, 40%, 50%) hex:
#66666680
> color name hx69-c 40,40,40,100
Color 'hx69-c' is opaque: gray(40%) hex: #666666
> color name hx38-t 34,42,36,50
Color 'hx38-t' is 50% transparent: rgba(34%, 42%, 36%, 50%) hex:
#576b5c80
> color name hx38-c 34,42,36,100
Color 'hx38-c' is opaque: rgb(34%, 42%, 36%) hex: #576b5c
> color name hx38-dt 34,42,36,50
Color 'hx38-dt' is 50% transparent: rgba(34%, 42%, 36%, 50%) hex:
#576b5c80
> color name hx38-dc 34,42,36,100
Color 'hx38-dc' is opaque: rgb(34%, 42%, 36%) hex: #576b5c
> color name ul5-t 55,62,67,50
Color 'ul5-t' is 50% transparent: rgba(55%, 62%, 67%, 50%) hex: #8c9eab80
> color name ul5-c 55,62,67,100
Color 'ul5-c' is opaque: rgb(55%, 62%, 67%) hex: #8c9eab
> color name ul5-dt 38,47,52,50
Color 'ul5-dt' is 50% transparent: rgba(38%, 47%, 52%, 50%) hex:
#61788580
> color name ul5-dc 38,47,52,100
Color 'ul5-dc' is opaque: rgb(38%, 47%, 52%) hex: #617885
> color name ul16-t 70,70,70,50
Color 'ul16-t' is 50% transparent: rgba(70%, 70%, 70%, 50%) hex:
#b3b3b380
> color name ul16-c 70,70,70,100
Color 'ul16-c' is opaque: gray(70%) hex: #b3b3b3
> color name srl-t 50,50,50,50
Color 'srl-t' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name srl-t 50,50,50,100
Color 'srl-t' is opaque: gray(50%) hex: #808080
> color name highlight-t 92,78,8,50
Color 'highlight-t' is 50% transparent: rgba(92%, 78%, 8%, 50%) hex:
#ebc71480
> color name highlight-c 92,78,8,100
Color 'highlight-c' is opaque: rgb(92%, 78%, 8%) hex: #ebc714
> color name tomato-t 100,39,28,50
Color 'tomato-t' is 50% transparent: rgba(100%, 39%, 28%, 50%) hex:
#ff634780
> color name tomato-c 100,39,28,100
Color 'tomato-c' is opaque: rgb(100%, 39%, 28%) hex: #ff6347
> color name lightgrayt 83,83,83,50
Color 'lightgrayt' is 50% transparent: rgba(83%, 83%, 83%, 50%) hex:
#d4d4d480
> color name silvert 75,75,75,50
Color 'silvert' is 50% transparent: rgba(75%, 75%, 75%, 50%) hex:
#bfbfbf80
> color name grayt 50,50,50,50
Color 'grayt' is 50% transparent: rgba(50%, 50%, 50%, 50%) hex: #80808080
> color name lightcyant 88,100,100,50
Color 'lightcyant' is 50% transparent: rgba(88%, 100%, 100%, 50%) hex:
#e0ffff80
> color name yellowt 100,90,0,50
Color 'yellowt' is 50% transparent: rgba(100%, 90%, 0%, 50%) hex:
#ffe60080
> color name deeppinkt 100,8,58,50
Color 'deeppinkt' is 50% transparent: rgba(100%, 8%, 58%, 50%) hex:
#ff149480
> color name oranget 100,65,0,50
Color 'oranget' is 50% transparent: rgba(100%, 65%, 0%, 50%) hex:
#ffa60080
> color name yellowgreent 60,80,20,50
Color 'yellowgreent' is 50% transparent: rgba(60%, 80%, 20%, 50%) hex:
#99cc3380
> color name darkmagentat 54,0,54,50
Color 'darkmagentat' is 50% transparent: rgba(54%, 0%, 54%, 50%) hex:
#8a008a80
> color name orchidt 86,44,84,50
Color 'orchidt' is 50% transparent: rgba(86%, 44%, 84%, 50%) hex:
#db70d680
> color name paleturquoiset 69,93,93,50
Color 'paleturquoiset' is 50% transparent: rgba(69%, 93%, 93%, 50%) hex:
#b0eded80
> color name pinkt 100,75,80,50
Color 'pinkt' is 50% transparent: rgba(100%, 75%, 80%, 50%) hex:
#ffbfcc80
> color name darkgreent 0,39,0,50
Color 'darkgreent' is 50% transparent: rgba(0%, 39%, 0%, 50%) hex:
#00630080
> color name limegreent 20,80,20,50
Color 'limegreent' is 50% transparent: rgba(20%, 80%, 20%, 50%) hex:
#33cc3380
> color name turquoiset 25,88,82,50
Color 'turquoiset' is 50% transparent: rgba(25%, 88%, 82%, 50%) hex:
#40e0d180
> color name tealt 0,50,50,50
Color 'tealt' is 50% transparent: rgba(0%, 50%, 50%, 50%) hex: #00808080
> color name darkoranget 100,50,0,50
Color 'darkoranget' is 50% transparent: rgba(100%, 50%, 0%, 50%) hex:
#ff800080
> color name lightyellowt 100,100,50,50
Color 'lightyellowt' is 50% transparent: rgba(100%, 100%, 50%, 50%) hex:
#ffff8080
> color name goldt 100,75,0,50
Color 'goldt' is 50% transparent: rgba(100%, 75%, 0%, 50%) hex: #ffbf0080
> color name plumt 87,63,87,50
Color 'plumt' is 50% transparent: rgba(87%, 63%, 87%, 50%) hex: #dea1de80
> color name ssubluet 68,86,90,50
Color 'ssubluet' is 50% transparent: rgba(68%, 86%, 90%, 50%) hex:
#addbe680
> color name p-prect 10,41,0,50
Color 'p-prect' is 50% transparent: rgba(10%, 41%, 0%, 50%) hex:
#1a690080
> color name p-h2t 23,59,0,50
Color 'p-h2t' is 50% transparent: rgba(23%, 59%, 0%, 50%) hex: #3b960080
> color name p-h1t 40,73,0,50
Color 'p-h1t' is 50% transparent: rgba(40%, 73%, 0%, 50%) hex: #66ba0080
> color name p-h1c 40,73,0,100
Color 'p-h1c' is opaque: rgb(40%, 73%, 0%) hex: #66ba00
> color name p-spct 68,81,0,50
Color 'p-spct' is 50% transparent: rgba(68%, 81%, 0%, 50%) hex: #adcf0080
> color name p-spcc 68,81,0,100
Color 'p-spcc' is opaque: rgb(68%, 81%, 0%) hex: #adcf00
> color name p-fat 82,92,0,50
Color 'p-fat' is 50% transparent: rgba(82%, 92%, 0%, 50%) hex: #d1eb0080
> color name p-postt 100,92,0,50
Color 'p-postt' is 50% transparent: rgba(100%, 92%, 0%, 50%) hex:
#ffeb0080
> color name d-t 100,80,4,50
Color 'd-t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
> color name d-prect 95,100,50,50
Color 'd-prect' is 50% transparent: rgba(95%, 100%, 50%, 50%) hex:
#f2ff8080
> color name d-h2t 100,90,4,50
Color 'd-h2t' is 50% transparent: rgba(100%, 90%, 4%, 50%) hex: #ffe60a80
> color name d-h1t 100,80,4,50
Color 'd-h1t' is 50% transparent: rgba(100%, 80%, 4%, 50%) hex: #ffcc0a80
> color name d-spct 100,70,4,50
Color 'd-spct' is 50% transparent: rgba(100%, 70%, 4%, 50%) hex:
#ffb30a80
> color name d-fat 100,55,4,50
Color 'd-fat' is 50% transparent: rgba(100%, 55%, 4%, 50%) hex: #ff8c0a80
> color name d-fac 100,55,4,100
Color 'd-fac' is opaque: rgb(100%, 55%, 4%) hex: #ff8c0a
> color name d-postt 100,40,4,50
Color 'd-postt' is 50% transparent: rgba(100%, 40%, 4%, 50%) hex:
#ff660a80
> color name m-t 95,43,62,50
Color 'm-t' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex: #f26e9e80
> color name m-prect 100,85,95,50
Color 'm-prect' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex:
#ffd9f280
> color name m-h2t 100,85,95,50
Color 'm-h2t' is 50% transparent: rgba(100%, 85%, 95%, 50%) hex:
#ffd9f280
> color name m-h1t 100,75,95,50
Color 'm-h1t' is 50% transparent: rgba(100%, 75%, 95%, 50%) hex:
#ffbff280
> color name m-spct 89,63,75,50
Color 'm-spct' is 50% transparent: rgba(89%, 63%, 75%, 50%) hex:
#e3a1bf80
> color name m-fat 95,51,75,50
Color 'm-fat' is 50% transparent: rgba(95%, 51%, 75%, 50%) hex: #f282bf80
> color name m-fac 95,51,75,100
Color 'm-fac' is opaque: rgb(95%, 51%, 75%) hex: #f282bf
> color name m-postt 95,43,62,50
Color 'm-postt' is 50% transparent: rgba(95%, 43%, 62%, 50%) hex:
#f26e9e80
executed 70S_colors.cxc
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_colorstandard.cxc
> color 100,100,100,50
> color lsu silvert
> color /3 lightgrayt
> color /5 lightgrayt
> color ssu ssu-t
> color head head-t
> color efg efg-t
> color dt d-t
> color pt p-t
> color pep p-t
> color mrna m-t
executed 70S_colorstandard.cxc
> windowsize 1000 1000
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_helices.cxc
> color h18 h18-t
> color h23 h23-t
> color h24 h24-t
> color h28 h28-t
> color h29 h29-t
> color h30 h30-t
> color h31 h31-t
> color h34 h34-t
> color h35 h35-t
> color h36 h36-t
> color h44 h44-t
> color H69 hx69-t
executed 70S_color_helices.cxc
> color h30|h36|h35 head-t
> view dc3
> surface cap true
> color zone #12.1 near #12.3,5 distance 5
> color zone #13.1 near #13.3,5 distance 5
> color zone #14.1 near #14.3,5 distance 5
> color zone #30.1 near #30.3,5 distance 5
> color zone #31.1 near #31.3,5 distance 5
> color zone #32.1 near #32.3,5 distance 5
> color zone #33.1 near #33.3,5 distance 5
> color zone #34.1 near #34.3,5 distance 5
> color zone #30.9 near #30.3,5 distance 5
> color zone #31.9 near #31.3,5 distance 5
> color zone #32.9 near #32.3,5 distance 5
> color zone #33.9 near #33.3,5 distance 5
> color zone #34.9 near #34.3,5 distance 5
> color h30|h36|h35 head-c
> color h28 h28-c
> color h29 h29-c
> color h34 h34-c
> color h23 h23-c
> color h24 h24-c
> color h31 h31-c
> hide #!100
> hide #101 models
> cartoon style nucleic xsection oval width 1.3 thickness 1.3
> transparency #*.3 0 target abc
> open
/data/EmilyRundlet/ChimeraX_70S/Scripts/colors/70S_color_helices-s.cxc
> color h18 h18-c
> color h23 h23-c
> color h24 h24-c
> color h28 h28-c
> color h29 h29-c
> color h30 h30-c
> color h31 h31-c
> color h34 h34-c
> color h35 h35-c
> color h44 h44-c
> color H69 hx69-c
executed 70S_color_helices-s.cxc
> color /v d-c
> color /y p-c
> color /w m-c
executed gtpys_dc.cxc
> surface cap true
> lighting gentle
> lighting intensity .2
> size stickRadius 0.17
Changed 1744812 bond radii
> nucribthin
> style ringFill thin
Changed 122200 residue ring styles
> graphics silhouettes true color black
> ~select
Nothing selected
> ~select
Nothing selected
> ~ribbon
> ~display
> ribbon
> ~ribbon mrna
> display mrna
> display antiplus
> display /x:504-514,584
> display /6:1492,1493,530,532,1054,1400,1397
> display /3:1913
> display #*.3/L:44
> color efg byhetero
> select efg
36728 atoms, 37417 bonds, 9 pseudobonds, 4797 residues, 16 models
selected
> hide models
> show #30.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_ysH1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_ysH1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #31.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_ysH1b.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_ysH1b.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #32.3,5 models
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_ysH1c.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_ysH1c.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #12.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_H1apo.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_H1bapo.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #33.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_ysI1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_ysI1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #34.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_I1bys.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_I1bys.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #13.3,5 models
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_I1spc.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_I1spc.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #14.3,5 models
> ~display #14.3/w:38,49
> view dc1
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc1_I2fa.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc2
> windowsize 1000 1000
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc2_I2fa.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> graphics silhouettes true color 25,25,25,15
> style ringFill thick
Changed 122200 residue ring styles
> ~cartoon /6/3
> display /6/3
> ~cartoon trna
> display trna
> volume emmaps style surface step 1 level 3
> surface dust emmaps size 2
> volume emmaps surfaceSmoothing true
> view dc3
> hide models
> show #30 models
> select #30.3
60930 atoms, 65574 bonds, 3 pseudobonds, 4887 residues, 3 models selected
> hide #30.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_ysH1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #31 models
> select #31.3
60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected
> hide #31.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_ysH1b.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #32 models
> select #32.3
60097 atoms, 64722 bonds, 4 pseudobonds, 4779 residues, 3 models selected
> hide #32.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_ysH1c.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #12 models
> select #12.3
55765 atoms, 60298 bonds, 4230 residues, 1 model selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_H1apo.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #33 models
> select #33.3
61025 atoms, 65674 bonds, 2 pseudobonds, 4898 residues, 3 models selected
> hide #33.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_ysI1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #34 models
> select #34.3
61064 atoms, 65713 bonds, 3 pseudobonds, 4898 residues, 3 models selected
> hide #34.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_I1bys.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #13 models
> select #13.3
61103 atoms, 65762 bonds, 4902 residues, 1 model selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_I1spc.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #14 models
> ~display #14.3/w:38,49
> select #14.3
60702 atoms, 65388 bonds, 1 pseudobond, 4855 residues, 2 models selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig3_I2fa.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc4
> hide models
> show #30 models
> select #30.3
60930 atoms, 65574 bonds, 3 pseudobonds, 4887 residues, 3 models selected
> hide #30.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig3_ysH1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #31 models
> select #31.3
60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected
> hide #31.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig3_ysH1b.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #32 models
> select #32.3
60097 atoms, 64722 bonds, 4 pseudobonds, 4779 residues, 3 models selected
> hide #32.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig3_ysH1c.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #12 models
> select #12.3
55765 atoms, 60298 bonds, 4230 residues, 1 model selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig3_H1apo.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #33 models
> select #33.3
61025 atoms, 65674 bonds, 2 pseudobonds, 4898 residues, 3 models selected
> hide #33.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig3_ysI1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #34 models
> select #34.3
61064 atoms, 65713 bonds, 3 pseudobonds, 4898 residues, 3 models selected
> hide #34.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig3_I1bys.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #13 models
> select #13.3
61103 atoms, 65762 bonds, 4902 residues, 1 model selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig3_I1spc.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #14 models
> ~display #14.3/w:38,49
> select #14.3
60702 atoms, 65388 bonds, 1 pseudobond, 4855 residues, 2 models selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig3_I2fa.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc5
> hide models
> show #30 models
> select #30.3
60930 atoms, 65574 bonds, 3 pseudobonds, 4887 residues, 3 models selected
> hide #30.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig3_ysH1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #31 models
> select #31.3
60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected
> hide #31.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig3_ysH1b.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #32 models
> select #32.3
60097 atoms, 64722 bonds, 4 pseudobonds, 4779 residues, 3 models selected
> hide #32.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig3_ysH1c.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #12 models
> select #12.3
55765 atoms, 60298 bonds, 4230 residues, 1 model selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig3_H1apo.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #33 models
> select #33.3
61025 atoms, 65674 bonds, 2 pseudobonds, 4898 residues, 3 models selected
> hide #33.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig3_ysI1a.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #34 models
> select #34.3
61064 atoms, 65713 bonds, 3 pseudobonds, 4898 residues, 3 models selected
> hide #34.9 models
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig3_I1bys.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #13 models
> select #13.3
61103 atoms, 65762 bonds, 4902 residues, 1 model selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig3_I1spc.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #14 models
> ~display #14.3/w:38,49
> select #14.3
60702 atoms, 65388 bonds, 1 pseudobond, 4855 residues, 2 models selected
> windowsize 1000 1000
> save
/data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig3_I2fa.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> volume emmaps style surface step 1 level 8
> surface dust emmaps size 2
> volume emmaps surfaceSmoothing true
> hide models
> show #30.3,5,9 models
> select #30.3
60930 atoms, 65574 bonds, 3 pseudobonds, 4887 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysH1a-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #31.3,5,9 models
> select #31.3
60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysH1b-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #32.3,5,9 models
> select #32.3
60097 atoms, 64722 bonds, 4 pseudobonds, 4779 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysH1c-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #33.3,5,9 models
> select #33.3
61025 atoms, 65674 bonds, 2 pseudobonds, 4898 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysI1a-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #34.3,5,9 models
> select #34.3
61064 atoms, 65713 bonds, 3 pseudobonds, 4898 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc3_sig8_ysI1b-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc4
> hide models
> show #30.3,5,9 models
> select #30.3
60930 atoms, 65574 bonds, 3 pseudobonds, 4887 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig8_ysH1a-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #31.3,5,9 models
> select #31.3
60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig8_ysH1b-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #32.3,5,9 models
> select #32.3
60097 atoms, 64722 bonds, 4 pseudobonds, 4779 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig8_ysH1c-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #33.3,5,9 models
> select #33.3
61025 atoms, 65674 bonds, 2 pseudobonds, 4898 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig8_ysI1a-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #34.3,5,9 models
> select #34.3
61064 atoms, 65713 bonds, 3 pseudobonds, 4898 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc4_sig8_ysI1b-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> view dc4
> hide models
> show #30.3,5,9 models
> select #30.3
60930 atoms, 65574 bonds, 3 pseudobonds, 4887 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig8_ysH1a-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #31.3,5,9 models
> select #31.3
60958 atoms, 65601 bonds, 3 pseudobonds, 4893 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig8_ysH1b-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #32.3,5,9 models
> select #32.3
60097 atoms, 64722 bonds, 4 pseudobonds, 4779 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig8_ysH1c-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #33.3,5,9 models
> select #33.3
61025 atoms, 65674 bonds, 2 pseudobonds, 4898 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig8_ysI1a-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> hide models
> show #34.3,5,9 models
> select #34.3
61064 atoms, 65713 bonds, 3 pseudobonds, 4898 residues, 3 models selected
> windowsize 1000 1000
> save
> /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/ys_dc5_sig8_ysI1b-
FR.tif
> format tiff width 1000 height 1000 supersample 20 transparentBackground
true
> save /data/EmilyRundlet/ChimeraX_70S/Sessions/gtpys/dc/gtpys_dc.cxs
Unable to save 'nucleotides' ->
<chimerax.nucleotides._data.NucleotideState
object at 0x7f33faefe1c0>". Session might not restore properly.
——— End of log from Mon Jul 31 16:31:22 2023 ———
opened ChimeraX session
OpenGL version: 4.5 (Core Profile) Mesa 23.1.0
OpenGL renderer: llvmpipe (LLVM 15.0.7, 256 bits)
OpenGL vendor: Mesa
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb
XDG_SESSION_TYPE=
DESKTOP_SESSION=
XDG_SESSION_DESKTOP=
XDG_CURRENT_DESKTOP=
DISPLAY=localhost:10.0
Manufacturer: TYAN
Model: B7105F48TV4HR-2T-N
OS: CentOS Stream 8 n/a
Architecture: 64bit ELF
Virtual Machine: none
CPU: 72 Intel(R) Xeon(R) Gold 5220 CPU @ 2.20GHz
Cache Size: 25344 KB
Memory:
total used free shared
buff/cache available
Mem: 376Gi 22Gi 296Gi 327Mi
57Gi 351Gi
Swap: 9Gi 0B 9Gi
Graphics:
04:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc.
ASPEED Graphics Family [1a03:2000] (rev 41)
Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family
[1a03:2000]
Kernel driver in use: ast
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
}}}
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Comment:
Can you send me the session file as an attachement? Either as a reply to
this ticket or directly to me at gregc@cgl.ucsf.edu. Thanks.
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ChimeraX
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ChimeraX Issue Tracker
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ChimeraX Issue Tracker
comment:5 by , 13 months ago
| Resolution: | → fixed |
|---|---|
| Status: | feedback → closed |
This was fixed on 26 October 2023 in the daily build. So it is in the 1.7 release and later.
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Can you send me the session file as an attachement? Either as a reply to this ticket or directly to me at gregc@…. Thanks.