Opened 4 years ago

Closed 4 years ago

#5803 closed defect (fixed)

MatchMaker chains within structure

Reported by: nxb318@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Comparison Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19043
ChimeraX Version: 1.3.dev202109080319 (2021-09-08 03:19:35 UTC)
Description
defined a chain C with one glycan as a selector with the name Cglyc. Then tried to match that chain to identical chain A (at different coordinates) in order to bring the glycan too. The error popped up. command: match Cglyc to #3/A        I guess I can use :match #3/C to 3/A bring #(glyc)?

Log:
UCSF ChimeraX version: 1.3.dev202109080319 (2021-09-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/cls1_model-
> map-corr-hotspots_dom.cxs

Opened run_class001-zflip.mrc as #1, grid size 420,420,420, pixel 1.06, shown
at level 0.0103, step 1, values float32  
Opened run_class001-zflip.mrc as #2, grid size 420,420,420, pixel 1.06, shown
at level 0.00729, step 2, values float32  
Opened run_class001-zflip.mrc gaussian as #4, grid size 420,420,420, pixel
1.06, shown at level 0.00815, step 1, values float32  
Opened map_wide_target-zflip.mrc as #5, grid size 420,420,420, pixel 1.06,
shown at level 0.227, step 1, values float32  
Opened mask.mrc as #6, grid size 420,420,420, pixel 1.06, shown at level
0.995, step 1, values float32  
Opened run_class001.mrc as #7, grid size 420,420,420, pixel 1.06, shown at
level 0.00856, step 1, values float32  
Opened run_class001_region_4511.mrc as #9, grid size 106,134,133, pixel 1.06,
shown at level 0.028, step 1, values float32  
Opened run_class001_region_4508.mrc as #10, grid size 58,55,70, pixel 1.06,
shown at level 0.0175, step 1, values float32  
Opened run_class001_region_4496.mrc as #11, grid size 101,98,112, pixel 1.06,
shown at level 0.0157, step 1, values float32  
Opened run_class001_region_4510.mrc as #12, grid size 59,52,70, pixel 1.06,
shown at level 0.0174, step 1, values float32  
Opened emdb 8289 as #15, grid size 300,300,300, pixel 1.32, shown at level
0.0337, step 1, values float32  
Opened postprocess-zlfip.mrc as #16, grid size 420,420,420, pixel 1.06, shown
at level 0.0135, step 1, values float32  
Opened postprocess-zlfip.mrc gaussian as #18, grid size 420,420,420, pixel
1.06, shown at level 0.0133, step 1, values float32  
Opened model_real_space_refined_006.pdb map 3.5 as #19, grid size 118,134,190,
pixel 1.17, shown at level 0.1, step 1, values float32  
Opened postprocess-zlfip_bfactor-100.mrc as #20, grid size 420,420,420, pixel
1.06, shown at level 0.0121, step 1, values float32  
Opened postprocess-zlfip.mrc gaussian as #26, grid size 420,420,420, pixel
1.06, shown at level 0.00862, step 1, values float32  
Log from Wed Dec 15 15:42:50 2021UCSF ChimeraX version: 1.3.dev202109080319
(2021-09-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

> alphafold predict
> KNISRKPGNVLKTLDPILITIIAMSALGVLLGAVCGVVLYCACWHNGMSERNLSALENYNFELVDGVKLKKDKLNTQSTYSEA

Running AlphaFold prediction  
[Repeated 5 time(s)]

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/Relion_maps/J067/run_class001.mrc

Opened run_class001.mrc as #1, grid size 420,420,420, pixel 1.06, shown at
level 0.0073, step 2, values float32  

> lighting soft

> volume #1 step 1

> volume #1 level 0.01378

> close

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/Relion_maps/J067/run_class001-zflip.mrc

Opened run_class001-zflip.mrc as #1, grid size 420,420,420, pixel 1.06, shown
at level 0.00729, step 2, values float32  

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/Relion_maps/J069/run_class001-zflip.mrc

Opened run_class001-zflip.mrc as #2, grid size 420,420,420, pixel 1.06, shown
at level 0.00729, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.01385

> open 5kuf

5kuf title:  
GluK2EM with 2S,4R-4-methylglutamate [more info...]  
  
Chain information for 5kuf #3  
---  
Chain | Description | UniProt  
A B C D | Glutamate receptor ionotropic, kainate 2 | GRIK2_RAT  
  
Non-standard residues in 5kuf #3  
---  
SYM — 2S,4R-4-methylglutamate  
  

> select /D:257

9 atoms, 8 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,1.828,0,1,0,3.2622,0,0,1,36.727

> view matrix models #3,1,0,0,25.225,0,1,0,17.775,0,0,1,36.252

> view matrix models #3,1,0,0,26.83,0,1,0,27.253,0,0,1,35.153

> volume gaussian #0 sDev3

Expected a keyword  

> volume gaussian #0 sDev 3

[Repeated 1 time(s)]

> volume gaussian #0 sDev3

Expected a keyword  

> volume gaussian #0 sDev2

Expected a keyword  

> volume gaussian #0 sDev 2

> volume gaussian #1 sDev 3

Opened run_class001-zflip.mrc gaussian as #4, grid size 420,420,420, pixel
1.06, shown at step 1, values float32  

> ui tool show "Fit in Map"

Fit molecule 5kuf (#3) to map run_class001-zflip.mrc gaussian (#4) using 23728
atoms  
average map value = 0.01334, steps = 140  
shifted from previous position = 1.95  
rotated from previous position = 16.4 degrees  
atoms outside contour = 943, contour level = 0.0081455  
  
Position of 5kuf (#3) relative to run_class001-zflip.mrc gaussian (#4)
coordinates:  
Matrix rotation and translation  
0.96348453 0.26449551 0.04170951 -27.69856620  
-0.26719499 0.95985080 0.08540068 70.25952441  
-0.01744681 -0.09342681 0.99547327 60.04897916  
Axis -0.31703139 0.10487430 -0.94259879  
Axis point 250.60948183 187.80794280 0.00000000  
Rotation angle (degrees) 16.38165949  
Shift along axis -40.45236161  
  

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/Relion_maps/J067/map_wide_target-
> zflip.mrc

Opened map_wide_target-zflip.mrc as #5, grid size 420,420,420, pixel 1.06,
shown at level -0.00608, step 2, values float32  

> volume #5 step 1

> volume #5 level 0.326

> volume #5 level 0.3019

> ui tool show "Hide Dust"

> surface dust #5 size 6.36

> select ligand

44 atoms, 40 bonds, 4 residues, 1 model selected  

> select ::name="ASN"

928 atoms, 812 bonds, 116 residues, 1 model selected  

> select ::name="SER"

1392 atoms, 1192 bonds, 232 residues, 1 model selected  

> volume #5 level 0.2273

> hide #!3 models

> hide #!5 models

> show #!1 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/Relion_maps/mask.mrc

Opened mask.mrc as #6, grid size 420,420,420, pixel 1.06, shown at level 1,
step 2, values float32  

> volume #6 level 0.9948

> volume #6 step 1

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/Relion_maps/J067/run_class001.mrc

Opened run_class001.mrc as #7, grid size 420,420,420, pixel 1.06, shown at
level 0.0073, step 2, values float32  

> volume #7 step 1

> ui tool show "Segment Map"

Segmenting run_class001.mrc, density threshold 0.007301  
Only showing 60 of 77 regions.  
Showing 60 of 77 region surfaces  
4410 watershed regions, grouped to 77 regions  
Showing run_class001.seg - 77 regions, 60 surfaces  
Segmenting run_class001.mrc, density threshold 0.007301  
Showing 19 region surfaces  
4410 watershed regions, grouped to 19 regions  
Showing run_class001.seg - 19 regions, 19 surfaces  

> volume #7 level 0.008563

Segmenting run_class001.mrc, density threshold 0.008563  
Only showing 60 of 508 regions.  
Showing 60 of 508 region surfaces  
3986 watershed regions, grouped to 508 regions  
Showing run_class001.seg - 508 regions, 60 surfaces  
Segmenting run_class001.mrc, density threshold 0.008563  
Showing 19 region surfaces  
3986 watershed regions, grouped to 19 regions  
Showing run_class001.seg - 19 regions, 19 surfaces  
Segmenting run_class001.mrc, density threshold 0.008563  
Showing 4 region surfaces  
3986 watershed regions, grouped to 4 regions  
Showing run_class001.seg - 4 regions, 4 surfaces  
Segmenting run_class001.mrc, density threshold 0.008563  
Only showing 60 of 3803 regions.  
Showing 60 of 3803 region surfaces  
Showing 4 region surfaces  
3803 watershed regions, grouped to 4 regions  
Showing run_class001.seg - 4 regions, 4 surfaces  

> select clear

Segmenting run_class001.mrc, density threshold 0.008563  
Showing 4 region surfaces  
3986 watershed regions, grouped to 4 regions  
Showing run_class001.seg - 4 regions, 4 surfaces  
Ungrouped to 4 regions  

> select clear

Ungrouped to 5 regions  
Ungrouped to 2 regions  
Grouped 2 regions  
[Repeated 1 time(s)]Grouped 3 regions  

> select clear

Grouped 2 regions  

> select clear

Grouped 4 regions  

> select clear

> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/Relion_maps/J067/run_class001.seg
> models #8

Saving 1 regions to mrc file...  
Opened run_class001_region_4511.mrc as #9, grid size 106,134,133, pixel 1.06,
shown at step 1, values float32  
Wrote run_class001_region_4511.mrc  
Saving 1 regions to mrc file...  
Opened run_class001_region_4508.mrc as #10, grid size 58,55,70, pixel 1.06,
shown at step 1, values float32  
Wrote run_class001_region_4508.mrc  
Saving 1 regions to mrc file...  
Opened run_class001_region_4496.mrc as #11, grid size 101,98,112, pixel 1.06,
shown at step 1, values float32  
Wrote run_class001_region_4496.mrc  
Saving 1 regions to mrc file...  
Opened run_class001_region_4510.mrc as #12, grid size 59,52,70, pixel 1.06,
shown at step 1, values float32  
Wrote run_class001_region_4510.mrc  
Segmenting run_class001.mrc, density threshold 0.008563  
Showing 4 region surfaces  
3986 watershed regions, grouped to 4 regions  
Showing run_class001.seg - 4 regions, 4 surfaces  
Segmenting mask.mrc, density threshold 0.994821  
Showing 4 region surfaces  
1521906 watershed regions, grouped to 4 regions  
Showing mask.seg - 4 regions, 4 surfaces  
Chain information for best_model.pdb #13  
---  
Chain | Description  
A | No description available  
  
AlphaFold prediction finished  
Results in C:\Users\nxb318/Downloads\ChimeraX\AlphaFold\prediction_7  

> ui tool show "Volume Viewer"

> show #!9 models

> show #!10 models

> show #!11 models

> show #!12 models

> hide #13 models

> close #13

> hide #!8 models

> show #!8 models

> hide #8.1 models

> show #8.1 models

> hide #8.1 models

> show #8.1 models

> hide #8.1 models

> show #8.1 models

> hide #8.1 models

> show #8.1 models

> close #8

> hide #!6 models

> show #!1 models

> hide #!9 models

> hide #!10 models

> hide #!11 models

> hide #!12 models

> 5kuf

Unknown command: 5kuf  

> open 5kuf

5kuf title:  
GluK2EM with 2S,4R-4-methylglutamate [more info...]  
  
Chain information for 5kuf #8  
---  
Chain | Description | UniProt  
A B C D | Glutamate receptor ionotropic, kainate 2 | GRIK2_RAT  
  
Non-standard residues in 5kuf #8  
---  
SYM — 2S,4R-4-methylglutamate  
  

> hide #!8 models

> color #8 white

> color #3 yellow

> show #!3 models

> select #1

2 models selected  

> transparency sel 50

> select clear

> hide #!1 models

> select #3/B:397

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select B:356

Expected an objects specifier or a keyword  

> interfaces sel /A,B contacting /C,D

Expected a keyword  

> interfaces sel /A,B contacting /C,D

Expected a keyword  

> interfaces sel #3 /A,B contacting /C,D

Expected a keyword  

> select sequence AACA

Nothing selected  

> select B:396

Expected an objects specifier or a keyword  

> select B/396

Expected an objects specifier or a keyword  

> select #3

23728 atoms, 24248 bonds, 8 pseudobonds, 3004 residues, 2 models selected  

> ~select:/isHelix

Unknown command: ~select:/isHelix  

> ~select :/isHelix

> select subtract :/isHelix

Expected an objects specifier or a keyword  

> select :/isHelix

Expected an objects specifier or a keyword  

> select #3 :/isHelix

Expected a keyword  

> ~select #3 :/isHelix

> select subtract #3 :/isHelix

Expected a keyword  

> select clear

> show #!1 models

> material transparentCastShadows true

> help select

> select #3

23728 atoms, 24248 bonds, 8 pseudobonds, 3004 residues, 2 models selected  

> select clear

> select #3/A

5932 atoms, 6062 bonds, 2 pseudobonds, 751 residues, 2 models selected  

> select clear

> select #3/A:422

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

> select #3/A:396-514

962 atoms, 981 bonds, 119 residues, 1 model selected  

> select #3/B:400-514

934 atoms, 953 bonds, 115 residues, 1 model selected  

> select #3/B:696

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/B:696

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select clear

> select #3/B:400-514

934 atoms, 953 bonds, 115 residues, 1 model selected  

> select add #3/B:692

943 atoms, 961 bonds, 116 residues, 1 model selected  

> select add #3/B:637-775

2029 atoms, 2067 bonds, 254 residues, 1 model selected  

> color sel blue

> color sel orange

> color sel red

> select #3/B:400-514

934 atoms, 953 bonds, 115 residues, 1 model selected  

> 637-775

Unknown command: 637-775  

> select #3/B:400-514,637-775

2029 atoms, 2067 bonds, 254 residues, 1 model selected  

> select clear

> select #3/C:400-514,637-775

2029 atoms, 2067 bonds, 254 residues, 1 model selected  

> select #3/B:400-514,637-775

2029 atoms, 2067 bonds, 254 residues, 1 model selected  

> select #3/B,D:400-514,637-775

4058 atoms, 4134 bonds, 508 residues, 1 model selected  

> hide #!3 models

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/RealSpaceRefine_3/aligned_model_real_space_refined_003a.pdb

Chain information for aligned_model_real_space_refined_003a.pdb #13  
---  
Chain | Description  
A B C D | No description available  
  

> select #13/D:805

11 atoms, 11 bonds, 1 residue, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #13,0.53992,0.83534,0.10343,-119.76,0.84119,-0.53983,-0.031232,183.76,0.029747,0.10387,-0.99415,450.85

> ui mousemode right "translate selected models"

> view matrix models
> #13,0.53992,0.83534,0.10343,-151.14,0.84119,-0.53983,-0.031232,159.45,0.029747,0.10387,-0.99415,458.24

> view matrix models
> #13,0.53992,0.83534,0.10343,-149.85,0.84119,-0.53983,-0.031232,154.59,0.029747,0.10387,-0.99415,434.55

> ui mousemode right "rotate selected models"

> view matrix models
> #13,0.91977,0.37983,0.098752,-130.11,0.38833,-0.91721,-0.08898,380.38,0.056779,0.12019,-0.99113,422.76

> view matrix models
> #13,0.96031,0.27126,0.06504,-104.69,0.27316,-0.96171,-0.022211,404.92,0.056525,0.039095,-0.99764,445.01

> view matrix models
> #13,0.93847,0.3383,0.06954,-117.24,0.34099,-0.93956,-0.031006,384.08,0.054847,0.05281,-0.9971,441.83

> view matrix models
> #13,0.93908,0.34151,-0.038785,-91.871,0.33724,-0.93731,-0.087859,398.29,-0.066358,0.069427,-0.99538,468.19

> show #!4 models

> ui tool show "Fit in Map"

Fit molecule aligned_model_real_space_refined_003a.pdb (#13) to map
run_class001-zflip.mrc gaussian (#4) using 23660 atoms  
average map value = 0.01329, steps = 84  
shifted from previous position = 7.06  
rotated from previous position = 2.82 degrees  
atoms outside contour = 1017, contour level = 0.0081455  
  
Position of aligned_model_real_space_refined_003a.pdb (#13) relative to
run_class001-zflip.mrc gaussian (#4) coordinates:  
Matrix rotation and translation  
0.92482441 0.37323340 -0.07346162 -88.15314091  
0.36673559 -0.92611813 -0.08837530 388.57975343  
-0.10101875 0.05479065 -0.99337463 487.28837345  
Axis 0.98100053 0.18882679 -0.04452423  
Axis point 0.00000000 193.72922142 249.00159772  
Rotation angle (degrees) 175.81544494  
Shift along axis -34.80015073  
  

> hide #!4 models

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/RealSpaceRefine_14/aligned_model_real_space_refined_003-deepEM_real_space_refined_014.pdb

Chain information for
aligned_model_real_space_refined_003-deepEM_real_space_refined_014.pdb #14  
---  
Chain | Description  
A B C D | No description available  
  

> color #14 #636073

> color #14 #734830

Fit molecule
aligned_model_real_space_refined_003-deepEM_real_space_refined_014.pdb (#14)
to map run_class001-zflip.mrc gaussian (#4) using 23660 atoms  
average map value = 0.01326, steps = 60  
shifted from previous position = 0.992  
rotated from previous position = 1.58 degrees  
atoms outside contour = 961, contour level = 0.0081455  
  
Position of
aligned_model_real_space_refined_003-deepEM_real_space_refined_014.pdb (#14)
relative to run_class001-zflip.mrc gaussian (#4) coordinates:  
Matrix rotation and translation  
0.99986415 0.01546082 0.00571314 -4.27698970  
-0.01558334 0.99963513 0.02206286 -1.69477296  
-0.00536995 -0.02214889 0.99974026 5.55607469  
Axis -0.80169906 0.20097158 -0.56292899  
Axis point -0.00000000 248.90445133 80.57293940  
Rotation angle (degrees) 1.58006147  
Shift along axis -0.03941810  
  

> hide #!13 models

> set bgColor white

> set bgColor black

> select #14/A:657

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select clear

> select #14/A:456

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #14/A:656

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #14/A:456

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select add #14/A:689

23 atoms, 20 bonds, 3 residues, 1 model selected  

> select add #14/A:459

28 atoms, 24 bonds, 4 residues, 1 model selected  

> select add #14/A:409

37 atoms, 32 bonds, 5 residues, 1 model selected  

> select add #14/A:491

44 atoms, 38 bonds, 6 residues, 1 model selected  

> select add #14/A:458

48 atoms, 41 bonds, 7 residues, 1 model selected  

> select add #14/A:457

60 atoms, 53 bonds, 8 residues, 1 model selected  

> show (sel-residues & sidechain) target ab

> set bgColor white

> show #!3 models

> hide #!14 models

> show #!14 models

> ui tool show "Side View"

> hide #!3 models

> show #!3 models

> hide #!14 models

> select ligand

88 atoms, 80 bonds, 8 residues, 2 models selected  

> volume #1 level 0.01719

> set bgColor black

> color (#!3 & sel) blue

> color (#!3 & sel) hot pink

> color (#!3 & sel) white

> lighting soft

[Repeated 1 time(s)]

> open 8289 from EMDB

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 71, in cmd_open  
provider_args = mgr.fetch_args(fetches[0][1], format_name=fetches[0][2])  
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\open_command\manager.py", line 170, in fetch_args  
args.update(provider_info.bundle_info.run_provider(self.session,  
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 381, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1287, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\map\\__init__.py", line 147, in run_provider  
class Info(OpenerInfo):  
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\map\\__init__.py", line 149, in Info  
_name=session.data_formats[name].nicknames[0], **kw):  
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\data_formats\manager.py", line 140, in __getitem__  
raise KeyError("No known data format '%s'" % key)  
KeyError: "No known data format 'EMDB'"  
  
KeyError: "No known data format 'EMDB'"  
  
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\data_formats\manager.py", line 140, in __getitem__  
raise KeyError("No known data format '%s'" % key)  
  
See log for complete Python traceback.  
  

> open 8289 fromDatabase emdb

Summary of feedback from opening 8289 fetched from emdb  
---  
note | Fetching compressed map 8289 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-8289/map/emd_8289.map.gz  
  
Opened emdb 8289 as #15, grid size 300,300,300, pixel 1.32, shown at level
0.0211, step 2, values float32  

> hide #!3 models

> hide #!1 models

> volume #15 step 1

> ui tool show "Hide Dust"

> surface dust #15 size 7.94

> volume #15 level 0.03371

> lighting soft

Fit map emdb 8289 in map run_class001-zflip.mrc gaussian using 83452 points  
correlation = 0.9636, correlation about mean = 0.4287, overlap = 53.61  
steps = 356, shift = 52.8, angle = 16.7 degrees  
  
Position of emdb 8289 (#15) relative to run_class001-zflip.mrc gaussian (#4)
coordinates:  
Matrix rotation and translation  
0.96208415 0.26912308 0.04434923 -28.98690147  
-0.27206070 0.95844814 0.08579124 71.42727634  
-0.01941803 -0.09460407 0.99532558 60.83184094  
Axis -0.31427152 0.11109065 -0.94281084  
Axis point 249.98231173 189.99831084 0.00000000  
Rotation angle (degrees) 16.67876411  
Shift along axis -40.30825871  
  

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!8 models

> hide #!8 models

> show #!3 models

> select #15

3 models selected  

> transparency sel 50

> select clear

> select ligand

88 atoms, 80 bonds, 8 residues, 2 models selected  

> show #!14 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #!15 models

> show #!1 models

> hide #!14 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!15 models

> hide #!1 models

> show #!1 models

> show #!3 models

> select clear

> hide #!15 models

> volume #1 level 0.01311

> volume #1 level 0.01367

> show #!8 models

> hide #!8 models

> show #!15 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> show #!3 models

> volume #1 level 0.01459

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> hide #!3 models

> hide #!1 models

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/run_class001-zflip.mrc

Opened run_class001-zflip.mrc as #16, grid size 420,420,420, pixel 1.06, shown
at level 0.00802, step 2, values float32  

> volume #16 step 1

> volume #16 level 0.01418

> close #16

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/postprocess-
> zlfip.mrc

Opened postprocess-zlfip.mrc as #16, grid size 420,420,420, pixel 1.06, shown
at level 0.00798, step 2, values float32  

> volume #16 step 1

> volume #16 color #fcff4e

> volume #16 level 0.01342

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/Swissprot/swissmodel/cls1_LBDdimer/model_real_space_refined_006.pdb

Chain information for model_real_space_refined_006.pdb #17  
---  
Chain | Description  
A B C D | No description available  
  

> select #16

2 models selected  

> transparency sel 50

> select clear

> volume #16 level 0.0135

> volume gaussian #16 bfactor-50

Expected a keyword  

> volume gaussian #16 Bfactor-50

Expected a keyword  

> volume gaussian #16 bFactor-50

Expected a keyword  

> select #16

2 models selected  

> volume gaussian #16 bFactor-50

Expected a keyword  

> volume gaussian #16 bactor-50

Expected a keyword  

> volume gaussian #16 bfactor-50

Expected a keyword  

> volume gaussian #16 bfactor -50

Opened postprocess-zlfip.mrc gaussian as #18, grid size 420,420,420, pixel
1.06, shown at step 1, values float32  

> select #18

2 models selected  

> transparency sel 50

> volume #18 level 0.01392

> select #17/D:723

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select clear

> slect #17:721-730

Unknown command: slect #17:721-730  

> select #17:721-730

320 atoms, 316 bonds, 40 residues, 1 model selected  

> show (sel-residues & sidechain) target ab

> volume #18 level 0.01531

> molmap #17

Missing or invalid "resolution" argument: Expected a number  

> molmap #17 3.5A

Missing or invalid "resolution" argument: Expected a number  

> molmap #17 3.5 A

Expected a keyword  

> molmap #17 3.5

Opened model_real_space_refined_006.pdb map 3.5 as #19, grid size 118,134,190,
pixel 1.17, shown at level 0.1, step 1, values float32  

> hide #17 models

> select #19

2 models selected  

> hide #!18 models

> show #17 models

> show #!18 models

> hide #!19 models

> select #17

25552 atoms, 26152 bonds, 3224 residues, 1 model selected  

> style sel sphere

Changed 25552 atom styles  

> undo

> cartoon style sel modeHelix tube sides 20

> hide #!18 models

> select clear

> select #17:424-427

116 atoms, 112 bonds, 16 residues, 1 model selected  

> color sel hot pink

> show #!19 models

> hide #!19 models

> show #!18 models

> volume #18 level 0.01297

> hide #!18 models

> show #!18 models

> select clear

> select #17/A:379

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show (sel-residues & sidechain) target ab

> select #17/A:380

7 atoms, 6 bonds, 1 residue, 1 model selected  

> show (sel-residues & sidechain) target ab

> select #17/C:380

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #17:380

28 atoms, 24 bonds, 4 residues, 1 model selected  

> show (sel-residues & sidechain) target ab

> color sel red

> style sel ball

Changed 28 atom styles  

> volume #18 level 0.01392

> select #17/C:275

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #17:275

32 atoms, 28 bonds, 4 residues, 1 model selected  

> color sel red

> style sel ball

Changed 32 atom styles  

> show (sel-residues & sidechain) target ab

> volume #18 level 0.00976

> volume #18 level 0.0134

> show #!16 models

> hide #!18 models

> select #17:492-496

140 atoms, 136 bonds, 20 residues, 1 model selected  

> color sel red

> show (sel-residues & sidechain) target ab

> style sel ball

Changed 140 atom styles  

> select #17/D:771

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #17/D:772

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select add #17/D:771

10 atoms, 8 bonds, 2 residues, 1 model selected  

> select add #17/D:770

18 atoms, 15 bonds, 3 residues, 1 model selected  

> select add #17/D:769

25 atoms, 22 bonds, 4 residues, 1 model selected  

> color sel red

> show (sel-residues & sidechain) target ab

> style sel ball

Changed 25 atom styles  

> select #17:769-772

100 atoms, 100 bonds, 16 residues, 1 model selected  

> hide #!16 models

> show #!18 models

> volume #18 level 0.01644

> style sel ball

Changed 100 atom styles  

> show (sel-residues & sidechain) target ab

> color sel yellow

> show #!9 models

> hide #!9 models

> show #!10 models

> hide #!10 models

> show #!11 models

> hide #!11 models

> show #!12 models

> hide #!12 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/cls1_model-
> map-corr-hotspots.cxs includeMaps true

> volume #18 level 0.01418

> volume gaussian #16 bfactor -150

Opened postprocess-zlfip.mrc gaussian as #20, grid size 420,420,420, pixel
1.06, shown at step 1, values float32  

> select #20

2 models selected  

> transparency sel 50

> volume #20 level 0.01406

> hide #!18 models

> select #17/A:715

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #17/B:760

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #17/A:715

14 atoms, 12 bonds, 2 residues, 1 model selected  

> hide #!20 models

> show #!20 models

> ui tool show "Hide Dust"

> surface dust #20 size 6.36

> help help:user/tools/modelpanel.html

> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/postprocess-
> zlfip_bfactor-100.mrc models #20

> select #17/D:531

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show (sel-residues & sidechain) target ab

> style sel ball

Changed 9 atom styles  

> select #17/D:523

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show (sel-residues & sidechain) target ab

> style sel ball

Changed 11 atom styles  

> volume #20 level 0.01211

> hide #!20 models

> show #!19 models

> hide #!19 models

> show #!18 models

> show #!12 models

> hide #!12 models

> select #17:771

16 atoms, 12 bonds, 4 residues, 1 model selected  

> select clear

> select #17/D:771

4 atoms, 3 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 4 atom styles  

> view matrix models
> #17,0.99675,-0.01814,-0.078475,22.218,0.021101,0.99909,0.037074,-12.723,0.077731,-0.03861,0.99623,-7.9766

> hide #!18 models

> hide #17 models

> show #17 models

> show #!18 models

> ui tool show "Fit in Map"

Fit molecule model_real_space_refined_006.pdb (#17) to map postprocess-
zlfip.mrc gaussian (#18) using 25552 atoms  
average map value = 0.01868, steps = 148  
shifted from previous position = 1.95  
rotated from previous position = 5.12 degrees  
atoms outside contour = 7479, contour level = 0.014184  
  
Position of model_real_space_refined_006.pdb (#17) relative to postprocess-
zlfip.mrc gaussian (#18) coordinates:  
Matrix rotation and translation  
0.99999993 -0.00019749 0.00032083 -0.04514043  
0.00019754 0.99999997 -0.00015763 -0.00363414  
-0.00032080 0.00015769 0.99999994 -0.01422802  
Axis 0.38603990 0.78554480 0.48362441  
Axis point -3.42520476 0.00000000 108.01509991  
Rotation angle (degrees) 0.02339956  
Shift along axis -0.02716181  
  

> select #17:777

36 atoms, 32 bonds, 4 residues, 1 model selected  

> color sel cyan

> style sel ball

Changed 36 atom styles  

> show sel target ab

> hide #!18 models

> select #17:423-426

124 atoms, 120 bonds, 16 residues, 1 model selected  

> show sel target ab

> select clear

> select #17:776

32 atoms, 28 bonds, 4 residues, 1 model selected  

> color sel cyan

> show sel target ab

> style sel ball

Changed 32 atom styles  

> show #!20 models

> hide #!20 models

> show #!18 models

> select clear

> ui tool show "Side View"

> hide #17 models

> show #17 models

> hide #!18 models

> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/cls1_model-
> map-corr-hotspots.cxs includeMaps true

> open 1YAE

Summary of feedback from opening 1YAE fetched from pdb  
---  
notes | Fetching compressed mmCIF 1yae from
http://files.rcsb.org/download/1yae.cif  
Fetching CCD FUC from http://ligand-expo.rcsb.org/reports/F/FUC/FUC.cif  
Fetching CCD DOQ from http://ligand-expo.rcsb.org/reports/D/DOQ/DOQ.cif  
  
1yae title:  
Structure of the Kainate Receptor Subunit GluR6 Agonist Binding Domain
Complexed with Domoic Acid [more info...]  
  
Chain information for 1yae #21  
---  
Chain | Description  
A B C D E F | Glutamate receptor, ionotropic kainate 2  
  
Non-standard residues in 1yae #21  
---  
DOQ —
(2S,3S,4S)-2-carboxy-4-[(1Z,3E,5R)-5-carboxy-1-methyl-1,3-hexadienyl]-3-pyrrolidineacetic
acid ((2S,3S,4S)-3-carboxymethyl-4-[(1Z,3E,5R)-5-carboxy-1-methyl-
hexa-1,3-dienyl]-pyrrolidine-2-carboxylic acid; domoic acid)  
FUC — alpha-L-fucopyranose  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  
1yae mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
4| author_defined_assembly  
5| author_defined_assembly  
6| author_and_software_defined_assembly  
7| software_defined_assembly  
8| software_defined_assembly  
9| software_defined_assembly  
  

> view #21

> select #21/B:543@CG

1 atom, 1 residue, 1 model selected  

> select #21

12512 atoms, 12663 bonds, 10 pseudobonds, 1616 residues, 2 models selected  

> hide (#!21 & sel) target a

> style (#!21 & sel) ball

Changed 12512 atom styles  

> show (#!21 & sel) target ab

> cartoon (#!21 & sel)

> hide (#!21 & sel) target a

> select ligand

370 atoms, 363 bonds, 25 residues, 3 models selected  

> select #21

12512 atoms, 12663 bonds, 10 pseudobonds, 1616 residues, 2 models selected  

> hide (#!21 & sel-residues & (protein|nucleic)) target a

> cartoon hide (#!21 & sel-residues)

> show (#!21 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab

> show (#!21 & sel-residues & sidechain) target ab

> cartoon (#!21 & sel)

> hide (#!21 & sel) target a

> ui tool show "Show Sequence Viewer"

> sequence chain #21/A

Alignment identifier is 21/A  

> select clear

> select
> #21/A:454-457,461-475,500-507,520-526,670-676,688-697,699-717,720-731,739-747,774-800

962 atoms, 968 bonds, 118 residues, 1 model selected  

> close #21

> view #17

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/G2-LBD-
> domoat-xray-1YAE.pdb

Chain information for G2-LBD-domoat-xray-1YAE.pdb #21  
---  
Chain | Description  
F | No description available  
  

> matchmaker #21 to #17/B

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
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 model_real_space_refined_006.pdb, chain B (#17) with G2-LBD-domoat-
xray-1YAE.pdb, chain F (#21), sequence alignment score = 845.8  
RMSD between 193 pruned atom pairs is 1.055 angstroms; (across all 226 pairs:
3.524)  
  

> show #!1 models

> hide #17 models

> hide #!1 models

> show #17 models

> matchmaker #21 to #17/C

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
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 model_real_space_refined_006.pdb, chain C (#17) with G2-LBD-domoat-
xray-1YAE.pdb, chain F (#21), sequence alignment score = 883.6  
RMSD between 210 pruned atom pairs is 1.121 angstroms; (across all 226 pairs:
1.340)  
  

> hide #17 models

> show #17 models

> select #21/F:1603@CAS

1 atom, 1 residue, 1 model selected  

> select ligand

110 atoms, 102 bonds, 9 residues, 3 models selected  

> color (#!21 & sel) yellow

> color (#!21 & sel) byelement

> hide #17 models

> show #!1 models

> transparency #1.1 0

> view matrix models
> #3,0.9505,0.30702,0.047804,-33.515,-0.31035,0.94553,0.098206,78.621,-0.015049,-0.10818,0.99402,62.281,#8,0.99899,0.044806,0.0023207,-9.1322,-0.044836,0.99888,0.014838,6.3071,-0.0016533,-0.014927,0.99989,3.2421,#21,0.97221,0.23269,-0.025747,-11.035,-0.22439,0.95756,0.18093,39.791,0.066755,-0.17013,0.98316,55.135

> hide #!1 models

> show #17 models

> matchmaker #21 to #17/C

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
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 model_real_space_refined_006.pdb, chain C (#17) with G2-LBD-domoat-
xray-1YAE.pdb, chain F (#21), sequence alignment score = 883.6  
RMSD between 210 pruned atom pairs is 1.121 angstroms; (across all 226 pairs:
1.340)  
  

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/domoat.pdb

> matchmaker #22 to #21

Reference and/or match model contains no nucleic or amino acid chains.  
Use the command-line 'align' command to superimpose small molecules/ligands.  

> align #22 toAtoms #21

Unequal number of atoms to pair, 22 and 1837  

> align #22 toAtoms sele

Invalid "toAtoms" argument: invalid atoms specifier  

> align #22 toAtoms #21/F DOQ

Expected a keyword  

> align #22 toAtoms #21/F

Unequal number of atoms to pair, 22 and 1837  

> select #17/C:488

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show (sel-residues & sidechain) target ab

> show #!1 models

> hide #!1 models

> show #!18 models

> hide #!18 models

> show #!18 models

> select #18

3 models selected  

> transparency sel 0

> select clear

> transparency #18.1 50

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/G2-LBD-
> domoat-xray-1YAE.pdb

Chain information for G2-LBD-domoat-xray-1YAE.pdb #23  
---  
Chain | Description  
F | No description available  
  

> color #21 #565711

> color #21 #a9ab21

> color #21 #b3b523

> color #21 #a8b515

> color #21 #b5aa14

> color #21 #d3c617

> color #23 #d3c617

> matchmaker #23 to #17/D

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
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 model_real_space_refined_006.pdb, chain D (#17) with G2-LBD-domoat-
xray-1YAE.pdb, chain F (#23), sequence alignment score = 838  
RMSD between 158 pruned atom pairs is 1.348 angstroms; (across all 226 pairs:
4.630)  
  

> volume #18 level 0.0133

> hide #!18 models

> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/cls1_model-
> map-corr-hotspots_dom.cxs includeMaps true

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/G2-LBD-
> domoat-xray-1YAE.pdb

Chain information for G2-LBD-domoat-xray-1YAE.pdb #24  
---  
Chain | Description  
F | No description available  
  

> color #24 #d3c617

> matchmaker #24 to #17/B

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
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 model_real_space_refined_006.pdb, chain B (#17) with G2-LBD-domoat-
xray-1YAE.pdb, chain F (#24), sequence alignment score = 845.8  
RMSD between 193 pruned atom pairs is 1.055 angstroms; (across all 226 pairs:
3.524)  
  

> show #!8 models

> hide #17 models

> show #17 models

> matchmaker #8 to #17

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
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 model_real_space_refined_006.pdb, chain C (#17) with 5kuf, chain A
(#8), sequence alignment score = 3831.8  
RMSD between 523 pruned atom pairs is 1.112 angstroms; (across all 749 pairs:
2.536)  
  

> hide #17 models

> hide #!21 models

> show #!21 models

> hide #!23 models

> show #!23 models

> show #17 models

> hide #!8 models

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/G2-LBD-
> domoat-xray-1YAE.pdb

Chain information for G2-LBD-domoat-xray-1YAE.pdb #25  
---  
Chain | Description  
F | No description available  
  

> color #25 #d3c617

> matchmaker #25 to #17/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
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 model_real_space_refined_006.pdb, chain A (#17) with G2-LBD-domoat-
xray-1YAE.pdb, chain F (#25), sequence alignment score = 869.8  
RMSD between 219 pruned atom pairs is 0.920 angstroms; (across all 226 pairs:
1.106)  
  

> matchmaker #24 to #17/B

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
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 model_real_space_refined_006.pdb, chain B (#17) with G2-LBD-domoat-
xray-1YAE.pdb, chain F (#24), sequence alignment score = 845.8  
RMSD between 193 pruned atom pairs is 1.055 angstroms; (across all 226 pairs:
3.524)  
  

> matchmaker #21 to #17/C

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
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 model_real_space_refined_006.pdb, chain C (#17) with G2-LBD-domoat-
xray-1YAE.pdb, chain F (#21), sequence alignment score = 883.6  
RMSD between 210 pruned atom pairs is 1.121 angstroms; (across all 226 pairs:
1.340)  
  

> matchmaker #23 to #17/D

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
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 model_real_space_refined_006.pdb, chain D (#17) with G2-LBD-domoat-
xray-1YAE.pdb, chain F (#23), sequence alignment score = 838  
RMSD between 158 pruned atom pairs is 1.348 angstroms; (across all 226 pairs:
4.630)  
  

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.3-cp39-cp39-win_amd64.whl  

> show #!15 models

> hide #17 models

> hide #!15 models

> hide #!24 models

> hide #!25 models

> hide #!23 models

> hide #22 models

> hide #!21 models

> show #!1 models

> hide #!1 models

> show #!8 models

> show #!15 models

> select ligand

176 atoms, 168 bonds, 12 residues, 6 models selected  

> volume #1 level 0.01477

> view matrix models
> #3,0.96314,0.26892,0.0066141,-21.211,-0.26899,0.96303,0.014993,82.446,-0.0023377,-0.016219,0.99987,40.665,#8,0.98287,0.18433,-0.0004728,-9.2607,-0.18432,0.98284,0.0069539,62.021,0.0017465,-0.0067476,0.99998,37.748,#21,0.98512,0.15259,-0.079136,11.159,-0.14642,0.98609,0.078714,38.684,0.090046,-0.065956,0.99375,28.177,#23,0.80596,0.22886,-0.54594,84.525,0.033016,0.90343,0.42746,-17.357,0.59105,-0.36254,0.72057,25.781,#24,0.1117,-0.99345,0.024262,396.54,0.99374,0.11167,-0.002869,-1.7422,0.00014099,0.02443,0.9997,31.465,#25,-0.98568,-0.16861,-0.0037711,456.76,0.16678,-0.97784,0.12657,358.64,-0.025028,0.12413,0.99195,23.062

> select clear

> volume gaussian #16 sDev 2

Opened postprocess-zlfip.mrc gaussian as #26, grid size 420,420,420, pixel
1.06, shown at step 1, values float32  

> ui tool show "Fit in Map"

Fit molecule 5kuf (#8) to map postprocess-zlfip.mrc gaussian (#26) using 23728
atoms  
average map value = 0.01479, steps = 116  
shifted from previous position = 4.4  
rotated from previous position = 7.36 degrees  
atoms outside contour = 1936, contour level = 0.0086179  
  
Position of 5kuf (#8) relative to postprocess-zlfip.mrc gaussian (#26)
coordinates:  
Matrix rotation and translation  
0.96460927 0.25873376 0.05085074 -28.87980803  
-0.26254876 0.96030068 0.09429080 66.90198132  
-0.02443579 -0.10430458 0.99424516 63.57505245  
Axis -0.35281467 0.13375031 -0.92608459  
Axis point 244.92423035 199.30981971 0.00000000  
Rotation angle (degrees) 16.34642612  
Shift along axis -39.73849567  
  

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls2_cryosparc/cls2_highRes-
> zflip.mrc

Opened cls2_highRes-zflip.mrc as #27, grid size 420,420,420, pixel 1.06, shown
at level -0.026, step 2, values float32  

> volume #27 step 1

> volume #27 level 0.006917

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!15 models

> hide #!8 models

> show #17 models

> close #27

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_cryosparc/cryosparc_P1_J3_004_volume_map-
> zflip.mrc

Opened cryosparc_P1_J3_004_volume_map-zflip.mrc as #27, grid size 420,420,420,
pixel 1.06, shown at level 0.154, step 2, values float32  

> volume #27 level 0.4581

> volume #27 step 1

> volume #27 level 0.3595

> ui tool show "Hide Dust"

> surface dust #27 size 6.36

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/model-
> coot-1-glycans.pdb

model-coot-1-glycans.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) cls1_LBD-dimer [more
info...]  
  
Chain information for model-coot-1-glycans.pdb #28  
---  
Chain | Description  
A B C D | No description available  
  
Non-standard residues in model-coot-1-glycans.pdb #28  
---  
BMA — (BMA)  
NAG — (NAG)  
  

> hide #17 models

> hide #!27 models

> show #!27 models

> transparency #27.1 50

> hide #!27 models

> close #27

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/G2-3m-dom-
> cls1_glyc.pdb

Chain information for G2-3m-dom-cls1_glyc.pdb #27  
---  
Chain | Description  
A B C D | No description available  
  

> hide #!28 models

> show #!1 models

> volume #1 level 0.01035

> hide #!1 models

> ui tool show "Show Sequence Viewer"

> sequence chain #27/A

Alignment identifier is 27/A  

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> select
> #27/A:2-11,42-51,96-98,113-115,138-143,165-170,192-196,220-223,242-247,335-337,340-342,356-361,366-372,399-404,444-449,503-510,648-651,700-705,719-721,727-729

1820 atoms, 1824 bonds, 108 residues, 1 model selected  

> select
> #27/A:19-33,55-67,79-92,120-134,146-151,153-156,158-160,176-188,199-212,228-230,234-239,254-269,285-302,323-332,422-425,429-441,467-473,488-491,520-523,528-549,573-575,598-626,628-630,638-643,656-662,667-679,688-697,706-715,742-755,757-766,773-775,777-779,788-802

5325 atoms, 5342 bonds, 330 residues, 1 model selected  

> select
> #27/A:2-11,42-51,96-98,113-115,138-143,165-170,192-196,220-223,242-247,335-337,340-342,356-361,366-372,399-404,444-449,503-510,648-651,700-705,719-721,727-729

1820 atoms, 1824 bonds, 108 residues, 1 model selected  

> select clear

> open "C:/Users/nxb318/Downloads/output_merged_1 (1).pdb"

Chain information for output_merged_1 (1).pdb #29  
---  
Chain | Description  
A B C D | No description available  
  

> hide #27 models

> open C:/Users/nxb318/Downloads/output_merged_1.pdb

Chain information for output_merged_1.pdb #30  
---  
Chain | Description  
A B C D | No description available  
  

> hide #29 models

> close #29

> show #!3 models

> hide #!3 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> close #3

> show #17 models

> hide #17 models

> show #17 models

> hide #17 models

> show #17 models

> hide #17 models

> show #17 models

> hide #30 models

> show #30 models

> hide #17 models

> cartoon style #30 modeHelix tube sides 20

> show #!25 models

> show #!24 models

> show #!23 models

> show #!21 models

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/G2-3m-dom-
> cls1_glyc.pdb

Chain information for G2-3m-dom-cls1_glyc.pdb #3  
---  
Chain | Description  
A B C D | No description available  
  

> hide #!23 models

> hide #!24 models

> hide #!25 models

> hide #!21 models

> hide #30 models

> show #30 models

> hide #30 models

> show #30 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #30 models

> show #30 models

> close #3

> hide #30 models

> show #17 models

> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/cls1_model-
> map-corr-hotspots_dom.cxs includeMaps true

——— End of log from Wed Dec 15 15:42:50 2021 ———

opened ChimeraX session  

> show #!18 models

> show #!2 models

> show #30 models

> hide #30 models

> hide #!2 models

> hide #!18 models

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/cls1_dimer-
> model_real_space_refined_006_real_space_refined_018.pdb

Chain information for cls1_dimer-
model_real_space_refined_006_real_space_refined_018.pdb #3  
---  
Chain | Description  
A B C D | No description available  
  

> matchmaker #3 to #17

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
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 model_real_space_refined_006.pdb, chain B (#17) with cls1_dimer-
model_real_space_refined_006_real_space_refined_018.pdb, chain B (#3),
sequence alignment score = 4048.9  
RMSD between 737 pruned atom pairs is 0.774 angstroms; (across all 806 pairs:
1.116)  
  

> hide #17 models

> show #!23 models

> show #!24 models

> show #!25 models

> hide #!25 models

> hide #!24 models

> hide #!23 models

> show #22 models

Drag select of 22 atoms, 22 bonds  

> ui mousemode right "translate selected models"

> view matrix models #22,1,0,0,13.901,0,1,0,30.176,0,0,1,65.768

> view matrix models #22,1,0,0,37.309,0,1,0,14.102,0,0,1,62.052

> view matrix models #22,1,0,0,39.347,0,1,0,20.372,0,0,1,63.319

> select #3/C:275

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel target ab

> hide #3 models

Drag select of 22 atoms, 22 bonds  

> ui mousemode right "rotate selected models"

> view matrix models
> #22,-0.45669,-0.85218,-0.2554,541.76,0.88768,-0.45549,-0.067509,98.108,-0.0588,-0.25754,0.96448,126.98

> view matrix models
> #22,-0.74933,0.6599,-0.055107,303.69,-0.6518,-0.7497,-0.11448,481.59,-0.11686,-0.049862,0.9919,98.053

> view matrix models
> #22,-0.23005,0.97317,0.0050809,128.87,-0.97298,-0.22989,-0.021529,441.5,-0.019783,-0.0098964,0.99976,69.234

> view matrix models
> #22,-0.066942,0.92462,0.37497,32.06,-0.96205,-0.15946,0.22145,380.46,0.26455,-0.34591,0.9002,86.584

> view matrix models
> #22,-0.51137,0.85898,0.025836,203.76,-0.85143,-0.50234,-0.15075,487.78,-0.11651,-0.099086,0.98823,107.19

> view matrix models
> #22,0.99937,0.035159,-0.0038077,34.135,0.034921,-0.96409,0.26327,301.83,0.0055853,-0.26324,-0.96472,484.24

> view matrix models
> #22,-0.18355,-0.79507,-0.57807,536.32,-0.72995,-0.28363,0.62188,276.35,-0.6584,0.53611,-0.5283,402.1

> view matrix models
> #22,-0.38817,-0.22247,-0.89433,541.06,-0.90259,-0.10423,0.41768,320.8,-0.18614,0.96935,-0.16034,157.44

> view matrix models
> #22,-0.61171,-0.2895,-0.7362,569.32,-0.70023,0.63117,0.33362,167.34,0.36809,0.71959,-0.58881,166.2

> show #3 models

> show #!18 models

> select #3/D:698

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:793

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:789

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select add #3/A:793

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select add #3/D:698

21 atoms, 18 bonds, 3 residues, 1 model selected  

> show (sel-residues & sidechain) target ab

> select #3/A:792

10 atoms, 10 bonds, 1 residue, 1 model selected  

> show (sel-residues & sidechain) target ab

> select #18

3 models selected  

> select #3/D:699

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show (sel-residues & sidechain) target ab

> select #3/D:522

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:783

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #3/D:522

15 atoms, 13 bonds, 2 residues, 1 model selected  

> show (sel-residues & sidechain) target ab

> select #3:698

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select #3:275

32 atoms, 28 bonds, 4 residues, 1 model selected  

> hide #22 models

> show #22 models

> hide #3 models

> show #3 models

> hide #!18 models

> hide #22 models

> hide #3 models

> show #17 models

> show #!18 models

> select #3:412

32 atoms, 28 bonds, 4 residues, 1 model selected  

> select #17:412

32 atoms, 28 bonds, 4 residues, 1 model selected  

> show (sel-residues & sidechain) target ab

> color sel red

> select #17:275

32 atoms, 28 bonds, 4 residues, 1 model selected  

> hide #!18 models

> show #!18 models

> select #17:430

32 atoms, 28 bonds, 4 residues, 1 model selected  

> show (sel-residues & sidechain) target ab

> color sel red

> volume #18 level 0.0109

> hide #17 models

> volume #18 level 0.009118

> show #17 models

> volume #18 level 0.01372

> hide #!18 models

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Glycans/DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAca1-OH/4ogg/structure.pdb

structure.pdb title:  
Generated by GMML [more info...]  
  
Non-standard residues in structure.pdb #29  
---  
0MA — (0MA)  
4YA — (4YA)  
4YB — (4YB)  
ROH — (ROH)  
VMB — (VMB)  
  

> view #29

> view matrix models
> #17,0.52814,0.0903,0.84434,-99.512,-0.40742,0.89935,0.15866,81.049,-0.74503,-0.42779,0.51178,375.95

> view matrix models
> #17,0.50396,0.2505,0.8266,-126.63,-0.46418,0.88562,0.014614,129.03,-0.72839,-0.39106,0.5626,352.52

Drag select of 120 atoms, 124 bonds  

> ui mousemode right "translate selected models"

> view matrix models #29,1,0,0,205.55,0,1,0,190.22,0,0,1,286.8

> ui tool show "Side View"

> view matrix models #29,1,0,0,259.34,0,1,0,207.41,0,0,1,235.98

> ui mousemode right "rotate selected models"

> view matrix models
> #29,0.39617,-0.91805,-0.01525,271.86,0.67151,0.30103,-0.6771,196,0.6262,0.25801,0.73574,224.01

> view matrix models
> #29,-0.10393,-0.95078,0.29192,281.45,0.50691,-0.30316,-0.80693,200.12,0.85571,0.06411,0.51347,219.94

> view matrix models
> #29,-0.011717,-0.97702,-0.21284,275.07,0.75114,0.1319,-0.64683,196.33,0.66004,-0.16745,0.73233,226.02

> view matrix models
> #29,-0.13375,-0.96864,-0.20941,276.55,0.7708,0.031131,-0.63632,196.79,0.62288,-0.24652,0.74246,227.04

> ui mousemode right "translate selected models"

> view matrix models
> #29,-0.13375,-0.96864,-0.20941,279.41,0.7708,0.031131,-0.63632,179.9,0.62288,-0.24652,0.74246,227.16

> view matrix models
> #29,-0.13375,-0.96864,-0.20941,269.19,0.7708,0.031131,-0.63632,178.58,0.62288,-0.24652,0.74246,221.44

> view matrix models
> #29,-0.13375,-0.96864,-0.20941,273.48,0.7708,0.031131,-0.63632,177.83,0.62288,-0.24652,0.74246,230.02

> view matrix models
> #29,-0.13375,-0.96864,-0.20941,269.79,0.7708,0.031131,-0.63632,172.99,0.62288,-0.24652,0.74246,232.64

> ui mousemode right "rotate selected models"

> view matrix models
> #29,0.012259,-0.99272,0.11985,271.67,0.8392,-0.054955,-0.54103,173.67,0.54368,0.10721,0.83242,232.52

> ui mousemode right "translate selected models"

> view matrix models
> #29,0.012259,-0.99272,0.11985,272.51,0.8392,-0.054955,-0.54103,177.37,0.54368,0.10721,0.83242,234.86

> view matrix models
> #29,0.012259,-0.99272,0.11985,265.88,0.8392,-0.054955,-0.54103,174.59,0.54368,0.10721,0.83242,235.08

> ui mousemode right "rotate selected models"

> view matrix models
> #29,0.53516,-0.84294,-0.055321,256.75,0.73164,0.49524,-0.46846,173.5,0.42228,0.21022,0.88175,236.5

> view matrix models
> #29,0.48472,-0.87446,0.019195,258.35,0.80235,0.4358,-0.40782,173.63,0.34826,0.21308,0.91286,237.72

> view matrix models
> #29,0.38085,-0.92133,0.078162,260.52,0.78746,0.27889,-0.54966,173.2,0.48462,0.27089,0.83172,234.85

> view matrix models
> #29,0.32554,-0.93165,0.16141,262.14,0.85226,0.21519,-0.47681,173.55,0.40949,0.29279,0.86406,235.98

> ui mousemode right "translate selected models"

> view matrix models
> #29,0.32554,-0.93165,0.16141,261.56,0.85226,0.21519,-0.47681,173.48,0.40949,0.29279,0.86406,235.8

> select clear

> hide HC

> select #17/C:275@CA

1 atom, 1 residue, 1 model selected  

> select #17/C:275@CB

1 atom, 1 residue, 1 model selected  

> select #17/C:275

8 atoms, 7 bonds, 1 residue, 1 model selected  

> color sel byhetero

> show #!18 models

> select #17 #27

76680 atoms, 77877 bonds, 6453 residues, 2 models selected  

> show #!23 models

> show #!16 models

> hide #!16 models

> ui mousemode right "rotate selected models"

> view matrix models
> #17,0.80244,-0.29952,0.51611,-0.63872,0.48034,0.8374,-0.26085,-15.011,-0.35406,0.45722,0.81584,17.255,#27,0.75599,-0.6302,-0.177,238.8,0.23622,0.51484,-0.8241,238.98,0.61048,0.5812,0.53808,-170.12

> view matrix models
> #17,0.82901,0.30822,0.46663,-134.5,-0.22317,0.94743,-0.2293,113.77,-0.51277,0.085957,0.85421,129.81,#27,0.88072,-0.10503,-0.46185,153.39,-0.064681,0.9393,-0.33695,103.16,0.46921,0.32663,0.82046,-142.15

> view matrix models
> #17,0.97481,0.2221,0.020189,-49.428,-0.22123,0.97447,-0.038376,64.914,-0.028197,0.032944,0.99906,-0.93718,#27,0.56359,-0.2555,-0.78555,331.83,0.10089,0.96514,-0.24152,38.3,0.81987,0.056864,0.56972,-105.29

> view matrix models
> #17,0.99913,-0.02301,0.034695,-2.2434,0.022233,0.9995,0.022609,-9.9638,-0.035198,-0.021818,0.99914,13.146,#27,0.52644,-0.48365,-0.69925,373.32,0.28027,0.87518,-0.39434,51.613,0.80269,0.011618,0.59628,-96.911

> show #!26 models

> hide #!26 models

> ui tool show "Fit in Map"

Fit molecules model_real_space_refined_006.pdb (#17), G2-3m-dom-cls1_glyc.pdb
(#27) to map postprocess-zlfip.mrc gaussian (#26) using 76680 atoms  
average map value = 0.008275, steps = 112  
shifted from previous position = 0.783  
rotated from previous position = 2.11 degrees  
atoms outside contour = 37703, contour level = 0.0086179  
  
Position of model_real_space_refined_006.pdb (#17) relative to postprocess-
zlfip.mrc gaussian (#26) coordinates:  
Matrix rotation and translation  
0.99995206 0.00021586 0.00978935 -2.29360096  
-0.00029680 0.99996578 0.00826768 -2.04255583  
-0.00978723 -0.00827019 0.99991791 4.10109578  
Axis -0.64520055 0.76375142 -0.02000069  
Axis point 416.62156911 0.00000000 247.02591872  
Rotation angle (degrees) 0.73432681  
Shift along axis -0.16219707  
  
Position of G2-3m-dom-cls1_glyc.pdb (#27) relative to postprocess-zlfip.mrc
gaussian (#26) coordinates:  
Matrix rotation and translation  
0.51208268 -0.46382513 -0.72293677 377.24893591  
0.25717798 0.88584777 -0.38617771 52.35828887  
0.81953085 0.01183149 0.57291290 -95.61320455  
Axis 0.22762109 -0.88213578 0.41234100  
Axis point 287.55889679 0.00000000 327.67093327  
Rotation angle (degrees) 60.95989697  
Shift along axis 0.25744824  
  

> select clear

> hide #!18 models

> select #27

51128 atoms, 51725 bonds, 3229 residues, 1 model selected  

> show #27 models

> hide #27 models

> show #!26 models

> hide #!26 models

> select #29

120 atoms, 124 bonds, 6 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #29,0.32554,-0.93165,0.16141,260.62,0.85226,0.21519,-0.47681,180.67,0.40949,0.29279,0.86406,251.55

> ui mousemode right "rotate selected models"

> view matrix models
> #29,0.13536,0.87001,0.47408,256.36,-0.77577,0.39071,-0.4955,199.64,-0.61632,-0.30071,0.72782,266.07

> view matrix models
> #29,0.52892,0.69178,-0.49162,242.4,-0.5451,-0.16707,-0.82156,196.45,-0.65047,0.70252,0.28872,256.41

> ui mousemode right "translate selected models"

> view matrix models
> #29,0.52892,0.69178,-0.49162,240.69,-0.5451,-0.16707,-0.82156,193.63,-0.65047,0.70252,0.28872,257.67

> view matrix models
> #29,0.52892,0.69178,-0.49162,240.22,-0.5451,-0.16707,-0.82156,194.16,-0.65047,0.70252,0.28872,258.11

> show #!18 models

> volume #18 level 0.01079

> ui mousemode right "rotate selected models"

> view matrix models
> #29,0.91199,0.41016,-0.0070817,242.08,-0.11613,0.24158,-0.96341,185.14,-0.39344,0.87944,0.26795,253.74

> ui mousemode right "translate selected models"

> view matrix models
> #29,0.91199,0.41016,-0.0070817,239.74,-0.11613,0.24158,-0.96341,187.65,-0.39344,0.87944,0.26795,253.7

> hide #!18 models

> save
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Glycans/DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAca1-OH/Glyc-
> C-Asn275.pdb models #29 relModel #18

> show #!18 models

> hide #!18 models

> select #29 #17

25672 atoms, 26276 bonds, 3230 residues, 2 models selected  

> combine sele

Expected a keyword  

> ui tool show "Build Structure"

> hide #29 models

> hide #17 models

> hide #!23 models

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Glycans/DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAca1-OH/Glyc-
> C-Asn275.pdb

Glyc-C-Asn275.pdb title:  
Generated by GMML [more info...]  
  
Non-standard residues in Glyc-C-Asn275.pdb #31  
---  
0MA — (0MA)  
4YA — (4YA)  
4YB — (4YB)  
ROH — (ROH)  
VMB — (VMB)  
  

> show #17 models

> hide #17 models

> close #29

> color #31 #5b42cd

Drag select of 111 atoms, 117 bonds  
Drag select of 120 atoms, 124 bonds  

> color sel byhetero

> hide HC

> show #17 models

> style sel ball

Changed 120 atom styles  

> select clear

> select #17/C

6388 atoms, 6538 bonds, 806 residues, 1 model selected  

> select add #31

6508 atoms, 6662 bonds, 812 residues, 2 models selected  

> show #3 models

> hide #17 models

> open
> C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/Glycans/DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAca1-OH/Glyc-
> C-Asn275.pdb

Glyc-C-Asn275.pdb title:  
Generated by GMML [more info...]  
  
Non-standard residues in Glyc-C-Asn275.pdb #29  
---  
0MA — (0MA)  
4YA — (4YA)  
4YB — (4YB)  
ROH — (ROH)  
VMB — (VMB)  
  

> hide #31 models

> select #3/C #29

6508 atoms, 6662 bonds, 812 residues, 2 models selected  

> matchmaker sele to #3/A

Missing or invalid "matchAtoms" argument: invalid atoms specifier  

> name frozen C+glyc sel

> matchmaker C+glyc to #3/A

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\match_maker\match.py", line 682, in cmd_match  
match_items = (refs[0], matches)  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\match_maker\match.py", line 682, in cmd_match  
match_items = (refs[0], matches)  
  
See log for complete Python traceback.  
  

> help help:user/menu.html#named-selections

> name frozen Cglyc sel

> matchmaker Cglyc sel to #3/A

Expected a keyword  

> matchmaker Cglyc to #3/A

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\match_maker\match.py", line 682, in cmd_match  
match_items = (refs[0], matches)  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\match_maker\match.py", line 682, in cmd_match  
match_items = (refs[0], matches)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 471.41
OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: OptiPlex 7071
OS: Microsoft Windows 10 Pro (Build 19043)
Memory: 34,140,291,072
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-9700 CPU @ 3.00GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.0
    chardet: 4.0.0
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.29.1
    ChimeraX-AtomicLibrary: 4.1.4
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.3
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.4.1
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202109080319
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.4
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.1
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.1
    ChimeraX-MDcrds: 2.5
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.1.1
    ChimeraX-ModelPanel: 1.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-Phenix: 0.3
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.12
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.10.0
    Cython: 0.29.23
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.4.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 2.11.3
    jupyter-client: 6.1.12
    jupyter-core: 4.7.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 1.1.1
    matplotlib: 3.4.2
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.6
    networkx: 2.6.2
    numexpr: 2.7.3
    numpy: 1.21.0
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pickleshare: 0.7.5
    Pillow: 8.2.0
    pip: 21.1.1
    pkginfo: 1.7.0
    prompt-toolkit: 3.0.20
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.9.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.2.1
    qtconsole: 5.1.0
    QtPy: 1.11.0
    RandomWords: 0.3.0
    requests: 2.25.1
    scipy: 1.6.3
    setuptools: 57.0.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.0.1
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.0
    urllib3: 1.26.6
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.2
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Structure Comparison
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → MatchMaker chains within structure

Hi Nebojsa,

It should give you a sensible error message instead of a stack trace, but you cannot MatchMaker one chain of a structure model onto another chain of the same structure model. You would need to open a second copy of the structure and use MatchMaker with one chain of the first structure and another chain of the second structure.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:2 by Eric Pettersen, 4 years ago

Resolution: → fixed
Status: accepted → closed

Fixed the code that detects this problem.

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