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#10377 closed defect (can't reproduce)
Color command syntax
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Depiction | Version: | |
| Keywords: | Cc: | Elaine Meng | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-14.1.1-arm64-arm-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
This command is not working right. The cartoon turns into blue instead of red. Also palette combinations keywords like red:blue:yellow are also not working.
Log:
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly__C-
> ring]/Figures/CCW and CW maps and models.cxs"
Opened C34-J412_Z-flip.mrc as #2, grid size 768,768,768, pixel 1.36, shown at
level 0.0856, step 1, values float32
Log from Tue Dec 19 14:18:47 2023UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly__C-
> ring]/EMDB and PDB Upload/C-ring/34-mer C-ring/C34_C-ring_RSR158.pdb"
Chain information for C34_C-ring_RSR158.pdb #1
---
Chain | Description
A BC BF DB DE F FA FD FG HC HF I JB JE LA LD LG NC NF PB PE RA RD RG S TC TF
VB VE XA XD Z ZC ZF | No description available
AA AD AG B CC CF EB EE G GA GD GG IC IF J KB KE MA MD MG OC OF QB QE SA SD SG
T UC UF WB WE YA YD | No description available
AB AE CA CD CG D EC EF GB GE IA ID IG KC KF L MB ME N OA OD OG QC QF SB SE UA
UD UG W WC WF YB YE | No description available
AC AF CB CE EA ED EG GC GF H IB IE KA KD KG MC MF OB OE Q QA QD QG R SC SF UB
UE WA WD WG Y YC YF | No description available
BA BD BG C DC DF FB FE HA HD HG JC JF K LB LE M NA ND NG PC PF RB RE TA TD TG
V VC VF XB XE ZA ZD | No description available
BB BE DA DD DG E FC FF HB HE JA JD JG LC LF NB NE O P PA PD PG RC RF TB TE VA
VD VG X XC XF ZB ZE | No description available
> select
> #10/A,BC,BF,DB,DE,F-FA,FD,FG,HC,HF,I,JB,JE,LA,LD,LG,NC,NF,PB,PE,RA,RD,RG-S,TC,TF,VB,VE,XA,XD,Z,ZC,ZF
Nothing selected
> color sel #0f98f7ff
> select
> #10/AA,AD,AG-B,CC,CF,EB,EE,G-GA,GD,GG,IC,IF,J,KB,KE,MA,MD,MG,OC,OF,QB,QE,SA,SD,SG-T,UC,UF,WB,WE,YA,YD
Nothing selected
> color sel #ed271dff
> select
> #10/BA,BD,BG-C,DC,DF,FB,FE,HA,HD,HG,JC,JF,K,LB,LE,M,NA,ND,NG,PC,PF,RB,RE,TA,TD,TG,V,VC,VF,XB,XE,ZA,ZD
Nothing selected
> color sel #ffb60aff
> select
> #10/AB,AE,CA,CD,CG-D,EC,EF,GB,GE,IA,ID,IG,KC,KF,L,MB,ME,N,OA,OD,OG,QC,QF,SB,SE,UA,UD,UG,W,WC,WF,YB,YE
Nothing selected
> color sel #8c15b7ff
> select
> #10/AC,AF,CB,CE,EA,ED,EG,GC,GF,H,IB,IE,KA,KD,KG,MC,MF,OB,OE,Q-QA,QD,QG-R,SC,SF,UB,UE,WA,WD,WG,Y,YC,YF
Nothing selected
> color sel #b581c5ff
> select
> #10/BB,BE,DA,DD,DG-E,FC,FF,HB,HE,JA,JD,JG,LC,LF,NB,NE,O,P-PA,PD,PG,RC,RF,TB,TE,VA,VD,VG,X,XC,XF,ZB,ZE
Nothing selected
> color sel #dc4166ff
> select
> /A,BC,BF,DB,DE,F-FA,FD,FG,HC,HF,I,JB,JE,LA,LD,LG,NC,NF,PB,PE,RA,RD,RG-S,TC,TF,VB,VE,XA,XD,Z,ZC,ZF
7956 atoms, 7922 bonds, 1598 residues, 1 model selected
> color sel #0f98f7ff
> select
> /AA,AD,AG-B,CC,CF,EB,EE,G-GA,GD,GG,IC,IF,J,KB,KE,MA,MD,MG,OC,OF,QB,QE,SA,SD,SG-T,UC,UF,WB,WE,YA,YD
84864 atoms, 85544 bonds, 10880 residues, 1 model selected
> color sel #ed271dff
> select
> /BA,BD,BG-C,DC,DF,FB,FE,HA,HD,HG,JC,JF,K,LB,LE,M,NA,ND,NG,PC,PF,RB,RE,TA,TD,TG,V,VC,VF,XB,XE,ZA,ZD
70924 atoms, 72182 bonds, 10064 residues, 1 model selected
> color sel #ffb60aff
> select
> /AB,AE,CA,CD,CG-D,EC,EF,GB,GE,IA,ID,IG,KC,KF,L,MB,ME,N,OA,OD,OG,QC,QF,SB,SE,UA,UD,UG,W,WC,WF,YB,YE
15504 atoms, 15470 bonds, 3162 residues, 1 model selected
> color sel #8c15b7ff
> select
> /AC,AF,CB,CE,EA,ED,EG,GC,GF,H,IB,IE,KA,KD,KG,MC,MF,OB,OE,Q-QA,QD,QG-R,SC,SF,UB,UE,WA,WD,WG,Y,YC,YF
12546 atoms, 12512 bonds, 2550 residues, 1 model selected
> color sel #b581c5ff
> select
> /BB,BE,DA,DD,DG-E,FC,FF,HB,HE,JA,JD,JG,LC,LF,NB,NE,O,P-PA,PD,PG,RC,RF,TB,TE,VA,VD,VG,X,XC,XF,ZB,ZE
13226 atoms, 13192 bonds, 2686 residues, 1 model selected
> color sel #dc4166ff
> select add #1
205020 atoms, 206822 bonds, 30940 residues, 1 model selected
> select subtract #1
Nothing selected
> hide atoms
> show cartoons
> set bgColor white
> open "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly__C-
> ring]/EMDB and PDB Upload/C-ring/34-mer C-ring/C34-J412_Z-flip.mrc"
MRC file is truncated. Failed reading 1 values, type int32
> open "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly__C-
> ring]/EMDB and PDB Upload/C-ring/34-mer C-ring/C34-J412_Z-flip.mrc"
Opened C34-J412_Z-flip.mrc as #2, grid size 768,768,768, pixel 1.36, shown at
step 1, values float32
> volume #2 region 0,0,0,767,767,767 step 4
[Repeated 1 time(s)]
> volume #2 step 1
> volume #2 change image level -0.01815,0 level 0.2025,0.8 level 0.2592,1
> volume #2 level 0.1155
> volume #2 style mesh
> volume #2 color #0f98f7
> material transparentCastShadows true
> select add #2
3 models selected
> transparency #2.2 50
> select add #2
3 models selected
> select add #2
3 models selected
> select add #1
205020 atoms, 206822 bonds, 30940 residues, 4 models selected
> select add #2
205020 atoms, 206822 bonds, 30940 residues, 4 models selected
> select subtract #1
3 models selected
> select #1
205020 atoms, 206822 bonds, 30940 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #2
3 models selected
> transparency #2.2 90
> select add #2
3 models selected
> select #1
205020 atoms, 206822 bonds, 30940 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #2
3 models selected
> transparency #2.2 40
> select #1
205020 atoms, 206822 bonds, 30940 residues, 1 model selected
> select subtract #1
Nothing selected
> volume #2 level 0.1188
> volume #2 level 0.1642
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> cartoon style width 3.5 thickness 2.8
> volume #2 level 0.08338
> volume #2 level 0.0856
> ui tool show "Hide Dust"
> surface dust #2 size 8.18
> surface dust #2 size 8.52
> surface dust #2 size 10.25
> surface dust #2 size 10.42
> surface dust #2 size 12.12
> lighting simple
> lighting soft
> lighting full
> lighting soft
> volume #2 color #0f98f764
> volume #2 color #0f98f762
> volume #2 color #0f98f7
> volume #2 color #0f98f78e
> graphics silhouettes true
> material transparentCastShadows false
> volume #2 color #0f98f75c
> volume #2 color #0f98f7
> volume #2 color #0f98f7cf
> volume #2 color #0f98f785
> volume #2 color #0f98f794
> volume #2 color #0f98f74c
> volume #2 color #0f98f769
> volume #2 color #0f98f75b
> volume #2 color #0f98f72e
> volume #2 color #0f98f75a
> save "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly__C-
> ring]/Figures/RAW Figures/Overview/C-ring_mesh.png" width 1344 height 1370
> supersample 3 transparentBackground true
> volume #2 style surface
> color #2 #919191ff models
> color #2 #929292ff models
> color #2 #92929285 models
> color #2 #92929244 models
> save "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly__C-
> ring]/Figures/RAW Figures/Overview/C-ring_surface.png" width 1344 height
> 1370 supersample 3 transparentBackground true
> hide #!2 models
> open "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly__C-
> ring]/Mutations, Maps and Models/CW_C-
> ring_Phenix/ApplyNCS_20/NoDensity_PAA_apply_ncs_20.pdb"
Summary of feedback from opening /Users/prash_mbp/Dropbox (VU Basic
Sciences)/[FiguresOnly__C-ring]/Mutations, Maps and Models/CW_C-
ring_Phenix/ApplyNCS_20/NoDensity_PAA_apply_ncs_20.pdb
---
warnings | Ignored bad PDB record found on line 237
Ignored bad PDB record found on line 2736
Ignored bad PDB record found on line 4781
Ignored bad PDB record found on line 5239
Ignored bad PDB record found on line 5630
1 messages similar to the above omitted
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 6237
Duplicate atom serial number found: 235
Duplicate atom serial number found: 236
Duplicate atom serial number found: 237
Duplicate atom serial number found: 238
Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 8736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 10781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 11239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 11630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 12001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 12237
Duplicate atom serial number found: 235
Duplicate atom serial number found: 236
Duplicate atom serial number found: 237
Duplicate atom serial number found: 238
Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 14736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 16781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 17239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 17630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 18001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 18237
Duplicate atom serial number found: 235
Duplicate atom serial number found: 236
Duplicate atom serial number found: 237
Duplicate atom serial number found: 238
Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 20736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 22781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 23239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 23630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 24001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 24237
Duplicate atom serial number found: 235
Duplicate atom serial number found: 236
Duplicate atom serial number found: 237
Duplicate atom serial number found: 238
Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 26736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 28781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 29239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 29630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 30001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 30237
Duplicate atom serial number found: 235
Duplicate atom serial number found: 236
Duplicate atom serial number found: 237
Duplicate atom serial number found: 238
Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 32736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 34781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 35239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 35630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 36001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 36237
Duplicate atom serial number found: 235
Duplicate atom serial number found: 236
Duplicate atom serial number found: 237
Duplicate atom serial number found: 238
Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 38736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 40781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 41239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 41630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 42001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 42237
Duplicate atom serial number found: 235
Duplicate atom serial number found: 236
Duplicate atom serial number found: 237
Duplicate atom serial number found: 238
Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 44736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 46781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 47239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 47630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 48001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 48237
Duplicate atom serial number found: 235
Duplicate atom serial number found: 236
Duplicate atom serial number found: 237
Duplicate atom serial number found: 238
Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 50736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 52781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 53239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 53630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 54001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 54237
Duplicate atom serial number found: 235
Duplicate atom serial number found: 236
Duplicate atom serial number found: 237
Duplicate atom serial number found: 238
Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 56736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 58781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 59239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 59630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 60001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 60237
Duplicate atom serial number found: 235
Duplicate atom serial number found: 236
Duplicate atom serial number found: 237
Duplicate atom serial number found: 238
Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 62736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 64781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 65239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 65630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 66001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 66237
Duplicate atom serial number found: 235
Duplicate atom serial number found: 236
Duplicate atom serial number found: 237
Duplicate atom serial number found: 238
Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 68736
Duplicate atom serial number found: 2732
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Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 70781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 71239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 71630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 72001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
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Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 72237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 74736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
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Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 76781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 77239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 77630
Duplicate atom serial number found: 5620
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Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 78001
Duplicate atom serial number found: 1
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Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 78237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 80736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
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Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 82781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 83239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
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Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 83630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 84001
Duplicate atom serial number found: 1
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Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 84237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 86736
Duplicate atom serial number found: 2732
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Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 88781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 89239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
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Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 89630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 90001
Duplicate atom serial number found: 1
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Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 90237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 92736
Duplicate atom serial number found: 2732
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Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 94781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 95239
Duplicate atom serial number found: 5231
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Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 95630
Duplicate atom serial number found: 5620
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Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 96001
Duplicate atom serial number found: 1
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229 messages similar to the above omitted
Ignored bad PDB record found on line 96237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 98736
Duplicate atom serial number found: 2732
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Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 100781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 101239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 101630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 102001
Duplicate atom serial number found: 1
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Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 102237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 104736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 106781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 107239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 107630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 108001
Duplicate atom serial number found: 1
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Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 108237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 110736
Duplicate atom serial number found: 2732
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Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 112781
Duplicate atom serial number found: 4775
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Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 113239
Duplicate atom serial number found: 5231
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Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 113630
Duplicate atom serial number found: 5620
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Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 114001
Duplicate atom serial number found: 1
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229 messages similar to the above omitted
Ignored bad PDB record found on line 114237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 116736
Duplicate atom serial number found: 2732
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Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 118781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 119239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
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Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 119630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 120001
Duplicate atom serial number found: 1
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Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 120237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 122736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
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Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 124781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 125239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 125630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 126001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
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Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 126237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 128736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 130781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 131239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 131630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 132001
Duplicate atom serial number found: 1
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Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 132237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 134736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 136781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 137239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 137630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 138001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 138237
Duplicate atom serial number found: 235
Duplicate atom serial number found: 236
Duplicate atom serial number found: 237
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 140736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 142781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 143239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 143630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 144001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 144237
Duplicate atom serial number found: 235
Duplicate atom serial number found: 236
Duplicate atom serial number found: 237
Duplicate atom serial number found: 238
Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 146736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 148781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 149239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 149630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 150001
Duplicate atom serial number found: 1
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Duplicate atom serial number found: 3
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Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 150237
Duplicate atom serial number found: 235
Duplicate atom serial number found: 236
Duplicate atom serial number found: 237
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 152736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 154781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 155239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 155630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 156001
Duplicate atom serial number found: 1
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Duplicate atom serial number found: 3
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Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 156237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 237
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 158736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 160781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 161239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 161630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 162001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 162237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 238
Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 164736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 166781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 167239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 167630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 168001
Duplicate atom serial number found: 1
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Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 168237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 170736
Duplicate atom serial number found: 2732
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Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 172781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 173239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
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Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 173630
Duplicate atom serial number found: 5620
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Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 174001
Duplicate atom serial number found: 1
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Duplicate atom serial number found: 3
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Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 174237
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Chain information for NoDensity_PAA_apply_ncs_20.pdb #3
---
Chain | Description
A BC BF DB DE F FA FD FG HC HF I JB JE LA LD LG NC NF PB PE RA RD RG S TC TF
VB VE XA XD Z ZC ZF | No description available
AA AD AG B CC CF EB EE G GA GD GG IC IF J KB KE MA MD MG OC OF QB QE SA SD SG
T UC UF WB WE YA YD | No description available
AB AE CA CD CG D EC EF GB GE IA ID IG KC KF L MB ME N OA OD OG QC QF SB SE UA
UD UG W WC WF YB YE | No description available
AC AF CB CE EA ED EG GC GF H IB IE KA KD KG MC MF OB OE Q QA QD QG R SC SF UB
UE WA WD WG Y YC YF | No description available
BA BD BG C DC DF FB FE HA HD HG JC JF K LB LE M NA ND NG PC PF RB RE TA TD TG
V VC VF XB XE ZA ZD | No description available
BB BE DA DD DG E FC FF HB HE JA JD JG LC LF NB NE O P PA PD PG RC RF TB TE VA
VD VG X XC XF ZB ZE | No description available
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> select add #3
203592 atoms, 205360 bonds, 30600 residues, 1 model selected
> view matrix models
> #3,0.061024,-0.97672,-0.20564,1099.3,-0.97734,-0.016633,-0.21102,1142.8,0.20269,0.21386,-0.95561,699.13
> view matrix models
> #3,0.061024,-0.97672,-0.20564,1119.3,-0.97734,-0.016633,-0.21102,1131.3,0.20269,0.21386,-0.95561,850.37
> view matrix models
> #3,0.0072251,-0.99885,-0.047368,1084.8,-0.99994,-0.007598,0.0076966,1035.8,-0.0080477,0.04731,-0.99885,1068.2
> view matrix models
> #3,0.0072251,-0.99885,-0.047368,1065.4,-0.99994,-0.007598,0.0076966,1048.8,-0.0080477,0.04731,-0.99885,1018.9
> ui tool show Matchmaker
> matchmaker #3/N#3/O#3/P to #1/N#1/O#1/P pairing ss
Parameters
---
Chain pairing | ss
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 C34_C-ring_RSR158.pdb, chain N (#1) with
NoDensity_PAA_apply_ncs_20.pdb, chain N (#3), sequence alignment score = 464
Matchmaker C34_C-ring_RSR158.pdb, chain O (#1) with
NoDensity_PAA_apply_ncs_20.pdb, chain O (#3), sequence alignment score = 380.9
Matchmaker C34_C-ring_RSR158.pdb, chain P (#1) with
NoDensity_PAA_apply_ncs_20.pdb, chain P (#3), sequence alignment score = 380.9
RMSD between 7 pruned atom pairs is 1.407 angstroms; (across all 251 pairs:
36.172)
> matchmaker #3/N#3/O#3/P#3/ID#3/JD#3/KD to #1/N#1/O#1/P#1/ID#1/JD#1/KD
> pairing ss
Parameters
---
Chain pairing | ss
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 C34_C-ring_RSR158.pdb, chain N (#1) with
NoDensity_PAA_apply_ncs_20.pdb, chain N (#3), sequence alignment score = 464
Matchmaker C34_C-ring_RSR158.pdb, chain O (#1) with
NoDensity_PAA_apply_ncs_20.pdb, chain O (#3), sequence alignment score = 380.9
Matchmaker C34_C-ring_RSR158.pdb, chain P (#1) with
NoDensity_PAA_apply_ncs_20.pdb, chain P (#3), sequence alignment score = 380.9
Matchmaker C34_C-ring_RSR158.pdb, chain ID (#1) with
NoDensity_PAA_apply_ncs_20.pdb, chain ID (#3), sequence alignment score = 464
Matchmaker C34_C-ring_RSR158.pdb, chain JD (#1) with
NoDensity_PAA_apply_ncs_20.pdb, chain JD (#3), sequence alignment score =
377.9
Matchmaker C34_C-ring_RSR158.pdb, chain KD (#1) with
NoDensity_PAA_apply_ncs_20.pdb, chain KD (#3), sequence alignment score =
359.6
RMSD between 3 pruned atom pairs is 0.986 angstroms; (across all 498 pairs:
37.850)
> select #3/ID/JD/KD
1214 atoms, 1211 bonds, 247 residues, 1 model selected
> view matrix models
> #3,-0.92335,0.36383,-0.12267,835.06,-0.33847,-0.92215,-0.1873,1266.7,-0.18126,-0.13142,0.97461,477.59
> view matrix models
> #3,0.49038,0.56302,0.66523,-378.83,0.32193,-0.82635,0.46208,566.27,0.80987,-0.012437,-0.58648,628.62
> view matrix models
> #3,0.70374,0.49526,0.50937,-381.95,0.48741,-0.8582,0.16102,637.52,0.51689,0.13496,-0.84535,826.23
> view matrix models
> #3,0.16536,0.98461,-0.056479,-90.917,0.95847,-0.14695,0.24441,-20.554,0.23235,-0.09455,-0.96802,1152.9
> view matrix models
> #3,0.16536,0.98461,-0.056479,-40.193,0.95847,-0.14695,0.24441,-13.736,0.23235,-0.09455,-0.96802,997.86
> view matrix models
> #3,0.10837,0.99399,-0.015439,-34.517,0.99275,-0.10902,-0.050605,86.829,-0.051984,-0.0098429,-0.9986,1116.7
> view matrix models
> #3,0.10837,0.99399,-0.015439,-42.301,0.99275,-0.10902,-0.050605,87.506,-0.051984,-0.0098429,-0.9986,1074.4
> matchmaker #3/N#3/O#3/P#3/ID#3/JD#3/KD to #1/N#1/O#1/P#1/ID#1/JD#1/KD
> pairing ss
Parameters
---
Chain pairing | ss
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 C34_C-ring_RSR158.pdb, chain N (#1) with
NoDensity_PAA_apply_ncs_20.pdb, chain N (#3), sequence alignment score = 464
Matchmaker C34_C-ring_RSR158.pdb, chain O (#1) with
NoDensity_PAA_apply_ncs_20.pdb, chain O (#3), sequence alignment score = 380.9
Matchmaker C34_C-ring_RSR158.pdb, chain P (#1) with
NoDensity_PAA_apply_ncs_20.pdb, chain P (#3), sequence alignment score = 380.9
Matchmaker C34_C-ring_RSR158.pdb, chain ID (#1) with
NoDensity_PAA_apply_ncs_20.pdb, chain ID (#3), sequence alignment score = 464
Matchmaker C34_C-ring_RSR158.pdb, chain JD (#1) with
NoDensity_PAA_apply_ncs_20.pdb, chain JD (#3), sequence alignment score =
377.9
Matchmaker C34_C-ring_RSR158.pdb, chain KD (#1) with
NoDensity_PAA_apply_ncs_20.pdb, chain KD (#3), sequence alignment score =
359.6
RMSD between 3 pruned atom pairs is 0.986 angstroms; (across all 498 pairs:
37.850)
> matchmaker #3/N#3/O#3/P#3/ID#3/JD#3/KD to #1/N#1/O#1/P#1/ID#1/JD#1/KD
> pairing ss
Parameters
---
Chain pairing | ss
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 C34_C-ring_RSR158.pdb, chain N (#1) with
NoDensity_PAA_apply_ncs_20.pdb, chain N (#3), sequence alignment score = 464
Matchmaker C34_C-ring_RSR158.pdb, chain O (#1) with
NoDensity_PAA_apply_ncs_20.pdb, chain O (#3), sequence alignment score = 380.9
Matchmaker C34_C-ring_RSR158.pdb, chain P (#1) with
NoDensity_PAA_apply_ncs_20.pdb, chain P (#3), sequence alignment score = 380.9
Matchmaker C34_C-ring_RSR158.pdb, chain ID (#1) with
NoDensity_PAA_apply_ncs_20.pdb, chain ID (#3), sequence alignment score = 464
Matchmaker C34_C-ring_RSR158.pdb, chain JD (#1) with
NoDensity_PAA_apply_ncs_20.pdb, chain JD (#3), sequence alignment score =
377.9
Matchmaker C34_C-ring_RSR158.pdb, chain KD (#1) with
NoDensity_PAA_apply_ncs_20.pdb, chain KD (#3), sequence alignment score =
359.6
RMSD between 3 pruned atom pairs is 0.986 angstroms; (across all 498 pairs:
37.850)
> view matrix models
> #3,-0.92335,0.36383,-0.12267,886.05,-0.33847,-0.92215,-0.1873,1299,-0.18126,-0.13142,0.97461,60.951
> select /ID/JD/KD
2428 atoms, 2422 bonds, 494 residues, 2 models selected
> select add #3
204806 atoms, 206571 bonds, 30847 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select subtract #3
1214 atoms, 1211 bonds, 247 residues, 1 model selected
> select /ID/JD/KD
2428 atoms, 2422 bonds, 494 residues, 2 models selected
> view matrix models
> #1,0.92815,-0.22753,0.29455,10.316,0.035008,0.84125,0.53951,-178.92,-0.37055,-0.49044,0.78877,493.75,#3,-0.83339,0.50879,0.21583,555.1,-0.41486,-0.83392,0.36396,977.77,0.36517,0.21378,0.90606,-423.58
> select add #3
204806 atoms, 206571 bonds, 30847 residues, 2 models selected
> view matrix models
> #1,0.96713,-0.22244,0.12324,86.489,0.18653,0.94991,0.25075,-122.04,-0.17285,-0.21952,0.96018,220.32,#3,-0.84005,0.5408,0.043139,661.97,-0.5392,-0.84105,0.043587,1292.5,0.059854,0.013354,0.99812,-159.46
> select add #1
408612 atoms, 412182 bonds, 61540 residues, 2 models selected
> select subtract #1
203592 atoms, 205360 bonds, 30600 residues, 1 model selected
> view matrix models
> #3,-0.28509,0.75679,0.5882,2.8787,0.7786,-0.17506,0.60261,-8.1044,0.55902,0.62977,-0.53933,-22.805
> view matrix models
> #3,0.40268,0.90412,-0.14288,-91.593,0.4033,-0.035123,0.91439,-31.056,0.8217,-0.42583,-0.37878,317.08
> view matrix models
> #3,0.65557,0.70961,-0.25823,-68.07,0.71328,-0.46964,0.52027,218.91,0.24791,-0.52526,-0.81403,873.53
> view matrix models
> #3,0.46205,0.71819,0.5203,-336.6,0.75942,-0.62341,0.18611,433.14,0.45803,0.30913,-0.83345,341.48
No reference and/or match structure/chain chosen
> matchmaker #!3 to #1
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 C34_C-ring_RSR158.pdb, chain KB (#1) with
NoDensity_PAA_apply_ncs_20.pdb, chain AA (#3), sequence alignment score =
1478.8
RMSD between 22 pruned atom pairs is 0.838 angstroms; (across all 317 pairs:
27.032)
> view matrix models
> #3,-0.78227,-0.61918,0.068319,1254.1,-0.62262,0.77364,-0.11759,587.92,0.019956,-0.13453,-0.99071,1166.3
> view matrix models
> #3,-0.78227,-0.61918,0.068319,1233.1,-0.62262,0.77364,-0.11759,559.2,0.019956,-0.13453,-0.99071,1116.4
> show #!2 models
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit molecule C34_C-ring_RSR158.pdb (#1) to map C34-J412_Z-flip.mrc (#2) using
205020 atoms
average map value = 0.2189, steps = 344
shifted from previous position = 95.4
rotated from previous position = 16.3 degrees
atoms outside contour = 3176, contour level = 0.085596
Position of C34_C-ring_RSR158.pdb (#1) relative to C34-J412_Z-flip.mrc (#2)
coordinates:
Matrix rotation and translation
0.98299857 -0.18361312 -0.00000189 105.02358542
0.18361313 0.98299858 0.00000022 -87.22643017
0.00000180 -0.00000056 0.99999999 0.01620323
Axis -0.00000214 -0.00001005 1.00000000
Axis point 523.52899692 523.50750282 0.00000000
Rotation angle (degrees) 10.58028565
Shift along axis 0.01685479
> fitmap #3 inMap #2
Fit molecule NoDensity_PAA_apply_ncs_20.pdb (#3) to map C34-J412_Z-flip.mrc
(#2) using 203592 atoms
average map value = 0.151, steps = 272
shifted from previous position = 61.9
rotated from previous position = 9.54 degrees
atoms outside contour = 49481, contour level = 0.085596
Position of NoDensity_PAA_apply_ncs_20.pdb (#3) relative to C34-J412_Z-
flip.mrc (#2) coordinates:
Matrix rotation and translation
-0.83742595 -0.54655082 0.00002263 1248.04878765
-0.54655080 0.83742593 0.00005725 371.22485949
-0.00005025 0.00003559 -1.00000001 1043.46878645
Axis -0.28488814 0.95856073 0.00026910
Axis point 679.19950682 0.00000000 521.66990978
Rotation angle (degrees) 179.99782171
Shift along axis 0.56807471
> select /f/g/m/n/p/q
12018 atoms, 12123 bonds, 1810 residues, 2 models selected
> turn #3 y -2
Expected an axis vector or a keyword
> turn #3 y -2
Expected an axis vector or a keyword
> turn #3 y -2
Expected an axis vector or a keyword
> turn #3 y -2
Expected an axis vector or a keyword
> turn #3 y -2
Expected an axis vector or a keyword
> turn #3 y -2
Expected an axis vector or a keyword
> turn #3 y -2
Expected an axis vector or a keyword
> turn #3 y -2
Expected an axis vector or a keyword
> turn #3 y -2
Expected an axis vector or a keyword
> turn #3 y -2
Expected an axis vector or a keyword
> turn #3 y -2
Expected an axis vector or a keyword
> turn #3 y -2
Expected an axis vector or a keyword
> turn #3 y -2
Expected an axis vector or a keyword
> turn #3 y -2
Expected an axis vector or a keyword
> turn #3 y -2
Expected an axis vector or a keyword
> turn #3 y -2
Expected an axis vector or a keyword
> turn #3 y -2
Expected an axis vector or a keyword
> turn #3 y -2
Expected an axis vector or a keyword
> turn #3 y -2
Expected an axis vector or a keyword
> turn #3 y -2
Expected an axis vector or a keyword
> turn #3 y -2
Expected an axis vector or a keyword
> turn #3 y -2
Expected an axis vector or a keyword
> turn #3 y -2
Expected an axis vector or a keyword
> select add #3
209622 atoms, 211443 bonds, 31510 residues, 2 models selected
> select add #1
408612 atoms, 412182 bonds, 61540 residues, 2 models selected
> select subtract #1
203592 atoms, 205360 bonds, 30600 residues, 1 model selected
> turn sel y -2
Expected an axis vector or a keyword
> hide #!2 models
> hide #1 models
> select /f/g/m/n/p/q
12018 atoms, 12123 bonds, 1810 residues, 2 models selected
> turn y -2
[Repeated 87 time(s)]
> view orient
> turn y -2
[Repeated 2 time(s)]
> view orient
[Repeated 1 time(s)]
> view
> view orient
> turn x
> turn y -2
[Repeated 84 time(s)]
> hide #!3 models
> show #1 models
> turn y -2
[Repeated 15 time(s)]
> show #!3 models
> hide #1 models
> select add #1
211008 atoms, 212862 bonds, 31840 residues, 2 models selected
> select subtract #1
5988 atoms, 6040 bonds, 900 residues, 1 model selected
> turn y 2
[Repeated 12 time(s)]
> select add #3
203592 atoms, 205360 bonds, 30600 residues, 1 model selected
> select subtract #3
Nothing selected
> hide #!3 models
> show #1 models
> select add #1
205020 atoms, 206822 bonds, 30940 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #1
205020 atoms, 206822 bonds, 30940 residues, 1 model selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select add #1
205020 atoms, 206822 bonds, 30940 residues, 1 model selected
> select /f/g/m/n/p/q
12018 atoms, 12123 bonds, 1810 residues, 2 models selected
> select add #3
209622 atoms, 211443 bonds, 31510 residues, 2 models selected
> select subtract #3
6030 atoms, 6083 bonds, 910 residues, 1 model selected
> turn y -2
[Repeated 64 time(s)]
> select add #1
205020 atoms, 206822 bonds, 30940 residues, 1 model selected
> select subtract #1
Nothing selected
> show #!3 models
> select /f/g/m/n/p/q
12018 atoms, 12123 bonds, 1810 residues, 2 models selected
> select add #1
211008 atoms, 212862 bonds, 31840 residues, 2 models selected
> select subtract #1
5988 atoms, 6040 bonds, 900 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.0803,0.99672,-0.010104,-35.586,0.99672,-0.080187,0.011189,38.539,0.010343,-0.01097,-0.99989,1043.7
> select /f/g/m/n/p/q
12018 atoms, 12123 bonds, 1810 residues, 2 models selected
> select /f/g/m/n/p/q
12018 atoms, 12123 bonds, 1810 residues, 2 models selected
> select add #1
211008 atoms, 212862 bonds, 31840 residues, 2 models selected
> select subtract #1
5988 atoms, 6040 bonds, 900 residues, 1 model selected
> view matrix models
> #3,0.22988,0.97316,0.010684,-111.3,0.97322,-0.22986,-0.0031422,135.92,-0.00060208,0.01112,-0.99994,1037.9
> fitmap #3 inMap #2
Fit molecule NoDensity_PAA_apply_ncs_20.pdb (#3) to map C34-J412_Z-flip.mrc
(#2) using 203592 atoms
average map value = 0.151, steps = 96
shifted from previous position = 0.0976
rotated from previous position = 1.38 degrees
atoms outside contour = 49493, contour level = 0.085596
Position of NoDensity_PAA_apply_ncs_20.pdb (#3) relative to C34-J412_Z-
flip.mrc (#2) coordinates:
Matrix rotation and translation
0.25068553 0.96806857 0.00000273 -114.52260105
0.96806857 -0.25068550 -0.00001442 147.96797966
-0.00001329 0.00000628 -1.00000001 1043.46667737
Axis 0.79088036 0.61197080 -0.00004918
Axis point -0.00000000 118.28756755 521.73039022
Rotation angle (degrees) 179.99925009
Shift along axis -0.07291252
> select add #3
203592 atoms, 205360 bonds, 30600 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #3
203592 atoms, 205360 bonds, 30600 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #3
203592 atoms, 205360 bonds, 30600 residues, 1 model selected
> select subtract #3
Nothing selected
> select
> /A,BC,BF,DB,DE,F-FA,FD,FG,HC,HF,I,JB,JE,LA,LD,LG,NC,NF,PB,PE,RA,RD,RG-S,TC,TF,VB,VE,XA,XD,Z,ZC,ZF
15912 atoms, 15844 bonds, 3196 residues, 2 models selected
> color sel #0f98f7ff
> select
> /AA,AD,AG-B,CC,CF,EB,EE,G-GA,GD,GG,IC,IF,J,KB,KE,MA,MD,MG,OC,OF,QB,QE,SA,SD,SG-T,UC,UF,WB,WE,YA,YD
169762 atoms, 171054 bonds, 21726 residues, 2 models selected
> color sel #ed271dff
> select
> /BA,BD,BG-C,DC,DF,FB,FE,HA,HD,HG,JC,JF,K,LB,LE,M,NA,ND,NG,PC,PF,RB,RE,TA,TD,TG,V,VC,VF,XB,XE,ZA,ZD
140386 atoms, 142936 bonds, 19822 residues, 2 models selected
> color sel #ffb60aff
> select
> /AB,AE,CA,CD,CG-D,EC,EF,GB,GE,IA,ID,IG,KC,KF,L,MB,ME,N,OA,OD,OG,QC,QF,SB,SE,UA,UD,UG,W,WC,WF,YB,YE
31008 atoms, 30940 bonds, 6324 residues, 2 models selected
> color sel #8c15b7ff
> select
> /AC,AF,CB,CE,EA,ED,EG,GC,GF,H,IB,IE,KA,KD,KG,MC,MF,OB,OE,Q-QA,QD,QG-R,SC,SF,UB,UE,WA,WD,WG,Y,YC,YF
25092 atoms, 25024 bonds, 5100 residues, 2 models selected
> color sel #b581c5ff
> select
> /BB,BE,DA,DD,DG-E,FC,FF,HB,HE,JA,JD,JG,LC,LF,NB,NE,O,P-PA,PD,PG,RC,RF,TB,TE,VA,VD,VG,X,XC,XF,ZB,ZE
26452 atoms, 26384 bonds, 5372 residues, 2 models selected
> color sel #dc4166ff
> cartoon style width 3.5 thickness 2.8
> select add #1
218246 atoms, 220014 bonds, 33626 residues, 2 models selected
> select subtract #1
13226 atoms, 13192 bonds, 2686 residues, 1 model selected
> select add #3
203592 atoms, 205360 bonds, 30600 residues, 1 model selected
> select subtract #3
Nothing selected
> hide #1 models
> save "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly__C-
> ring]/Figures/CCW and CW maps and models.cxs"
——— End of log from Tue Dec 19 14:18:47 2023 ———
opened ChimeraX session
> hide #!3 models
> show #!2 models
> show #1 models
> hide #!2 models
> close #3
> select /f/g/m/n/p/q
6030 atoms, 6083 bonds, 910 residues, 1 model selected
> select ~sel & ##selected
198990 atoms, 200739 bonds, 30030 residues, 1 model selected
> color sel dim gray
> color sel dark gray
> select add #1
205020 atoms, 206822 bonds, 30940 residues, 1 model selected
> select subtract #1
Nothing selected
> turn z 10
[Repeated 9 time(s)]
> close session
> open "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly__C-
> ring]/Mutations, Maps and Models/CW_C-
> ring_Phenix/ApplyNCS_20/NoDensity_PAA_apply_ncs_20.pdb"
Summary of feedback from opening /Users/prash_mbp/Dropbox (VU Basic
Sciences)/[FiguresOnly__C-ring]/Mutations, Maps and Models/CW_C-
ring_Phenix/ApplyNCS_20/NoDensity_PAA_apply_ncs_20.pdb
---
warnings | Ignored bad PDB record found on line 237
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Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 88781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 89239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 89630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 90001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
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Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 90237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 92736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 94781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 95239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 95630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 96001
Duplicate atom serial number found: 1
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Duplicate atom serial number found: 3
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Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 96237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 98736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 100781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 101239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 101630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 102001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
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Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 102237
Duplicate atom serial number found: 235
Duplicate atom serial number found: 236
Duplicate atom serial number found: 237
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 104736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 106781
[deleted to fit within ticket limits]
Duplicate atom serial number found: 2732
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Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 82781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 83239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 83630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 84001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
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Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 84237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 237
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 86736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 88781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 89239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 89630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 90001
Duplicate atom serial number found: 1
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Duplicate atom serial number found: 3
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Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 90237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 92736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 94781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 95239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 95630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 96001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 96237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 237
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 98736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 100781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 101239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 101630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 102001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 102237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 237
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 104736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 106781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 107239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 107630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 108001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 108237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 237
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 110736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 112781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 113239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 113630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 114001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 114237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 116736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 118781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 119239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 119630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 120001
Duplicate atom serial number found: 1
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Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 120237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 237
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 122736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 124781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 125239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 125630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 126001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
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Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 126237
Duplicate atom serial number found: 235
Duplicate atom serial number found: 236
Duplicate atom serial number found: 237
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 128736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 130781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 131239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 131630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 132001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 132237
Duplicate atom serial number found: 235
Duplicate atom serial number found: 236
Duplicate atom serial number found: 237
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 134736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 136781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 137239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 137630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 138001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 138237
Duplicate atom serial number found: 235
Duplicate atom serial number found: 236
Duplicate atom serial number found: 237
Duplicate atom serial number found: 238
Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 140736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 142781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 143239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 143630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 144001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 144237
Duplicate atom serial number found: 235
Duplicate atom serial number found: 236
Duplicate atom serial number found: 237
Duplicate atom serial number found: 238
Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 146736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 148781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 149239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 149630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 150001
Duplicate atom serial number found: 1
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Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 150237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 237
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 152736
Duplicate atom serial number found: 2732
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Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 154781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 155239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 155630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 156001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 156237
Duplicate atom serial number found: 235
Duplicate atom serial number found: 236
Duplicate atom serial number found: 237
Duplicate atom serial number found: 238
Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 158736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 160781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 161239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 161630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 162001
Duplicate atom serial number found: 1
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Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 162237
Duplicate atom serial number found: 235
Duplicate atom serial number found: 236
Duplicate atom serial number found: 237
Duplicate atom serial number found: 238
Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 164736
Duplicate atom serial number found: 2732
Duplicate atom serial number found: 2733
Duplicate atom serial number found: 2734
Duplicate atom serial number found: 2735
Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 166781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 167239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 167630
Duplicate atom serial number found: 5620
Duplicate atom serial number found: 5621
Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 168001
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
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Chain information for NoDensity_PAA_apply_ncs_20.pdb #2
---
Chain | Description
A BC BF DB DE F FA FD FG HC HF I JB JE LA LD LG NC NF PB PE RA RD RG S TC TF
VB VE XA XD Z ZC ZF | No description available
AA AD AG B CC CF EB EE G GA GD GG IC IF J KB KE MA MD MG OC OF QB QE SA SD SG
T UC UF WB WE YA YD | No description available
AB AE CA CD CG D EC EF GB GE IA ID IG KC KF L MB ME N OA OD OG QC QF SB SE UA
UD UG W WC WF YB YE | No description available
AC AF CB CE EA ED EG GC GF H IB IE KA KD KG MC MF OB OE Q QA QD QG R SC SF UB
UE WA WD WG Y YC YF | No description available
BA BD BG C DC DF FB FE HA HD HG JC JF K LB LE M NA ND NG PC PF RB RE TA TD TG
V VC VF XB XE ZA ZD | No description available
BB BE DA DD DG E FC FF HB HE JA JD JG LC LF NB NE O P PA PD PG RC RF TB TE VA
VD VG X XC XF ZB ZE | No description available
> show sel cartoons
> hide sel atoms
> show sel cartoons
> hide sel atoms
[Repeated 1 time(s)]
> select add #1
5988 atoms, 6040 bonds, 900 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #2
203592 atoms, 205360 bonds, 30600 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select subtract #2
Nothing selected
> open "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly__C-
> ring]/Mutations, Maps and
> Models/CheY/CheY_PAA_LocalRef_HighRes_Aligned_1.mrc"
Opened CheY_PAA_LocalRef_HighRes_Aligned_1.mrc as #3, grid size 512,512,512,
pixel 2.05, shown at level 0.146, step 2, values float32
> volume #3 level 0.3557
> volume #3 step 1
> volume #3 level 0.4044
> volume #3 level 0.2841
> open "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly__C-
> ring]/Mutations, Maps and Models/PAA/MSC_PAA_LocalRef_HighRes_Aligned.mrc"
Opened MSC_PAA_LocalRef_HighRes_Aligned.mrc as #4, grid size 512,512,512,
pixel 2.05, shown at level 0.0798, step 2, values float32
> hide #!2 models
> show #!2 models
> hide #!3 models
> volume #4 level 0.2264
> volume #4 step 1
> show #!3 models
> hide #!4 models
> open "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly__C-
> ring]/Mutations, Maps and Models/CheY/cryosparc_P23_J53_005_volume_map.mrc"
Opened cryosparc_P23_J53_005_volume_map.mrc as #5, grid size 512,512,512,
pixel 2.05, shown at level 0.146, step 2, values float32
> volume #5 level 0.3371
> hide #!3 models
> volume #5 level 0.4806
> open "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly__C-
> ring]/Mutations, Maps and
> Models/CheY/CheY_PAA_C34_LocalRef_Flip_HighRes_Aligned.mrc"
Opened CheY_PAA_C34_LocalRef_Flip_HighRes_Aligned.mrc as #6, grid size
512,512,512, pixel 2.05, shown at level 0.151, step 2, values float32
> volume #6 level 0.187
> hide #!5 models
> volume #6 level 0.1973
> open "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly__C-
> ring]/Mutations, Maps and Models/final/CW-coot-pan.pdb"
Chain information for CW-coot-pan.pdb #7
---
Chain | Description
F | No description available
G | No description available
M | No description available
N | No description available
P | No description available
Q | No description available
> hide #!6 models
> hide #!1 models
> hide #!2 models
> show #!7 cartoons
> hide #!7 atoms
> open "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly__C-
> ring]/Mutations, Maps and Models/CW_C-
> ring_Phenix/ApplyNCS_15/Density_PAA_apply_ncs_15.pdb"
Summary of feedback from opening /Users/prash_mbp/Dropbox (VU Basic
Sciences)/[FiguresOnly__C-ring]/Mutations, Maps and Models/CW_C-
ring_Phenix/ApplyNCS_15/Density_PAA_apply_ncs_15.pdb
---
warnings | Ignored bad PDB record found on line 237
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1 messages similar to the above omitted
Duplicate atom serial number found: 1
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384 messages similar to the above omitted
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Ignored bad PDB record found on line 59630
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364 messages similar to the above omitted
Ignored bad PDB record found on line 60001
Duplicate atom serial number found: 1
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Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 60237
Duplicate atom serial number found: 235
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2492 messages similar to the above omitted
Ignored bad PDB record found on line 62736
Duplicate atom serial number found: 2732
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Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 64781
Duplicate atom serial number found: 4775
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Duplicate atom serial number found: 4777
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Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 65239
Duplicate atom serial number found: 5231
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Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 65630
Duplicate atom serial number found: 5620
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Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 66001
Duplicate atom serial number found: 1
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229 messages similar to the above omitted
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Duplicate atom serial number found: 235
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2492 messages similar to the above omitted
Ignored bad PDB record found on line 68736
Duplicate atom serial number found: 2732
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2038 messages similar to the above omitted
Ignored bad PDB record found on line 70781
Duplicate atom serial number found: 4775
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Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 71239
Duplicate atom serial number found: 5231
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Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 71630
Duplicate atom serial number found: 5620
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Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 72001
Duplicate atom serial number found: 1
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229 messages similar to the above omitted
Ignored bad PDB record found on line 72237
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2492 messages similar to the above omitted
Ignored bad PDB record found on line 74736
Duplicate atom serial number found: 2732
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2038 messages similar to the above omitted
Ignored bad PDB record found on line 76781
Duplicate atom serial number found: 4775
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Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 77239
Duplicate atom serial number found: 5231
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Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 77630
Duplicate atom serial number found: 5620
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Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 78001
Duplicate atom serial number found: 1
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229 messages similar to the above omitted
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2492 messages similar to the above omitted
Ignored bad PDB record found on line 80736
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2038 messages similar to the above omitted
Ignored bad PDB record found on line 82781
Duplicate atom serial number found: 4775
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Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 83239
Duplicate atom serial number found: 5231
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Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 83630
Duplicate atom serial number found: 5620
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Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 84001
Duplicate atom serial number found: 1
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229 messages similar to the above omitted
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2492 messages similar to the above omitted
Ignored bad PDB record found on line 86736
Duplicate atom serial number found: 2732
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2038 messages similar to the above omitted
Ignored bad PDB record found on line 88781
Duplicate atom serial number found: 4775
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Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 89239
Duplicate atom serial number found: 5231
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Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 89630
Duplicate atom serial number found: 5620
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364 messages similar to the above omitted
Ignored bad PDB record found on line 90001
Duplicate atom serial number found: 1
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229 messages similar to the above omitted
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2492 messages similar to the above omitted
Ignored bad PDB record found on line 92736
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2038 messages similar to the above omitted
Ignored bad PDB record found on line 94781
Duplicate atom serial number found: 4775
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Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 95239
Duplicate atom serial number found: 5231
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Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 95630
Duplicate atom serial number found: 5620
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Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 96001
Duplicate atom serial number found: 1
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229 messages similar to the above omitted
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2492 messages similar to the above omitted
Ignored bad PDB record found on line 98736
Duplicate atom serial number found: 2732
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2038 messages similar to the above omitted
Ignored bad PDB record found on line 100781
Duplicate atom serial number found: 4775
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Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 101239
Duplicate atom serial number found: 5231
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Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 101630
Duplicate atom serial number found: 5620
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Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 102001
Duplicate atom serial number found: 1
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229 messages similar to the above omitted
Ignored bad PDB record found on line 102237
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2492 messages similar to the above omitted
Ignored bad PDB record found on line 104736
Duplicate atom serial number found: 2732
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2038 messages similar to the above omitted
Ignored bad PDB record found on line 106781
Duplicate atom serial number found: 4775
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Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 107239
Duplicate atom serial number found: 5231
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Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 107630
Duplicate atom serial number found: 5620
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Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 108001
Duplicate atom serial number found: 1
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229 messages similar to the above omitted
Ignored bad PDB record found on line 108237
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2492 messages similar to the above omitted
Ignored bad PDB record found on line 110736
Duplicate atom serial number found: 2732
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2038 messages similar to the above omitted
Ignored bad PDB record found on line 112781
Duplicate atom serial number found: 4775
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Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 113239
Duplicate atom serial number found: 5231
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Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 113630
Duplicate atom serial number found: 5620
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Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 114001
Duplicate atom serial number found: 1
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229 messages similar to the above omitted
Ignored bad PDB record found on line 114237
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2492 messages similar to the above omitted
Ignored bad PDB record found on line 116736
Duplicate atom serial number found: 2732
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Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 118781
Duplicate atom serial number found: 4775
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Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 119239
Duplicate atom serial number found: 5231
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Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 119630
Duplicate atom serial number found: 5620
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Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 120001
Duplicate atom serial number found: 1
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229 messages similar to the above omitted
Ignored bad PDB record found on line 120237
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2492 messages similar to the above omitted
Ignored bad PDB record found on line 122736
Duplicate atom serial number found: 2732
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Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 124781
Duplicate atom serial number found: 4775
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Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 125239
Duplicate atom serial number found: 5231
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Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 125630
Duplicate atom serial number found: 5620
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Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 126001
Duplicate atom serial number found: 1
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229 messages similar to the above omitted
Ignored bad PDB record found on line 126237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 128736
Duplicate atom serial number found: 2732
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Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 130781
Duplicate atom serial number found: 4775
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Duplicate atom serial number found: 4777
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Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 131239
Duplicate atom serial number found: 5231
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Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 131630
Duplicate atom serial number found: 5620
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Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 132001
Duplicate atom serial number found: 1
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229 messages similar to the above omitted
Ignored bad PDB record found on line 132237
Duplicate atom serial number found: 235
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2492 messages similar to the above omitted
Ignored bad PDB record found on line 134736
Duplicate atom serial number found: 2732
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Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 136781
Duplicate atom serial number found: 4775
Duplicate atom serial number found: 4776
Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 137239
Duplicate atom serial number found: 5231
Duplicate atom serial number found: 5232
Duplicate atom serial number found: 5233
Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 137630
Duplicate atom serial number found: 5620
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Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 138001
Duplicate atom serial number found: 1
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Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 138237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 140736
Duplicate atom serial number found: 2732
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Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 142781
Duplicate atom serial number found: 4775
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Duplicate atom serial number found: 4777
Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 143239
Duplicate atom serial number found: 5231
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Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 143630
Duplicate atom serial number found: 5620
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Duplicate atom serial number found: 5622
Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 144001
Duplicate atom serial number found: 1
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229 messages similar to the above omitted
Ignored bad PDB record found on line 144237
Duplicate atom serial number found: 235
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2492 messages similar to the above omitted
Ignored bad PDB record found on line 146736
Duplicate atom serial number found: 2732
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Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 148781
Duplicate atom serial number found: 4775
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Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 149239
Duplicate atom serial number found: 5231
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Duplicate atom serial number found: 5234
Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 149630
Duplicate atom serial number found: 5620
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Duplicate atom serial number found: 5623
Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 150001
Duplicate atom serial number found: 1
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229 messages similar to the above omitted
Ignored bad PDB record found on line 150237
Duplicate atom serial number found: 235
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2492 messages similar to the above omitted
Ignored bad PDB record found on line 152736
Duplicate atom serial number found: 2732
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Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 154781
Duplicate atom serial number found: 4775
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Duplicate atom serial number found: 4778
Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 155239
Duplicate atom serial number found: 5231
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Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 155630
Duplicate atom serial number found: 5620
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Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 156001
Duplicate atom serial number found: 1
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229 messages similar to the above omitted
Ignored bad PDB record found on line 156237
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 239
2492 messages similar to the above omitted
Ignored bad PDB record found on line 158736
Duplicate atom serial number found: 2732
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Duplicate atom serial number found: 2736
2038 messages similar to the above omitted
Ignored bad PDB record found on line 160781
Duplicate atom serial number found: 4775
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Duplicate atom serial number found: 4779
451 messages similar to the above omitted
Ignored bad PDB record found on line 161239
Duplicate atom serial number found: 5231
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Duplicate atom serial number found: 5235
384 messages similar to the above omitted
Ignored bad PDB record found on line 161630
Duplicate atom serial number found: 5620
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Duplicate atom serial number found: 5624
364 messages similar to the above omitted
Ignored bad PDB record found on line 162001
Duplicate atom serial number found: 1
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229 messages similar to the above omitted
Ignored bad PDB record found on line 162237
Duplicate atom serial number found: 235
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2492 messages similar to the above omitted
Ignored bad PDB record found on line 164736
Duplicate atom serial number found: 2732
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2038 messages similar to the above omitted
Ignored bad PDB record found on line 166781
Duplicate atom serial number found: 4775
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451 messages similar to the above omitted
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Chain information for Density_PAA_apply_ncs_15.pdb #8
---
Chain | Description
A BC BF DB DE F FA FD FG HC HF I JB JE LA LD LG NC NF PB PE RA RD RG S TC TF
VB VE XA XD Z ZC ZF | No description available
AA AD AG B CC CF EB EE G GA GD GG IC IF J KB KE MA MD MG OC OF QB QE SA SD SG
T UC UF WB WE YA YD | No description available
AB AE CA CD CG D EC EF GB GE IA ID IG KC KF L MB ME N OA OD OG QC QF SB SE UA
UD UG W WC WF YB YE | No description available
AC AF CB CE EA ED EG GC GF H IB IE KA KD KG MC MF OB OE Q QA QD QG R SC SF UB
UE WA WD WG Y YC YF | No description available
BA BD BG C DC DF FB FE HA HD HG JC JF K LB LE M NA ND NG PC PF RB RE TA TD TG
V VC VF XB XE ZA ZD | No description available
BB BE DA DD DG E FC FF HB HE JA JD JG LC LF NB NE O P PA PD PG RC RF TB TE VA
VD VG X XC XF ZB ZE | No description available
> show #!5 models
> show #!4 models
> show #!3 models
> hide #!4 models
> hide #!5 models
> hide #!3 models
> show #!6 models
> marker segment #9 position 485.8,307.7,456.7 toPosition 509.1,371,524.4
> color yellow radius 0.5113 label 95.58 labelHeight 9.558 labelColor yellow
> close #9
> open "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly__C-
> ring]/Mutations, Maps and Models/PAA/MSC_PAA_LocalRef_HighRes_Aligned.mrc"
Opened MSC_PAA_LocalRef_HighRes_Aligned.mrc as #9, grid size 512,512,512,
pixel 2.05, shown at level 0.0798, step 2, values float32
> hide #!6 models
> volume #9 level 0.2142
> show #!7-8 cartoons
> hide #!7-8 atoms
[Repeated 1 time(s)]
> volume #9 step 1
> volume #9 level 0.1334
> volume #9 level 0.2853
> hide #!7 models
> hide #!8 models
> hide #!9 models
> show #!1 models
> close #2-9
> color sequential polymers target c red:blue
Expected a keyword
> color sequential polymers target c
> color sequential polymers target c palette
Missing "palette" keyword's argument
> color sequential polymers target c palette red-white-blue
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,1
Model Number: MK183LL/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 10151.41.12
OS Loader Version: 10151.41.12
Software:
System Software Overview:
System Version: macOS 14.1.1 (23B81)
Kernel Version: Darwin 23.1.0
Time since boot: 8 hours, 59 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
LG HDR WQHD:
Resolution: 3840 x 1600 (Ultra-wide 4K)
UI Looks like: 3840 x 1600 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Television: Yes
LG HDR WQHD:
Resolution: 3840 x 1600 (Ultra-wide 4K)
UI Looks like: 3840 x 1600 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Television: Yes
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
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: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
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: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7
ChimeraX-CoreFormats: 1.2
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: 1.1.3
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: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBImages: 1.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-QScore: 1.0
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.3
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: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-XMAS: 1.1.2
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
et-xmlfile: 1.1.0
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.0
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openpyxl: 3.1.2
openvr: 1.23.701
packaging: 21.3
pandas: 2.1.0
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
QtRangeSlider: 0.1.5
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
seaborn: 0.12.2
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (5)
comment:1 by , 23 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Depiction |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Color command syntax |
comment:2 by , 23 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
comment:3 by , 23 months ago
Dear Tom
Thank you for responding. You are correct that I I should not be using polymer in my command.
I realized today that I was using the wrong command when I started backtracking myself. The correct command to be used here should have been:
color seq #1/G:107-168 targ c palette yellow:cyan
Apologies for the false alarm.
Thank you
Prash
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, December 20, 2023 2:07:39 PM
To: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Singh, Prashant Kumar <Prashant.k.singh@vanderbilt.edu>
Cc: meng@cgl.ucsf.edu <meng@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #10377: Color command syntax
#10377: Color command syntax
-----------------------------------------+-------------------------
Reporter: Prashant.k.singh@… | Owner: Tom Goddard
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Depiction | Version:
Resolution: can't reproduce | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-----------------------------------------+-------------------------
Changes (by Tom Goddard):
* resolution: => can't reproduce
* status: assigned => closed
Comment:
You say "The cartoon turns into blue instead of red." Apparently you mean
with this command
> color sequential polymers target c palette red-white-blue
This command is coloring each chain of atomic models a single color and
the chains will be colored I think in alphabetical order using chain id
from red to blue. Since I have no idea what model you are coloring I
can't advise on whether it is doing is right. Possibly you misunderstand
what the command is supposed to do.
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comment:4 by , 23 months ago
Correction "color sequential polymers" colors by each unique amino acid sequence a unique color. It does not color each chain id a unique color. Since the polymers are not in any specific order the colors used from the palette is not predictable. Here is the documentation
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html#sequential
Note:
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for help on using tickets.
You say "The cartoon turns into blue instead of red." Apparently you mean with this command
This command is coloring each chain of atomic models a single color and the chains will be colored I think in alphabetical order using chain id from red to blue. Since I have no idea what model you are coloring I can't advise on whether it is doing is right. Possibly you misunderstand what the command is supposed to do.