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#3309 closed defect (wontfix)
some color commands should only target atomic models
| Reported by: | Tristan Croll | Owned by: | Tom Goddard |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Depiction | Version: | |
| Keywords: | Cc: | Elaine Meng, pett | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 1.0rc202005242323 (2020-05-24 23:23:37 UTC)
Description
Color by attribute commands probably shouldn't apply to markers. I just did "color bychain; color byhet" and all my colour-coded markers turned white.
Log:
UCSF ChimeraX version: 1.0rc202005242323 (2020-05-24)
© 2016-2020 Regents of the University of California. All rights reserved.
> open working_renumbered_and_renamed.cxs
restore_snapshot for "RotamerRestraintMgr" returned None
Log from Mon May 25 23:00:27 2020UCSF ChimeraX version: 1.0rc202005242323
(2020-05-24)
© 2016-2020 Regents of the University of California. All rights reserved.
> open working.cxs
restore_snapshot for "RotamerRestraintMgr" returned None
Log from Mon May 25 22:28:45 2020
> save working.cxs
> save working.cxs
> sequence chain /aa
Alignment identifier is 1.2.aa
> sequence chain /BA
Alignment identifier is 1.2.BA
> sequence chain /AA
Alignment identifier is 1.2.AA
> sequence chain /AA
Alignment identifier is 1.2.AA
> view lse
Expected an objects specifier or a view name or a keyword
> view sel
> sequence chain /BA
Alignment identifier is 1.2.BA
> sequence chain /BB
Alignment identifier is 1.2.BB
> sequence chain /ba
Alignment identifier is 1.2.ba
> view sel
> isolde stepto /BA
Multiple residues selected! Going to the first...
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> isolde stepto /ba
Multiple residues selected! Going to the first...
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> select clear
> isolde stepto /bb
Multiple residues selected! Going to the first...
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> select clear
> isolde stepto /bc
Multiple residues selected! Going to the first...
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> select clear
> isolde stepto /bd
Multiple residues selected! Going to the first...
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> view sel
> select up
7 atoms, 6 bonds, 1 model selected
> delete sel
> isolde stepto /bd
Multiple residues selected! Going to the first...
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> isolde stepto /be
Multiple residues selected! Going to the first...
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> isolde stepto /bf
Multiple residues selected! Going to the first...
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> isolde stepto /bg
Multiple residues selected! Going to the first...
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> select clear
> isolde stepto /bh
Multiple residues selected! Going to the first...
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> view sel
> select up
7 atoms, 6 bonds, 1 model selected
> delete sel
> isolde stepto /bh
Multiple residues selected! Going to the first...
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> select clear
> isolde stepto /bg
Multiple residues selected! Going to the first...
> isolde stepto /bg
Multiple residues selected! Going to the first...
> isolde stepto /bh
Multiple residues selected! Going to the first...
> isolde stepto /bi
Multiple residues selected! Going to the first...
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> select clear
> isolde stepto /bj
Multiple residues selected! Going to the first...
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> select clear
> isolde stepto /bk
Multiple residues selected! Going to the first...
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> select clear
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
> isolde stepto /bl
Multiple residues selected! Going to the first...
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> isolde stepto /bm
Multiple residues selected! Going to the first...
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> select clear
> isolde stepto /bn
Multiple residues selected! Going to the first...
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> select clear
> select clear
> isolde stepto /bo
Multiple residues selected! Going to the first...
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> view sel
> select up
7 atoms, 6 bonds, 1 model selected
> delete sel
> isolde stepto /bo
Multiple residues selected! Going to the first...
> isolde stepto /bo
Multiple residues selected! Going to the first...
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> select clear
> isolde stepto /bp
Multiple residues selected! Going to the first...
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> isolde stepto /bq
Selection contains no residues!
> select clear
> save working.cxs
opened ChimeraX session
> setattr /AF c chain_id QF
Assigning chain_id attribute to 1 item
> setattr /AF r chain_id QF
Assigning chain_id attribute to 2 items
> setattr /BF c chain_id RF
Assigning chain_id attribute to 1 item
> setattr /BF r chain_id RF
Assigning chain_id attribute to 1 item
> setattr /QF c chain_id BF
Assigning chain_id attribute to 1 item
> setattr /QF r chain_id BF
Assigning chain_id attribute to 2 items
> setattr /RF r chain_id AF
Assigning chain_id attribute to 46 items
Cannot set attribute 'chain_id' to 'AF'
> setattr /RF c chain_id AF
Assigning chain_id attribute to 1 item
> setattr /RF r chain_id AF
Assigning chain_id attribute to 1 item
> select /AD,AE,AF
2589 atoms, 2655 bonds, 13 pseudobonds, 3 models selected
> select /AD,AE,AF,AG
3455 atoms, 3541 bonds, 17 pseudobonds, 3 models selected
> select clear
> setattr /AG c chain_id QG
Assigning chain_id attribute to 1 item
> setattr /AG r chain_id QG
Assigning chain_id attribute to 2 items
> setattr /BG c chain_id RG
Assigning chain_id attribute to 1 item
> setattr /BG r chain_id RG
Assigning chain_id attribute to 1 item
> setattr /QG c chain_id BG
Assigning chain_id attribute to 1 item
> setattr /QG r chain_id BG
Assigning chain_id attribute to 2 items
> setattr /RG c chain_id /AG
Assigning chain_id attribute to 1 item
> setattr /RG r chain_id /AG
Assigning chain_id attribute to 1 item
> select /AD,AE,AF,AG
2589 atoms, 2655 bonds, 13 pseudobonds, 3 models selected
> select clear
> select /AG
Nothing selected
> select /AD
863 atoms, 885 bonds, 4 pseudobonds, 2 models selected
> select /AD,AE,AF
2589 atoms, 2655 bonds, 13 pseudobonds, 3 models selected
> select /AG
Nothing selected
> select clear
> ui tool show Shell
/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved
warn("IPython History requires SQLite, your history will not be saved")
> isolde start
> set selectionWidth 4
Done loading forcefield
> select /AA-AW
19950 atoms, 20455 bonds, 93 pseudobonds, 3 models selected
> select /AA-AX
20813 atoms, 21340 bonds, 97 pseudobonds, 3 models selected
> select clear
> isolde stepto /AA
Multiple residues selected! Going to the first...
> select /AA-AX
20813 atoms, 21340 bonds, 97 pseudobonds, 3 models selected
> select clear
> isolde stepto /BA
Multiple residues selected! Going to the first...
> select /B*,b*
34747 atoms, 35556 bonds, 161 pseudobonds, 4 models selected
> select /B
369 atoms, 375 bonds, 1 pseudobond, 2 models selected
> view sel
Traceback (most recent call last):
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/isolde.py", line 2570, in _xtal_mask_to_selection
self._xtal_mask_to_atoms(sel, focus)
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/isolde.py", line 2579, in _xtal_mask_to_atoms
atoms, 0, context, cutoff, focus=focus)
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/symmetry.py", line 972, in
isolate_and_cover_selection
extra_padding=extra_padding)
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/map_mgr.py", line 358, in cover_atoms
zm.set_symmetry_map(atoms, transforms, transform_indices)
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 111, in set_symmetry_map
self.structure = self._unique_structure(atoms)
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 177, in
_unique_structure
raise TypeError('All atoms for zone mask must be from a single model!')
TypeError: All atoms for zone mask must be from a single model!
TypeError: All atoms for zone mask must be from a single model!
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 177, in
_unique_structure
raise TypeError('All atoms for zone mask must be from a single model!')
See log for complete Python traceback.
> select /B
369 atoms, 375 bonds, 1 pseudobond, 2 models selected
> isolde stepto /BX
Multiple residues selected! Going to the first...
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
No template found for residue AA57 (BCL)
Doing nothing
> isolde stepto /BX
Multiple residues selected! Going to the first...
> save working_renumbered_and_renamed.cxs
opened ChimeraX session
> select :UA
Nothing selected
> select /UA
320 atoms, 319 bonds, 1 model selected
> isolde start
> set selectionWidth 4
Done loading forcefield
> clipper spotlight radius 13.00
> clipper spotlight radius 14.00
> clipper spotlight radius 15.00
> clipper spotlight radius 16.00
> clipper spotlight radius 17.00
> ui tool show "Build Structure"
> build start peptide #1.2 AAAAAAAAAAAAAAA -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> rotLib Dunbrack chainId UB
> select /UB
76 atoms, 75 bonds, 1 model selected
> style sel stick
Changed 76 atom styles
> show sel cartoons
> color sel bychain
> color sel byhetero
> ui tool show Shell
/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved
warn("IPython History requires SQLite, your history will not be saved")
> isolde ignore ~sel
ISOLDE: currently ignoring 4889 residues in model 1.2
ISOLDE: currently ignoring 3824 residues in model 2
ISOLDE: currently ignoring 40 residues in model 3
No template found for residue UB1 (ALA)
Adding hydrogens
Summary of feedback from adding hydrogens to extended_rough.cif #1.2
---
notes | No usable SEQRES records for extended_rough.cif (#1.2) chain AA;
guessing termini instead
No usable SEQRES records for extended_rough.cif (#1.2) chain AB; guessing
termini instead
No usable SEQRES records for extended_rough.cif (#1.2) chain AC; guessing
termini instead
No usable SEQRES records for extended_rough.cif (#1.2) chain AD; guessing
termini instead
No usable SEQRES records for extended_rough.cif (#1.2) chain AE; guessing
termini instead
82 messages similar to the above omitted
Chain-initial residues that are actual N termini: extended_rough.cif #1.2/C
ALA 15, extended_rough.cif #1.2/H1 MET 1, extended_rough.cif #1.2/H2 SER 1,
extended_rough.cif #1.2/L ALA 1, extended_rough.cif #1.2/M MET 1,
extended_rough.cif #1.2/aa HIS 2, extended_rough.cif #1.2/ab MET 1,
extended_rough.cif #1.2/ac MET 1, extended_rough.cif #1.2/ad MET 1,
extended_rough.cif #1.2/ae MET 1, extended_rough.cif #1.2/af MET 1,
extended_rough.cif #1.2/ag MET 1, extended_rough.cif #1.2/ah MET 1,
extended_rough.cif #1.2/ai MET 1, extended_rough.cif #1.2/aj MET 1,
extended_rough.cif #1.2/ak MET 1, extended_rough.cif #1.2/al MET 1,
extended_rough.cif #1.2/am MET 1, extended_rough.cif #1.2/an MET 1,
extended_rough.cif #1.2/ao MET 1, extended_rough.cif #1.2/ap MET 1,
extended_rough.cif #1.2/UB ALA 1
Chain-initial residues that are not actual N termini: extended_rough.cif
#1.2/AA HIS 2, extended_rough.cif #1.2/AB HIS 2, extended_rough.cif #1.2/AC
HIS 2, extended_rough.cif #1.2/AD HIS 2, extended_rough.cif #1.2/AE HIS 2,
extended_rough.cif #1.2/BF GLY 6, extended_rough.cif #1.2/BG GLY 6,
extended_rough.cif #1.2/AH HIS 2, extended_rough.cif #1.2/AI HIS 2,
extended_rough.cif #1.2/AJ HIS 2, extended_rough.cif #1.2/AK HIS 2,
extended_rough.cif #1.2/AL HIS 2, extended_rough.cif #1.2/AM HIS 2,
extended_rough.cif #1.2/AN HIS 2, extended_rough.cif #1.2/AO HIS 2,
extended_rough.cif #1.2/AP HIS 2, extended_rough.cif #1.2/AQ HIS 2,
extended_rough.cif #1.2/AR HIS 2, extended_rough.cif #1.2/AS HIS 2,
extended_rough.cif #1.2/AT HIS 2, extended_rough.cif #1.2/AU HIS 2,
extended_rough.cif #1.2/AV HIS 2, extended_rough.cif #1.2/AW HIS 2,
extended_rough.cif #1.2/AX HIS 2, extended_rough.cif #1.2/BA GLY 6,
extended_rough.cif #1.2/BB GLY 5, extended_rough.cif #1.2/BC GLY 6,
extended_rough.cif #1.2/BD GLY 5, extended_rough.cif #1.2/BE GLY 5,
extended_rough.cif #1.2/AF HIS 2, extended_rough.cif #1.2/AG HIS 2,
extended_rough.cif #1.2/BH GLY 6, extended_rough.cif #1.2/BI GLY 5,
extended_rough.cif #1.2/BJ GLY 6, extended_rough.cif #1.2/BK GLY 6,
extended_rough.cif #1.2/BL GLY 6, extended_rough.cif #1.2/BM GLY 6,
extended_rough.cif #1.2/BN GLY 6, extended_rough.cif #1.2/BO GLY 6,
extended_rough.cif #1.2/BP GLY 6, extended_rough.cif #1.2/BQ GLY 6,
extended_rough.cif #1.2/BR GLY 6, extended_rough.cif #1.2/BS GLY 6,
extended_rough.cif #1.2/BT GLY 6, extended_rough.cif #1.2/BU GLY 6,
extended_rough.cif #1.2/BV GLY 5, extended_rough.cif #1.2/BW GLY 5,
extended_rough.cif #1.2/BX GLY 6, extended_rough.cif #1.2/H2 ASP 9,
extended_rough.cif #1.2/ba GLY 6, extended_rough.cif #1.2/bb GLY 6,
extended_rough.cif #1.2/bc GLY 6, extended_rough.cif #1.2/bd GLY 6,
extended_rough.cif #1.2/be GLY 6, extended_rough.cif #1.2/bf GLY 6,
extended_rough.cif #1.2/bg GLY 6, extended_rough.cif #1.2/bh GLY 6,
extended_rough.cif #1.2/bi GLY 6, extended_rough.cif #1.2/bj GLY 6,
extended_rough.cif #1.2/bk GLY 6, extended_rough.cif #1.2/bl GLY 6,
extended_rough.cif #1.2/bm GLY 6, extended_rough.cif #1.2/bn GLY 5,
extended_rough.cif #1.2/bo GLY 6, extended_rough.cif #1.2/bp GLY 6,
extended_rough.cif #1.2/UA ALA 2
Chain-final residues that are actual C termini: extended_rough.cif #1.2/BF PHE
44, extended_rough.cif #1.2/BG PHE 44, extended_rough.cif #1.2/BA PHE 44,
extended_rough.cif #1.2/BB PHE 44, extended_rough.cif #1.2/BC PHE 44,
extended_rough.cif #1.2/BD PHE 44, extended_rough.cif #1.2/BE PHE 44,
extended_rough.cif #1.2/BH PHE 44, extended_rough.cif #1.2/BI PHE 44,
extended_rough.cif #1.2/BJ PHE 44, extended_rough.cif #1.2/BK PHE 44,
extended_rough.cif #1.2/BL PHE 44, extended_rough.cif #1.2/BM PHE 44,
extended_rough.cif #1.2/BN PHE 44, extended_rough.cif #1.2/BO PHE 44,
extended_rough.cif #1.2/BP PHE 44, extended_rough.cif #1.2/BQ PHE 44,
extended_rough.cif #1.2/BR PHE 44, extended_rough.cif #1.2/BS PHE 44,
extended_rough.cif #1.2/BT PHE 44, extended_rough.cif #1.2/BU PHE 44,
extended_rough.cif #1.2/BV PHE 44, extended_rough.cif #1.2/BW PHE 44,
extended_rough.cif #1.2/BX PHE 44, extended_rough.cif #1.2/C ARG 302,
extended_rough.cif #1.2/L LYS 273, extended_rough.cif #1.2/ba PHE 44,
extended_rough.cif #1.2/bb PHE 44, extended_rough.cif #1.2/bc PHE 44,
extended_rough.cif #1.2/bd PHE 44, extended_rough.cif #1.2/be PHE 44,
extended_rough.cif #1.2/bf PHE 44, extended_rough.cif #1.2/bg PHE 44,
extended_rough.cif #1.2/bh PHE 44, extended_rough.cif #1.2/bi PHE 44,
extended_rough.cif #1.2/bj PHE 44, extended_rough.cif #1.2/bk PHE 44,
extended_rough.cif #1.2/bl PHE 44, extended_rough.cif #1.2/bm PHE 44,
extended_rough.cif #1.2/bn PHE 44, extended_rough.cif #1.2/bo PHE 44,
extended_rough.cif #1.2/bp PHE 44, extended_rough.cif #1.2/UB ALA 15
Chain-final residues that are not actual C termini: extended_rough.cif #1.2/AA
TYR 46, extended_rough.cif #1.2/AB TYR 46, extended_rough.cif #1.2/AC TYR 46,
extended_rough.cif #1.2/AD TYR 46, extended_rough.cif #1.2/AE TYR 46,
extended_rough.cif #1.2/AH TYR 46, extended_rough.cif #1.2/AI TYR 46,
extended_rough.cif #1.2/AJ TYR 46, extended_rough.cif #1.2/AK TYR 46,
extended_rough.cif #1.2/AL TYR 46, extended_rough.cif #1.2/AM TYR 46,
extended_rough.cif #1.2/AN TYR 46, extended_rough.cif #1.2/AO TYR 46,
extended_rough.cif #1.2/AP TYR 46, extended_rough.cif #1.2/AQ TYR 46,
extended_rough.cif #1.2/AR TYR 46, extended_rough.cif #1.2/AS TYR 46,
extended_rough.cif #1.2/AT TYR 46, extended_rough.cif #1.2/AU TYR 46,
extended_rough.cif #1.2/AV TYR 46, extended_rough.cif #1.2/AW TYR 46,
extended_rough.cif #1.2/AX TYR 46, extended_rough.cif #1.2/AF TYR 46,
extended_rough.cif #1.2/AG TYR 46, extended_rough.cif #1.2/H1 LYS 53,
extended_rough.cif #1.2/H2 ALA 8, extended_rough.cif #1.2/H2 PRO 7,
extended_rough.cif #1.2/M TYR 324, extended_rough.cif #1.2/aa ALA 60,
extended_rough.cif #1.2/ab ALA 60, extended_rough.cif #1.2/ac ALA 60,
extended_rough.cif #1.2/ad ALA 60, extended_rough.cif #1.2/ae ALA 60,
extended_rough.cif #1.2/af ALA 60, extended_rough.cif #1.2/ag ALA 60,
extended_rough.cif #1.2/ah ALA 60, extended_rough.cif #1.2/ai ALA 60,
extended_rough.cif #1.2/aj ALA 60, extended_rough.cif #1.2/ak ALA 60,
extended_rough.cif #1.2/al ALA 60, extended_rough.cif #1.2/am ALA 60,
extended_rough.cif #1.2/an ALA 60, extended_rough.cif #1.2/ao ALA 60,
extended_rough.cif #1.2/ap ALA 60, extended_rough.cif #1.2/UA ALA 33
4893 hydrogen bonds
extended_rough.cif #1.2/AA TYR 46 is not terminus, removing H atom from 'C'
extended_rough.cif #1.2/AB TYR 46 is not terminus, removing H atom from 'C'
extended_rough.cif #1.2/AC TYR 46 is not terminus, removing H atom from 'C'
extended_rough.cif #1.2/AD TYR 46 is not terminus, removing H atom from 'C'
extended_rough.cif #1.2/AE TYR 46 is not terminus, removing H atom from 'C'
38 messages similar to the above omitted
96 hydrogens added
> select clear
> select up
10 atoms, 9 bonds, 1 model selected
> select up
130 atoms, 129 bonds, 1 model selected
> select /UB
153 atoms, 152 bonds, 1 model selected
> select /UA
320 atoms, 319 bonds, 1 model selected
> select /UB
153 atoms, 152 bonds, 1 model selected
> clipper spotlight radius 18.00
> clipper spotlight radius 19.00
> clipper spotlight radius 20.00
> clipper spotlight radius 21.00
> clipper spotlight radius 22.00
> clipper spotlight radius 23.00
> clipper spotlight radius 24.00
> clipper spotlight radius 25.00
> ui mousemode right "mark point"
> marker #3 position 141.5,132.2,158.9 color #ef2929 radius 1
> select /UB
153 atoms, 152 bonds, 1 model selected
> isolde ~ignore
No template found for residue bg7 (MET)
Doing nothing
> delete sel
> select /UA
320 atoms, 319 bonds, 1 model selected
> select /UB
153 atoms, 152 bonds, 1 model selected
> select clear
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
> select up
12 atoms, 11 bonds, 1 model selected
> select up
172 atoms, 171 bonds, 1 model selected
> select down
12 atoms, 11 bonds, 1 model selected
> select up
172 atoms, 171 bonds, 1 model selected
> select clear
> ui mousemode right swapaa
> swapaa mousemode #1.2/UB:4 ALA
> delete sel
> select up
6 atoms, 5 bonds, 1 model selected
> select up
126 atoms, 125 bonds, 1 model selected
No template found for residue UB4 (ALA)
Doing nothing
> delete sel
> select up
5 atoms, 4 bonds, 1 model selected
> select up
125 atoms, 124 bonds, 1 model selected
> delete sel
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> select /UB
175 atoms, 174 bonds, 1 model selected
> select clear
> save working.cxs
> build start peptide #1.2 AAAAAAAAAAAAAAA -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> rotLib Dunbrack chainId UC
> select /UC
76 atoms, 75 bonds, 1 model selected
> color sel bychain
> color sel byhetero
> style sel stick
Changed 76 atom styles
> show sel cartoons
> addh
Summary of feedback from adding hydrogens to multiple structures
---
warning | Not adding hydrogens to extended_rough.cif #1.2/UB ALA 4 CA because
it is missing heavy-atom bond partners
notes | No usable SEQRES records for extended_rough.cif (#1.2) chain AA;
guessing termini instead
No usable SEQRES records for extended_rough.cif (#1.2) chain AB; guessing
termini instead
No usable SEQRES records for extended_rough.cif (#1.2) chain AC; guessing
termini instead
No usable SEQRES records for extended_rough.cif (#1.2) chain AD; guessing
termini instead
No usable SEQRES records for extended_rough.cif (#1.2) chain AE; guessing
termini instead
83 messages similar to the above omitted
Chain-initial residues that are actual N termini: extended_rough.cif #1.2/C
ALA 15, extended_rough.cif #1.2/H1 MET 1, extended_rough.cif #1.2/H2 SER 1,
extended_rough.cif #1.2/L ALA 1, extended_rough.cif #1.2/M MET 1,
extended_rough.cif #1.2/aa HIS 2, extended_rough.cif #1.2/ab MET 1,
extended_rough.cif #1.2/ac MET 1, extended_rough.cif #1.2/ad MET 1,
extended_rough.cif #1.2/ae MET 1, extended_rough.cif #1.2/af MET 1,
extended_rough.cif #1.2/ag MET 1, extended_rough.cif #1.2/ah MET 1,
extended_rough.cif #1.2/ai MET 1, extended_rough.cif #1.2/aj MET 1,
extended_rough.cif #1.2/ak MET 1, extended_rough.cif #1.2/al MET 1,
extended_rough.cif #1.2/am MET 1, extended_rough.cif #1.2/an MET 1,
extended_rough.cif #1.2/ao MET 1, extended_rough.cif #1.2/ap MET 1,
extended_rough.cif #1.2/UC ALA 1
Chain-initial residues that are not actual N termini: extended_rough.cif
#1.2/AA HIS 2, extended_rough.cif #1.2/AB HIS 2, extended_rough.cif #1.2/AC
HIS 2, extended_rough.cif #1.2/AD HIS 2, extended_rough.cif #1.2/AE HIS 2,
extended_rough.cif #1.2/BF GLY 6, extended_rough.cif #1.2/BG GLY 6,
extended_rough.cif #1.2/AH HIS 2, extended_rough.cif #1.2/AI HIS 2,
extended_rough.cif #1.2/AJ HIS 2, extended_rough.cif #1.2/AK HIS 2,
extended_rough.cif #1.2/AL HIS 2, extended_rough.cif #1.2/AM HIS 2,
extended_rough.cif #1.2/AN HIS 2, extended_rough.cif #1.2/AO HIS 2,
extended_rough.cif #1.2/AP HIS 2, extended_rough.cif #1.2/AQ HIS 2,
extended_rough.cif #1.2/AR HIS 2, extended_rough.cif #1.2/AS HIS 2,
extended_rough.cif #1.2/AT HIS 2, extended_rough.cif #1.2/AU HIS 2,
extended_rough.cif #1.2/AV HIS 2, extended_rough.cif #1.2/AW HIS 2,
extended_rough.cif #1.2/AX HIS 2, extended_rough.cif #1.2/BA GLY 6,
extended_rough.cif #1.2/BB GLY 5, extended_rough.cif #1.2/BC GLY 6,
extended_rough.cif #1.2/BD GLY 5, extended_rough.cif #1.2/BE GLY 5,
extended_rough.cif #1.2/AF HIS 2, extended_rough.cif #1.2/AG HIS 2,
extended_rough.cif #1.2/BH GLY 6, extended_rough.cif #1.2/BI GLY 5,
extended_rough.cif #1.2/BJ GLY 6, extended_rough.cif #1.2/BK GLY 6,
extended_rough.cif #1.2/BL GLY 6, extended_rough.cif #1.2/BM GLY 6,
extended_rough.cif #1.2/BN GLY 6, extended_rough.cif #1.2/BO GLY 6,
extended_rough.cif #1.2/BP GLY 6, extended_rough.cif #1.2/BQ GLY 6,
extended_rough.cif #1.2/BR GLY 6, extended_rough.cif #1.2/BS GLY 6,
extended_rough.cif #1.2/BT GLY 6, extended_rough.cif #1.2/BU GLY 6,
extended_rough.cif #1.2/BV GLY 5, extended_rough.cif #1.2/BW GLY 5,
extended_rough.cif #1.2/BX GLY 6, extended_rough.cif #1.2/H2 ASP 9,
extended_rough.cif #1.2/ba GLY 6, extended_rough.cif #1.2/bb GLY 6,
extended_rough.cif #1.2/bc GLY 6, extended_rough.cif #1.2/bd GLY 6,
extended_rough.cif #1.2/be GLY 6, extended_rough.cif #1.2/bf GLY 6,
extended_rough.cif #1.2/bg GLY 6, extended_rough.cif #1.2/bh GLY 6,
extended_rough.cif #1.2/bi GLY 6, extended_rough.cif #1.2/bj GLY 6,
extended_rough.cif #1.2/bk GLY 6, extended_rough.cif #1.2/bl GLY 6,
extended_rough.cif #1.2/bm GLY 6, extended_rough.cif #1.2/bn GLY 5,
extended_rough.cif #1.2/bo GLY 6, extended_rough.cif #1.2/bp GLY 6,
extended_rough.cif #1.2/UA ALA 2, extended_rough.cif #1.2/UB ALA 18
Chain-final residues that are actual C termini: extended_rough.cif #1.2/BF PHE
44, extended_rough.cif #1.2/BG PHE 44, extended_rough.cif #1.2/BA PHE 44,
extended_rough.cif #1.2/BB PHE 44, extended_rough.cif #1.2/BC PHE 44,
extended_rough.cif #1.2/BD PHE 44, extended_rough.cif #1.2/BE PHE 44,
extended_rough.cif #1.2/BH PHE 44, extended_rough.cif #1.2/BI PHE 44,
extended_rough.cif #1.2/BJ PHE 44, extended_rough.cif #1.2/BK PHE 44,
extended_rough.cif #1.2/BL PHE 44, extended_rough.cif #1.2/BM PHE 44,
extended_rough.cif #1.2/BN PHE 44, extended_rough.cif #1.2/BO PHE 44,
extended_rough.cif #1.2/BP PHE 44, extended_rough.cif #1.2/BQ PHE 44,
extended_rough.cif #1.2/BR PHE 44, extended_rough.cif #1.2/BS PHE 44,
extended_rough.cif #1.2/BT PHE 44, extended_rough.cif #1.2/BU PHE 44,
extended_rough.cif #1.2/BV PHE 44, extended_rough.cif #1.2/BW PHE 44,
extended_rough.cif #1.2/BX PHE 44, extended_rough.cif #1.2/C ARG 302,
extended_rough.cif #1.2/L LYS 273, extended_rough.cif #1.2/ba PHE 44,
extended_rough.cif #1.2/bb PHE 44, extended_rough.cif #1.2/bc PHE 44,
extended_rough.cif #1.2/bd PHE 44, extended_rough.cif #1.2/be PHE 44,
extended_rough.cif #1.2/bf PHE 44, extended_rough.cif #1.2/bg PHE 44,
extended_rough.cif #1.2/bh PHE 44, extended_rough.cif #1.2/bi PHE 44,
extended_rough.cif #1.2/bj PHE 44, extended_rough.cif #1.2/bk PHE 44,
extended_rough.cif #1.2/bl PHE 44, extended_rough.cif #1.2/bm PHE 44,
extended_rough.cif #1.2/bn PHE 44, extended_rough.cif #1.2/bo PHE 44,
extended_rough.cif #1.2/bp PHE 44, extended_rough.cif #1.2/UC ALA 15
Chain-final residues that are not actual C termini: extended_rough.cif #1.2/AA
TYR 46, extended_rough.cif #1.2/AB TYR 46, extended_rough.cif #1.2/AC TYR 46,
extended_rough.cif #1.2/AD TYR 46, extended_rough.cif #1.2/AE TYR 46,
extended_rough.cif #1.2/AH TYR 46, extended_rough.cif #1.2/AI TYR 46,
extended_rough.cif #1.2/AJ TYR 46, extended_rough.cif #1.2/AK TYR 46,
extended_rough.cif #1.2/AL TYR 46, extended_rough.cif #1.2/AM TYR 46,
extended_rough.cif #1.2/AN TYR 46, extended_rough.cif #1.2/AO TYR 46,
extended_rough.cif #1.2/AP TYR 46, extended_rough.cif #1.2/AQ TYR 46,
extended_rough.cif #1.2/AR TYR 46, extended_rough.cif #1.2/AS TYR 46,
extended_rough.cif #1.2/AT TYR 46, extended_rough.cif #1.2/AU TYR 46,
extended_rough.cif #1.2/AV TYR 46, extended_rough.cif #1.2/AW TYR 46,
extended_rough.cif #1.2/AX TYR 46, extended_rough.cif #1.2/AF TYR 46,
extended_rough.cif #1.2/AG TYR 46, extended_rough.cif #1.2/H1 LYS 53,
extended_rough.cif #1.2/H2 ALA 8, extended_rough.cif #1.2/H2 PRO 7,
extended_rough.cif #1.2/M TYR 324, extended_rough.cif #1.2/aa ALA 60,
extended_rough.cif #1.2/ab ALA 60, extended_rough.cif #1.2/ac ALA 60,
extended_rough.cif #1.2/ad ALA 60, extended_rough.cif #1.2/ae ALA 60,
extended_rough.cif #1.2/af ALA 60, extended_rough.cif #1.2/ag ALA 60,
extended_rough.cif #1.2/ah ALA 60, extended_rough.cif #1.2/ai ALA 60,
extended_rough.cif #1.2/aj ALA 60, extended_rough.cif #1.2/ak ALA 60,
extended_rough.cif #1.2/al ALA 60, extended_rough.cif #1.2/am ALA 60,
extended_rough.cif #1.2/an ALA 60, extended_rough.cif #1.2/ao ALA 60,
extended_rough.cif #1.2/ap ALA 60, extended_rough.cif #1.2/UA ALA 33,
extended_rough.cif #1.2/UB ALA 17
4911 hydrogen bonds
extended_rough.cif #1.2/AA TYR 46 is not terminus, removing H atom from 'C'
extended_rough.cif #1.2/AB TYR 46 is not terminus, removing H atom from 'C'
extended_rough.cif #1.2/AC TYR 46 is not terminus, removing H atom from 'C'
extended_rough.cif #1.2/AD TYR 46 is not terminus, removing H atom from 'C'
extended_rough.cif #1.2/AE TYR 46 is not terminus, removing H atom from 'C'
39 messages similar to the above omitted
Termini for 5y5s (#2) chain C determined from SEQRES records
Termini for 5y5s (#2) chain L determined from SEQRES records
Termini for 5y5s (#2) chain M determined from SEQRES records
Termini for 5y5s (#2) chain H determined from SEQRES records
Termini for 5y5s (#2) chain A determined from SEQRES records
31 messages similar to the above omitted
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: 5y5s #2/C CYS 23, 5y5s
#2/L ALA 2, 5y5s #2/M PRO 2, 5y5s #2/H ILE 5, 5y5s #2/A ALA 6, 5y5s #2/B SER
5, 5y5s #2/D ASN 5, 5y5s #2/E LEU 9, 5y5s #2/F ASN 5, 5y5s #2/G SER 5, 5y5s
#2/I THR 3, 5y5s #2/J SER 5, 5y5s #2/K THR 3, 5y5s #2/N SER 5, 5y5s #2/O MET
4, 5y5s #2/P SER 5, 5y5s #2/Q THR 3, 5y5s #2/R LEU 6, 5y5s #2/S THR 3, 5y5s
#2/T LYS 4, 5y5s #2/U THR 3, 5y5s #2/V SER 5, 5y5s #2/W ASN 5, 5y5s #2/X LEU
6, 5y5s #2/Y THR 3, 5y5s #2/Z THR 7, 5y5s #2/1 MET 4, 5y5s #2/2 LEU 6, 5y5s
#2/3 MET 4, 5y5s #2/4 SER 5, 5y5s #2/5 ALA 6, 5y5s #2/6 SER 5, 5y5s #2/7 THR
3, 5y5s #2/8 LEU 6, 5y5s #2/9 THR 3, 5y5s #2/0 LYS 4
Chain-final residues that are actual C termini: 5y5s #2/L TRP 281, 5y5s #2/H
LEU 259, 5y5s #2/B LEU 46, 5y5s #2/E LEU 46, 5y5s #2/G LEU 46, 5y5s #2/J LEU
46, 5y5s #2/N LEU 46, 5y5s #2/P LEU 46, 5y5s #2/R LEU 46, 5y5s #2/T LEU 46,
5y5s #2/V LEU 46, 5y5s #2/X LEU 46, 5y5s #2/Z LEU 46, 5y5s #2/2 LEU 46, 5y5s
#2/4 LEU 46, 5y5s #2/6 LEU 46, 5y5s #2/8 LEU 46, 5y5s #2/0 LEU 46
Chain-final residues that are not actual C termini: 5y5s #2/C THR 333, 5y5s
#2/M THR 319, 5y5s #2/A GLY 59, 5y5s #2/D GLY 59, 5y5s #2/F GLY 59, 5y5s #2/I
GLY 59, 5y5s #2/K GLY 59, 5y5s #2/O GLY 59, 5y5s #2/Q GLY 59, 5y5s #2/S LEU
58, 5y5s #2/U LYS 60, 5y5s #2/W LYS 60, 5y5s #2/Y GLY 59, 5y5s #2/1 GLY 59,
5y5s #2/3 GLY 59, 5y5s #2/5 GLY 59, 5y5s #2/7 GLY 59, 5y5s #2/9 GLY 59
Missing OXT added to C-terminal residue 5y5s #2/H LEU 259
5782 hydrogen bonds
Adding 'H' to 5y5s #2/C CYS 23
Adding 'H' to 5y5s #2/L ALA 2
Adding 'H' to 5y5s #2/H ILE 5
Adding 'H' to 5y5s #2/A ALA 6
Adding 'H' to 5y5s #2/B SER 5
30 messages similar to the above omitted
5y5s #2/C THR 333 is not terminus, removing H atom from 'C'
5y5s #2/M THR 319 is not terminus, removing H atom from 'C'
5y5s #2/A GLY 59 is not terminus, removing H atom from 'C'
5y5s #2/D GLY 59 is not terminus, removing H atom from 'C'
5y5s #2/F GLY 59 is not terminus, removing H atom from 'C'
13 messages similar to the above omitted
30197 hydrogens added
> isolde ignore ~sel
ISOLDE: currently ignoring 3824 residues in model 2
ISOLDE: currently ignoring 4922 residues in model 1.2
ISOLDE: currently ignoring 41 residues in model 3
> select up
10 atoms, 9 bonds, 1 model selected
> select up
130 atoms, 129 bonds, 1 model selected
Traceback (most recent call last):
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/isolde.py", line 2697, in _start_sim_or_toggle_pause
self.start_sim()
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/isolde.py", line 2717, in start_sim
self.params, self.sim_params, excluded_residues = self.ignored_residues)
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 586, in __init__
self._prepare_mdff_managers()
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 862, in
_prepare_mdff_managers
focus = False)
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/symmetry.py", line 972, in
isolate_and_cover_selection
extra_padding=extra_padding)
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/map_mgr.py", line 358, in cover_atoms
zm.set_symmetry_map(atoms, transforms, transform_indices)
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 111, in set_symmetry_map
self.structure = self._unique_structure(atoms)
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 177, in
_unique_structure
raise TypeError('All atoms for zone mask must be from a single model!')
TypeError: All atoms for zone mask must be from a single model!
TypeError: All atoms for zone mask must be from a single model!
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 177, in
_unique_structure
raise TypeError('All atoms for zone mask must be from a single model!')
See log for complete Python traceback.
> isolde ~ignore
> color bychain
> color byhetero
> select /UC
153 atoms, 152 bonds, 1 model selected
> isolde ignore ~sel
ISOLDE: currently ignoring 3824 residues in model 2
ISOLDE: currently ignoring 4907 residues in model 1.2
ISOLDE: currently ignoring 41 residues in model 3
OpenGL version: 3.3.0 NVIDIA 440.33.01
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
total used free shared buff/cache available
Mem: 62G 5.2G 48G 142M 8.6G 56G
Swap: 4.9G 0B 4.9G
Graphics:
03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:11df]
Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
Change History (8)
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Depiction |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → some color commands should only target atomic models |
comment:2 by , 5 years ago
| Resolution: | → wontfix |
|---|---|
| Status: | assigned → closed |
comment:3 by , 5 years ago
I'm kind of wishy washy on this one. If Tristan's desired usage scenario is the 95% case, you should probably make it default to working the way he wants, but possible to color the marker sets with a slightly longer command. If it's 70/30, then suddenly consistency might be more important. At any rate, marker sets are Tom's baby, so I'm going to defer to him one this one.
follow-up: 4 comment:4 by , 5 years ago
I'm open to persuasion. An important factor is that adding the special mechanisms to over-ride the guessing what the user wanted adds complexity and takes time. Given that we are maintaining a feature set that use to have more than double the funding in days of yore, it will be hard to get me to spend time on making obscure uses work their best.
follow-up: 5 comment:5 by , 5 years ago
I would think the most common use would be the “Marker” right-mouse-button tool, which doesn’t signal to the user in any way that the things being added are atoms. The way I was using that was to mark points of interest (unfilled regions corresponding to unknown ligands) with each colour corresponding to a set of symmetry-related sites. The problem was that I’d already made a number of different commands before I realised their colours had been wiped, so undo was not an option. That’s unexpected behaviour, and I think it’ll come out looking like a bug to the average user.
follow-up: 6 comment:6 by , 5 years ago
The problem isn't just what is the most common use case. I agree that in most cases the user does not intend "color bychain" to color markers. But when a user does have multichain marker set with 200 actin filaments in a tomogram each as a separate chain and does want "color bychain" to work on them, how do they do it? Of course I could add a special option to let them do it. I could add those special options to the many commands where it makes sense, but I don't have time to fix such rare cases. We have come up against this before with what ISOLDE needs versus what the broad ChimeraX user community needs. ISOLDE is a well-defined and complex work-flow. That has never been Chimera or ChimeraX's strength, which is flexibility for doing non-well-defined work flows.
follow-up: 7 comment:7 by , 5 years ago
Is there a model attribute that can be used for command-line specification? Yeah, you'd still have to be "advanced" but at least it wouldn't require entering the specific model numbers... e.g. "color bychain ##is_atomic" or something like that?
comment:8 by , 5 years ago
There is no such attribute, though we could easily make one if we wanted to.
Note:
See TracTickets
for help on using tickets.
MarkerSet is a Structure. There is another class called AtomicStructure with base class Structure. AtomicStructure is for chemically sensible models, ones you might run MD on, or swap an amino acid. Structure is for everything else. MarkerSet is the main reason for Structure. So some commands could decide to only work on AtomicStructure and not Structure.
That is the background. In general I've found it very powerful if almost everything that works on atoms can work on MarkerSet and Structure. Structure can have separate chains so I definitely want "color bychain" to work on MarkerSet. So already your first example command is going to do something you don't want. You should use "color #1 bychain" if specificity is needed. "color byhet" one could argue should only act on AtomicStructure. But I think for simplicity all coloring should act on all Structures. In order to make Markers very flexible it is best not to have to guess which commands are allowed to work on markers. My rule is everything is allowed to work on Markers unless it is never going to work.
I understand your point that if you can guess what the user intends you can provide a better experience. But guessing what they intend unfortunately limits what they can do. Markers are intended to be very flexible so I don't wish to disable any commands on them without a compelling reason.
I give you a long answer because Eric will surely disagree, reflecting that he only works on real molecules while I often use markers in very flexible ways, for example I just made a sars-cov-2 full RNA model from markers.