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#3296 closed defect (wontfix)
volume "subregion" keyword inconsistent with documentation
| Reported by: | Tristan Croll | Owned by: | Tom Goddard |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | Elaine Meng | |
| 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: 1.0 (2020-05-09)
Description
The "subregion" argument of volume commands doesn't appear consistent with the documentation. According to the documentation, it should accept a name previously assigned with "volume #model nameRegion {name}", but looking at MapRegionArg it currently only accepts "all", "shown", or an explicit list of 6 integers.
Log:
UCSF ChimeraX version: 1.0rc202005090702 (2020-05-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open working.cxs
Log from Sat May 23 20:58:17 2020UCSF ChimeraX version: 1.0rc202005090702
(2020-05-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Successfully installed 'ChimeraX_ISOLDE-1.0rc1-cp37-cp37m-linux_x86_64.whl'
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing
/home/tic20/.cache/ChimeraX/1.0/installers/ChimeraX_ISOLDE-1.0rc1-cp37-cp37m-linux_x86_64.whl
Requirement already satisfied, skipping upgrade: ChimeraX-Arrays~=1.0 in
/opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0rc1)
(1.0)
Requirement already satisfied, skipping upgrade: ChimeraX-Clipper~=0.13.0 in
/home/tic20/.local/share/ChimeraX/1.0/site-packages (from ChimeraX-
ISOLDE==1.0rc1) (0.13.0)
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=1.0 in
/opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0rc1)
(1.0)
Requirement already satisfied, skipping upgrade: ChimeraX-
Core~=1.0rc202005052344 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages
(from ChimeraX-ISOLDE==1.0rc1) (1.0rc202005090702)
Requirement already satisfied, skipping upgrade: ChimeraX-Geometry~=1.0 in
/opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-
Atomic>=1.0->ChimeraX-ISOLDE==1.0rc1) (1.0)
Requirement already satisfied, skipping upgrade: ChimeraX-Graphics~=1.0 in
/opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-
Atomic>=1.0->ChimeraX-ISOLDE==1.0rc1) (1.0)
Installing collected packages: ChimeraX-ISOLDE
Attempting uninstall: ChimeraX-ISOLDE
Found existing installation: ChimeraX-ISOLDE 1.0rc1
Uninstalling ChimeraX-ISOLDE-1.0rc1:
Successfully uninstalled ChimeraX-ISOLDE-1.0rc1
Successfully installed ChimeraX-ISOLDE-1.0rc1
Lock 139835417529040 acquired on
/home/tic20/.cache/ChimeraX/1.0/toolshed/bundle_info.cache.lock
Lock 139835417529040 released on
/home/tic20/.cache/ChimeraX/1.0/toolshed/bundle_info.cache.lock
WARNING: You are using pip version 20.1; however, version 20.1.1 is available.
You should consider upgrading via the '/usr/bin/chimerax -m pip install
--upgrade pip' command.
> open working.cif
Summary of feedback from opening working.cif
---
warnings | Unknown polymer entity '1' near line 589
Unknown polymer entity '2' near line 4494
Unknown polymer entity '3' near line 39973
Unknown polymer entity '4' near line 44683
Unknown polymer entity '5' near line 45557
4 messages similar to the above omitted
Atom H1 is not in the residue template for MET #3 in chain AA
Atom H1 is not in the residue template for MET #3 in chain AB
Atom H1 is not in the residue template for MET #3 in chain AC
Atom H1 is not in the residue template for MET #3 in chain AD
Atom H1 is not in the residue template for MET #3 in chain AE
1 messages similar to the above omitted
Atom C1 is not in the residue template for GPC #101 in chain AF
Atom H1 is not in the residue template for MET #1 in chain AG
Atom C1 is not in the residue template for GPC #101 in chain AG
Atom H1 is not in the residue template for MET #3 in chain AH
Atom H1 is not in the residue template for MET #3 in chain AI
Atom H1 is not in the residue template for MET #3 in chain AJ
Atom H1 is not in the residue template for MET #3 in chain AK
Atom H1 is not in the residue template for MET #3 in chain AL
10 messages similar to the above omitted
Atom C1 is not in the residue template for GPC #101 in chain AV
Atom H1 is not in the residue template for MET #3 in chain AW
Atom H1 is not in the residue template for MET #3 in chain AX
Atom H1 is not in the residue template for MET #1 in chain BA
Atom C1 is not in the residue template for GPC #101 in chain BA
Atom H1 is not in the residue template for MET #1 in chain BB
Atom C1 is not in the residue template for GPC #101 in chain BB
Atom H1 is not in the residue template for MET #1 in chain BC
Atom C1 is not in the residue template for GPC #101 in chain BC
Atom H1 is not in the residue template for MET #1 in chain BD
Atom C1 is not in the residue template for GPC #101 in chain BD
Atom H1 is not in the residue template for MET #1 in chain BE
Atom C1 is not in the residue template for GPC #101 in chain BE
Atom H1 is not in the residue template for MET #3 in chain BF
Atom H1 is not in the residue template for MET #3 in chain BG
Atom H1 is not in the residue template for MET #1 in chain BH
Atom C1 is not in the residue template for GPC #101 in chain BH
Atom H1 is not in the residue template for MET #1 in chain BI
Atom C1 is not in the residue template for GPC #101 in chain BI
Atom H1 is not in the residue template for MET #1 in chain BJ
Atom C1 is not in the residue template for GPC #101 in chain BJ
Atom H1 is not in the residue template for MET #1 in chain BK
Atom C1 is not in the residue template for GPC #101 in chain BK
Atom H1 is not in the residue template for MET #1 in chain BL
Atom C1 is not in the residue template for GPC #101 in chain BL
Atom H1 is not in the residue template for MET #1 in chain BM
Atom C1 is not in the residue template for GPC #101 in chain BM
Atom H1 is not in the residue template for MET #1 in chain BN
Atom C1 is not in the residue template for GPC #101 in chain BN
Atom H1 is not in the residue template for MET #1 in chain BO
Atom C1 is not in the residue template for GPC #101 in chain BO
Atom H1 is not in the residue template for MET #1 in chain BP
Atom C1 is not in the residue template for GPC #101 in chain BP
Atom H1 is not in the residue template for MET #1 in chain BQ
Atom C1 is not in the residue template for GPC #101 in chain BQ
Atom H1 is not in the residue template for MET #1 in chain BR
Atom C1 is not in the residue template for GPC #101 in chain BR
Atom H1 is not in the residue template for MET #1 in chain BS
Atom C1 is not in the residue template for GPC #101 in chain BS
Atom H1 is not in the residue template for MET #1 in chain BT
Atom C1 is not in the residue template for GPC #101 in chain BT
Atom H1 is not in the residue template for MET #1 in chain BU
Atom C1 is not in the residue template for GPC #101 in chain BU
Atom H1 is not in the residue template for MET #1 in chain BV
Atom H1 is not in the residue template for MET #1 in chain BW
Atom C1 is not in the residue template for GPC #101 in chain BW
Atom H1 is not in the residue template for MET #1 in chain BX
Atom C1 is not in the residue template for GPC #101 in chain BX
Atom H1 is not in the residue template for ALA #15 in chain C
Atom H1 is not in the residue template for MET #1 in chain H1
Atom CH1 is not in the residue template for TRP #47 in chain H1
Atom H1 is not in the residue template for SER #1 in chain H2
Atom H1 is not in the residue template for ALA #1 in chain L
Atom H11 is not in the residue template for BPH #606 in chain L
Atom H1 is not in the residue template for MET #1 in chain M
Atom H11 is not in the residue template for BPH #605 in chain M
Atom C1 is not in the residue template for GP1 #701 in chain M
Atom H1 is not in the residue template for HIS #2 in chain aa
Atom H1 is not in the residue template for MET #1 in chain ab
Atom H1 is not in the residue template for MET #1 in chain ac
Atom H1 is not in the residue template for MET #1 in chain ad
Atom H1 is not in the residue template for MET #1 in chain ae
5 messages similar to the above omitted
Atom C1 is not in the residue template for GPC #101 in chain aj
Atom H1 is not in the residue template for MET #1 in chain ak
Atom H1 is not in the residue template for MET #1 in chain al
Atom H1 is not in the residue template for MET #1 in chain am
Atom H1 is not in the residue template for MET #1 in chain an
Atom C1 is not in the residue template for GPC #101 in chain an
Atom H1 is not in the residue template for MET #1 in chain ao
Atom H1 is not in the residue template for MET #1 in chain ap
Atom H1 is not in the residue template for MET #1 in chain ba
Atom C1 is not in the residue template for GPC #101 in chain ba
Atom H1 is not in the residue template for MET #1 in chain bb
Atom C1 is not in the residue template for GPC #101 in chain bb
Atom H1 is not in the residue template for MET #1 in chain bc
Atom C1 is not in the residue template for GPC #101 in chain bc
Atom H1 is not in the residue template for MET #1 in chain bd
Atom C1 is not in the residue template for GPC #101 in chain bd
Atom H1 is not in the residue template for MET #1 in chain be
Atom C1 is not in the residue template for GPC #101 in chain be
Atom H1 is not in the residue template for MET #1 in chain bf
Atom C1 is not in the residue template for GPC #101 in chain bf
Atom H1 is not in the residue template for MET #1 in chain bg
Atom C1 is not in the residue template for GPC #101 in chain bg
Atom H1 is not in the residue template for MET #1 in chain bh
Atom C1 is not in the residue template for GPC #101 in chain bh
Atom H1 is not in the residue template for MET #1 in chain bi
Atom H1 is not in the residue template for MET #1 in chain bj
Atom C1 is not in the residue template for GPC #101 in chain bj
Atom H1 is not in the residue template for MET #1 in chain bk
Atom C1 is not in the residue template for GPC #101 in chain bk
Atom H1 is not in the residue template for MET #1 in chain bl
Atom C1 is not in the residue template for GPC #101 in chain bl
Atom H1 is not in the residue template for MET #1 in chain bm
Atom H1 is not in the residue template for MET #1 in chain bn
Atom C1 is not in the residue template for GPC #101 in chain bn
Atom H1 is not in the residue template for MET #1 in chain bo
Atom C1 is not in the residue template for GPC #101 in chain bo
Atom H1 is not in the residue template for MET #1 in chain bp
Atom C1 is not in the residue template for GPC #101 in chain bp
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for working.cif #1
---
Chain | Description
AA AB AC AD AE AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX BF BG | ?
AF AG BA BB BC BD BE BH BI BJ BK BL BM BN BO BP BQ BR BS BT BU BV BW BX ba bb
bc bd be bf bg bh bi bj bk bl bm bn bo bp | ?
C | ?
H1 | ?
H2 | ?
L | ?
M | ?
aa | ?
ab ac ad ae af ag ah ai aj ak al am an ao ap | ?
> isolde start
> set selectionWidth 4
Chain information for working.cif
---
Chain | Description
1.2/AA 1.2/AB 1.2/AC 1.2/AD 1.2/AE 1.2/AH 1.2/AI 1.2/AJ 1.2/AK 1.2/AL 1.2/AM
1.2/AN 1.2/AO 1.2/AP 1.2/AQ 1.2/AR 1.2/AS 1.2/AT 1.2/AU 1.2/AV 1.2/AW 1.2/AX
1.2/BF 1.2/BG | ?
1.2/AF 1.2/AG 1.2/BA 1.2/BB 1.2/BC 1.2/BD 1.2/BE 1.2/BH 1.2/BI 1.2/BJ 1.2/BK
1.2/BL 1.2/BM 1.2/BN 1.2/BO 1.2/BP 1.2/BQ 1.2/BR 1.2/BS 1.2/BT 1.2/BU 1.2/BV
1.2/BW 1.2/BX 1.2/ba 1.2/bb 1.2/bc 1.2/bd 1.2/be 1.2/bf 1.2/bg 1.2/bh 1.2/bi
1.2/bj 1.2/bk 1.2/bl 1.2/bm 1.2/bn 1.2/bo 1.2/bp | ?
1.2/C | ?
1.2/H1 | ?
1.2/H2 | ?
1.2/L | ?
1.2/M | ?
1.2/aa | ?
1.2/ab 1.2/ac 1.2/ad 1.2/ae 1.2/af 1.2/ag 1.2/ah 1.2/ai 1.2/aj 1.2/ak 1.2/al
1.2/am 1.2/an 1.2/ao 1.2/ap | ?
Done loading forcefield
> open
> /run/media/tic20/storage/structure_dump/pu_qian/running/gprclh1-338aleft.mrc
Opened gprclh1-338aleft.mrc, grid size 300,300,300, pixel 1.05, shown at level
0.0201, step 2, values float32
> volume gaussian #2 bfactor 50
> clipper associate #2,3 toModel #1
> clipper associate #2,3 toModel #1
> set bgColor white
> toolshed 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 stepto /M:140
> isolde stepto
> isolde stepto interpolateFrames 4
> isolde stepto
No template found for residue L602 (BCL)
Doing nothing
> isolde stepto
> isolde stepto
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> select clear
> isolde stepto
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> select clear
> isolde stepto
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> save working.cxs
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde add ligand MYR
> color sel bychain
> color sel byhetero
> select up
44 atoms, 43 bonds, 1 model selected
> delete sel
> isolde stepto
> select clear
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
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> isolde stepto
> select :H2
Nothing selected
> select /H2
2763 atoms, 2801 bonds, 2 pseudobonds, 2 models selected
> usage isolde stepto
isolde stepto [residue] [viewDistance a number] [interpolateFrames
interpolateFrames] [polymericOnly true or false]
— Step the view forward or backward through the chain, or jump to a specific
residue
residue: a residues specifier or a text string
interpolateFrames: an integer ≥ 1
> isolde stepto sel
Multiple residues selected! Going to the first...
> select clear
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> clipper set contourSensitivity 0.25
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> select clear
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> select up
21 atoms, 21 bonds, 1 model selected
> select up
293 atoms, 296 bonds, 1 model selected
> isolde stepto
> isolde stepto
> isolde stepto
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> isolde stepto
> select up
11 atoms, 10 bonds, 1 model selected
> select up
108 atoms, 108 bonds, 1 model selected
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
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> isolde stepto
> isolde stepto
> select clear
> isolde stepto
> isolde stepto
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> isolde stepto
> sequence chain /H2
Alignment identifier is 1.2.H2
> toolshed show "Blast Protein"
> blastprotein /H2 database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp1
Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service
Opal job id: appBlastProtein2Service15902541592991149924067
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service15902541592991149924067
stdout.txt = standard output
stderr.txt = standard error
BlastProtein finished.
> open 5y5s
5y5s title:
Structure of photosynthetic LH1-RC super-complex at 1.9 angstrom resolution
[more info...]
Chain information for 5y5s #2
---
Chain | Description
0 2 4 6 8 B E G J N P R T V X Z | LH1 β polypeptide
1 3 5 7 9 A D F I K O Q S U W Y | LH1 α polypeptide
C | Photosynthetic reaction center cytochrome c subunit
H | Photosynthetic reaction center H subunit
L | Photosynthetic reaction center L subunit
M | Photosynthetic reaction center M subunit
Non-standard residues in 5y5s #2
---
BCL — bacteriochlorophyll A
BPH — bacteriopheophytin A
CA — calcium ion
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
CRT — spirilloxanthin (rhodoviolascin)
FE — Fe (III) ion
GOL — glycerol (glycerin; propane-1,2,3-triol)
HEM — protoporphyrin IX containing Fe (HEME)
LDA — lauryl dimethylamine-N-oxide
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
LMT — dodecyl-β-D-maltoside
MG — magnesium ion
MQ8 — menaquinone 8 (2-methyl-3-(3,7,11,15,19,23,27,31-octamethyl-
dotriaconta-2,6,10,14,18,22,26,30-octaenyl)-[1,4]napthoquinone)
PEF — di-palmitoyl-3-Sn-phosphatidylethanolamine
(3-[aminoethylphosphoryl]-[1,2-di-palmitoyl]-Sn-glycerol)
PGV —
(1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl
(11E)-octadec-11-enoate (phosphatidylglycerol, 2-vaccenoyl-1-palmitoyl-Sn-
glycerol-3-phosphoglycerol)
SO4 — sulfate ion
UNL — unknown ligand
UQ8 — Ubiquinone-8
(2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaen-1-yl]cyclohexa-2,5-diene-1,4-dione)
> matchmaker #2 to #1/H2
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 working.cif, chain H2 (#1.2) with 5y5s, chain H (#2), sequence
alignment score = 516.9
RMSD between 154 pruned atom pairs is 0.932 angstroms; (across all 174 pairs:
1.750)
> select #2
27922 atoms, 27717 bonds, 276 pseudobonds, 2 models selected
> style sel stick
Changed 27922 atom styles
> show sel cartoons
> color #2 tan
> color #2 byhetero
> select clear
> hide #2&~/H
> ~cartoon #2&~/H
> select up
24 atoms, 25 bonds, 1 model selected
> select up
252 atoms, 258 bonds, 1 model selected
> isolde restrain torsions #1/H2 templateResidues #2/H angleRange 120
> select up
7 atoms, 6 bonds, 1 model selected
> select up
252 atoms, 258 bonds, 1 model selected
> isolde release torsions sel
> hide #!2 models
> select #1/H2
2773 atoms, 2812 bonds, 1 pseudobond, 2 models selected
> select clear
> isolde stepto
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> show #!2 models
> ~cartoon #2
> hide #!2 models
> select up
17 atoms, 16 bonds, 1 model selected
> isolde release torsions sel
> isolde stepto #1/H1
Multiple residues selected! Going to the first...
> show #!2 models
> show #2
> hide #2
> isolde stepto
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> select up
138 atoms, 139 bonds, 1 model selected
> show sel
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
> isolde stepto
> isolde stepto
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> isolde restrain torsions #1/H1 templateResidues #2/H angleRange 120
> select #1/H1
874 atoms, 890 bonds, 1 model selected
> select clear
> isolde stepto #1/H1
Multiple residues selected! Going to the first...
> isolde stepto
> isolde stepto
> isolde stepto
> select clear
> select up
21 atoms, 21 bonds, 1 model selected
> isolde release torsions sel
> isolde stepto
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> hide #!2 models
> show #!2 models
> show #2
> hide #!2 models
> isolde stepto
> isolde stepto
> isolde stepto
> isolde stepto
> show #!2 models
> hide #!2 models
> show #!2 models
> matchmaker #2 to #1/H1
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 working.cif, chain H1 (#1.2) with 5y5s, chain H (#2), sequence
alignment score = 163.6
RMSD between 37 pruned atom pairs is 0.514 angstroms; (across all 53 pairs:
5.177)
> hide #!2 models
> isolde stepto
> isolde release torsions sel
> isolde release torsions sel
> isolde stepto #1/AA
Multiple residues selected! Going to the first...
> save working.cxs
> sequence chain #1/AA
Alignment identifier is 1.2.AA
> sequence chain #1/aa
Alignment identifier is 1.2.aa
> open
> /run/media/tic20/storage/structure_dump/pu_qian/RealSpaceRefine_23/rebonded.cif
Summary of feedback from opening
/run/media/tic20/storage/structure_dump/pu_qian/RealSpaceRefine_23/rebonded.cif
---
warnings | Unknown polymer entity '1' near line 473
Unknown polymer entity '2' near line 19217
Unknown polymer entity '3' near line 36481
Unknown polymer entity '4' near line 71001
Unknown polymer entity '5' near line 75713
3 messages similar to the above omitted
Atom H1 is not in the residue template for MET #3 in chain AA
Atom H1 is not in the residue template for MET #3 in chain AB
Atom H1 is not in the residue template for MET #3 in chain AC
Atom H1 is not in the residue template for MET #3 in chain AD
Atom H1 is not in the residue template for MET #3 in chain AE
80 messages similar to the above omitted
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for rebonded.cif #3
---
Chain | Description
AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | ?
Aa Ab Ac Ad Ae Af Ag Ah Ai Aj Ak Al Am An Ao Ap | ?
BA BB BC BD BE BF BG BH BI BJ BK BL BM BN BO BP BQ BR BS BT BU BV BW BX Ba Bb
Bc Bd Be Bf Bg Bh Bi Bj Bk Bl Bm Bn Bo Bp | ?
C | ?
H1 | ?
H2 | ?
L | ?
M | ?
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> isolde stepto
> isolde stepto
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> isolde restrain distances #1/AB templateAtoms #1/AA
RMSD between 41 pruned atom pairs is 0.696 angstroms; (across all 41 pairs:
0.696)
> isolde restrain torsions #1/AB templateResidues #1/AA angleRange 180
The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.
> select /AB
1562 atoms, 1596 bonds, 8 pseudobonds, 4 models selected
> isolde stepto #1/AC
Multiple residues selected! Going to the first...
> isolde restrain torsions #1/AC templateResidues #1/AA angleRange 180
The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.
> isolde restrain distances #1/AC templateAtoms #1/AA
RMSD between 41 pruned atom pairs is 0.711 angstroms; (across all 41 pairs:
0.711)
> select #1/AC
781 atoms, 800 bonds, 4 pseudobonds, 2 models selected
> select clear
> view #1/AA:3
> view #1/AD:3
> isolde restrain distances #1/AD templateAtoms #1/AA
RMSD between 41 pruned atom pairs is 1.011 angstroms; (across all 41 pairs:
1.011)
> isolde restrain torsions #1/AD templateResidues #1/AA angleRange 180
The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.
> select #1/AD
781 atoms, 800 bonds, 4 pseudobonds, 2 models selected
> isolde stepto #1/AE
Multiple residues selected! Going to the first...
> isolde restrain torsions #1/AE templateResidues #1/AA angleRange 180
The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.
> isolde restrain distances #1/AE templateAtoms #1/AA
RMSD between 41 pruned atom pairs is 0.541 angstroms; (across all 41 pairs:
0.541)
> select #1/AE
781 atoms, 800 bonds, 4 pseudobonds, 2 models selected
> select up
19 atoms, 18 bonds, 1 model selected
> isolde release distances sel
> isolde release torsions sel
> isolde stepto #1/AA
Multiple residues selected! Going to the first...
> isolde stepto #1/AE
Multiple residues selected! Going to the first...
> isolde restrain distances #1/AE templateAtoms #1/AA
RMSD between 41 pruned atom pairs is 0.687 angstroms; (across all 41 pairs:
0.687)
> isolde stepto #1/AA
Multiple residues selected! Going to the first...
> isolde stepto #1/AE
Multiple residues selected! Going to the first...
> select clear
> isolde release distances sel
> isolde restrain distances #1/AE templateAtoms #1/AA
RMSD between 41 pruned atom pairs is 0.768 angstroms; (across all 41 pairs:
0.768)
> isolde restrain torsions #1/AE templateResidues #1/AA angleRange 180
The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.
> isolde release distances sel
> isolde release torsions sel
> isolde stepto #1/AF
Multiple residues selected! Going to the first...
> sequence chain /AF
Chains must have same sequence
> sequence chain #1/AF
Alignment identifier is 1.2.AF
> sequence chain #1/BF
Alignment identifier is 1.2.BF
> sequence chain /AA
Alignment identifier is 1
> sequence chain #1/AA
Alignment identifier is 1.2.AA
> sequence chain #1/AB
Alignment identifier is 1.2.AB
> sequence chain #1/AC
Alignment identifier is 1.2.AC
> sequence chain #1/AD
Alignment identifier is 1.2.AD
> sequence chain #1/AE
Alignment identifier is 1.2.AE
> isolde stepto #1/AE
Multiple residues selected! Going to the first...
> sequence chain #1/AF
Alignment identifier is 1.2.AF
> isolde stepto #1/AF
Multiple residues selected! Going to the first...
> select #1/BF
781 atoms, 800 bonds, 4 pseudobonds, 2 models selected
> select #1/AA,AB,AC,AD,AE
3905 atoms, 4000 bonds, 20 pseudobonds, 2 models selected
> select #1/AA,AB,AC,AD,AE,BF
4686 atoms, 4800 bonds, 24 pseudobonds, 2 models selected
> select clear
> isolde stepto #1/AA
Multiple residues selected! Going to the first...
> isolde stepto #1/AF
Multiple residues selected! Going to the first...
> select up
14 atoms, 13 bonds, 1 model selected
> select up
33 atoms, 32 bonds, 1 model selected
> select #1/AF
860 atoms, 880 bonds, 4 pseudobonds, 2 models selected
> select clear
> select #1/AF
860 atoms, 880 bonds, 4 pseudobonds, 2 models selected
> isolde stepto #1/AG
Multiple residues selected! Going to the first...
> select #1/AG
860 atoms, 880 bonds, 4 pseudobonds, 2 models selected
> select clear
> isolde stepto #1/AH
Multiple residues selected! Going to the first...
> isolde restrain torsions #1/AH templateResidues #1/AA angleRange 180
The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.
> select #1/AH
781 atoms, 800 bonds, 4 pseudobonds, 2 models selected
> view #1/AA
> isolde stepto #1/AA
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
> 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
Profile for last activation of changes trigger:
483 function calls (450 primitive calls) in 0.003 seconds
Ordered by: internal time
List reduced from 90 to 20 due to restriction <20>
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.001 0.001 0.001 0.001 /home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/molobject.py:2812(visible_restraints)
1 0.000 0.000 0.000 0.000 /home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/molarray.py:500(_bond_transforms)
18 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/molc.py:319(pointer)
10 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/molc.py:189(get_prop)
29/7 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py:227(__setattr__)
18 0.000 0.000 0.000 0.000
/opt/UCSF/ChimeraX/lib/python3.7/ctypes/__init__.py:497(cast)
1 0.000 0.000 0.001 0.001 /home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/openmm_interface.py:2205(update_adaptive_distance_restraints)
1 0.000 0.000 0.000 0.000 /home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/custom_forces.py:865(update_targets)
1 0.000 0.000 0.001 0.001 /home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/openmm_interface.py:1106(_adr_changed_cb)
15 0.000 0.000 0.000 0.000 {built-in method numpy.empty}
1 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/numpy/lib/arraysetops.py:298(_unique1d)
1 0.000 0.000 0.001 0.001 /home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/molobject.py:3121(update_graphics)
18 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/numpy/core/_internal.py:251(__init__)
2 0.000 0.000 0.000 0.000 {built-in method
numpy.core._multiarray_umath.implement_array_function}
1 0.000 0.000 0.003 0.003 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py:197(_activate)
1 0.000 0.000 0.000 0.000 {method 'argsort' of 'numpy.ndarray' objects}
4 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/molarray.py:1420(remove_deleted_pointers)
4 0.000 0.000 0.000 0.000
/opt/UCSF/ChimeraX/lib/python3.7/weakref.py:530(__init__)
2 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py:336(set_display)
18 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/numpy/core/_internal.py:268(data_as)
Profile for last activation of changes trigger:
685 function calls (636 primitive calls) in 0.004 seconds
Ordered by: internal time
List reduced from 102 to 20 due to restriction <20>
ncalls tottime percall cumtime percall filename:lineno(function)
2 0.003 0.001 0.003 0.001 /home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/molobject.py:3637(visible_restraints)
24 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/molc.py:319(pointer)
1 0.000 0.000 0.000 0.000 /home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/molarray.py:657(_annotation_transforms)
38/10 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py:227(__setattr__)
24 0.000 0.000 0.000 0.000
/opt/UCSF/ChimeraX/lib/python3.7/ctypes/__init__.py:497(cast)
10 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/molc.py:189(get_prop)
24 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/numpy/core/_internal.py:251(__init__)
8 0.000 0.000 0.000 0.000
/opt/UCSF/ChimeraX/lib/python3.7/weakref.py:530(__init__)
8 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/molarray.py:1420(remove_deleted_pointers)
1 0.000 0.000 0.001 0.001 /home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/openmm_interface.py:1170(_adaptive_dihe_r_changed_cb)
1 0.000 0.000 0.000 0.000 /home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/openmm_interface.py:2001(update_adaptive_dihedral_restraints)
8 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/molarray.py:101(__init__)
1 0.000 0.000 0.000 0.000 /home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/custom_forces.py:1513(update_targets)
16 0.000 0.000 0.000 0.000 {built-in method numpy.empty}
1 0.000 0.000 0.003 0.003 /home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/molobject.py:3845(disable_mutually_exclusive_restraints)
24 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/numpy/core/_internal.py:268(data_as)
8 0.000 0.000 0.000 0.000
/opt/UCSF/ChimeraX/lib/python3.7/weakref.py:567(__call__)
1 0.000 0.000 0.004 0.004 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py:197(_activate)
3 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/molarray.py:152(__getitem__)
1 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/numpy/lib/arraysetops.py:298(_unique1d)
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.
> delete sel
Profile for last activation of changes done trigger:
269 function calls (241 primitive calls) in 0.001 seconds
Ordered by: internal time
List reduced from 73 to 20 due to restriction <20>
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 0.000 0.000 /home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/molobject.py:1039(_ca_positions_colors_and_selecteds)
1 0.000 0.000 0.001 0.001 /home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/rama_annotation.py:226(update_graphics)
8 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/molc.py:319(pointer)
20/5 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py:227(__setattr__)
1 0.000 0.000 0.000 0.000 /home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/molobject.py:1086(_draw_cis_and_twisted_omegas)
8 0.000 0.000 0.000 0.000
/opt/UCSF/ChimeraX/lib/python3.7/ctypes/__init__.py:497(cast)
9 0.000 0.000 0.000 0.000 {built-in method numpy.empty}
2/1 0.000 0.000 0.001 0.001 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py:197(_activate)
8 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/numpy/core/_internal.py:251(__init__)
19 0.000 0.000 0.000 0.000 {built-in method builtins.hasattr}
1 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py:492(set_positions)
1 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py:1413(opaque_count)
2 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py:336(set_display)
8 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/numpy/core/_internal.py:268(data_as)
1 0.000 0.000 0.000 0.000 /home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/symmetry.py:1561(_model_changed_cb)
8 0.000 0.000 0.000 0.000 <frozen importlib._bootstrap>:1009(_handle_fromlist)
2 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/molc.py:27(c_function)
12 0.000 0.000 0.000 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/drawing.py:186(redraw_needed)
27/18 0.000 0.000 0.000 0.000 {built-in method builtins.len}
3/2 0.000 0.000 0.001 0.000 /opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py:128(invoke)
> color sel bychain
> color sel byhetero
> color sel bychain
> color sel byhetero
> select up
17 atoms, 16 bonds, 1 model selected
> delete sel
> save working.cxs
Summary of feedback from opening working.cxs
---
warning | restore_snapshot for "RotamerRestraintMgr" returned None
opened ChimeraX session
> 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
> clipper spotlight radius 18.00
> clipper spotlight radius 19.00
> clipper spotlight radius 20.00
> isolde stepto /aa
Multiple residues selected! Going to the first...
> usage volume
volume [volumes] [style style] [change change] [show] [hide] [toggle] [close
close] [level level] [rmsLevel rmsLevel] [sdLevel sdLevel] [encloseVolume
encloseVolume] [fastEncloseVolume fastEncloseVolume] [color color] [brightness
a number] [transparency a number] [appearance appearance] [nameAppearance a
text string] [nameForget nameForget] [step map step] [region map region]
[nameRegion a text string] [expandSinglePlane true or false] [origin 1 or 3
floats] [originIndex 1 or 3 floats] [voxelSize 1 or 3 floats] [planes planes
x|y|z[,<start>[,<end>[,<increment>[,<depth>]]]]] [dumpHeader true or false]
[pickable true or false] [symmetry symmetry] [center center point]
[centerIndex 1 or 3 floats] [axis an axis vector] [coordinateSystem a
coordinate-system] [dataCacheSize a number] [showOnOpen true or false]
[voxelLimitForOpen a number] [showPlane true or false] [voxelLimitForPlane a
number] [showOutlineBox true or false] [outlineBoxRgb a color]
[limitVoxelCount true or false] [voxelLimit a number] [colorMode colorMode]
[colormapOnGpu true or false] [colormapSize an integer] [colormapExtendLeft
true or false] [colormapExtendRight true or false] [backingColor backingColor]
[blendOnGpu true or false] [projectionMode projectionMode] [planeSpacing
planeSpacing] [fullRegionOnGpu true or false] [btCorrection true or false]
[minimalTextureMemory true or false] [maximumIntensityProjection true or
false] [linearInterpolation true or false] [dimTransparency true or false]
[dimTransparentVoxels true or false] [smoothLines true or false] [meshLighting
true or false] [twoSidedLighting true or false] [flipNormals true or false]
[subdivideSurface true or false] [subdivisionLevels an integer]
[surfaceSmoothing true or false] [smoothingIterations an integer]
[smoothingFactor a number] [squareMesh true or false] [capFaces true or false]
[boxFaces true or false] [orthoplanes orthoplanes] [positionPlanes
positionPlanes] [tiltedSlab true or false] [tiltedSlabAxis an axis vector]
[tiltedSlabOffset a number] [tiltedSlabSpacing a number] [tiltedSlabPlaneCount
an integer] [imageMode imageMode] [calculateSurfaces true or false]
— set volume model parameters, display style and colors
style: one of image, mesh, solid, or surface
change: one of image or surface
close: one of image or surface
level: some numbers, repeatable
rmsLevel: some numbers, repeatable
sdLevel: some numbers, repeatable
encloseVolume: some numbers
fastEncloseVolume: some numbers
color: a color, repeatable
appearance: one of Airways, airways, Airways II, Black & White, Bone + Skin,
Bone + Skin II, brain, chest, CT_Bones, CT_Kidneys, CT_Liver, CT_Lungs,
CT_Muscles, CT_Skin, CT_Soft_Tissue, CT_Vessels, CT_w_Contrast, Dark Bone,
Glossy, Glossy II, Gold Bone, High Contrast, initial, Low Contrast, Mid
Contrast, No Shading, Pencil, Red on White, Skin On Blue, Skin On Blue II,
Soft, Soft + Skin, Soft + Skin II, Soft + Skin III, Soft On Blue, Soft on
White, Standard, Vascular, Vascular II, Vascular III, Vascular IV, or Yellow
Bone
nameForget: one of Airways, airways, Airways II, Black & White, Bone + Skin,
Bone + Skin II, brain, chest, CT_Bones, CT_Kidneys, CT_Liver, CT_Lungs,
CT_Muscles, CT_Skin, CT_Soft_Tissue, CT_Vessels, CT_w_Contrast, Dark Bone,
Glossy, Glossy II, Gold Bone, High Contrast, initial, Low Contrast, Mid
Contrast, No Shading, Pencil, Red on White, Skin On Blue, Skin On Blue II,
Soft, Soft + Skin, Soft + Skin II, Soft + Skin III, Soft On Blue, Soft on
White, Standard, Vascular, Vascular II, Vascular III, Vascular IV, or Yellow
Bone
colorMode: one of auto12, auto16, auto4, auto8, l12, l16, l4, l8, la12, la16,
la4, la8, opaque12, opaque16, opaque4, opaque8, rgb12, rgb16, rgb4, rgb8,
rgba12, rgba16, rgba4, or rgba8
backingColor: a color or none
projectionMode: one of 2d-x, 2d-xyz, 2d-y, 2d-z, 3d, or auto
planeSpacing: one of max, mean, or min or a number
orthoplanes: one of off, xy, xyz, xz, or yz
positionPlanes: some integers
imageMode: one of box faces, full region, orthoplanes, or tilted slab
Subcommands are:
* volume add
* volume bin
* volume boxes
* volume copy
* volume cover
* volume erase
* volume falloff
* volume flatten
* volume flip
* volume fourier
* volume gaussian
* volume laplacian
* volume localCorrelation
* volume mask
* volume maximum
* volume median
* volume minimum
* volume morph
* volume multiply
* volume new
* volume octant
* volume ~octant
* volume onesmask
* volume permuteAxes
* volume resample
* volume ridges
* volume scale
* volume settings
* volume splitbyzone
* volume subtract
* volume threshold
* volume tile
* volume unbend
* volume unroll
* volume unzone
* volume zone
> volume #1.1.1.1 nameRegion asu_aa
> volume copy #1.1.1.1 region asu_aa
Expected a keyword
Must specify 6 comma-separated integers, got asu_aa
Must specify 6 comma-separated integers, got asu_aa
> usage volume copy
volume copy volumes [valueType numeric value type] [subregion map region]
[step map step] [modelId modelId]
— Copy a map or a map subregio
modelId: a model id
> volume #1.1.1.1 nameRegion shown
> volume copy #1.1.1.1 subregion shown
> volume #1.1.1.1 nameRegion asu
Must specify 6 comma-separated integers, got asu
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 3.0G 49G 36M 9.9G 59G
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
Change History (5)
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Volume Data |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → volume "subregion" keyword inconsistent with documentation |
comment:2 by , 5 years ago
comment:3 by , 5 years ago
| Resolution: | → wontfix |
|---|---|
| Status: | assigned → closed |
Named volume regions are a Chimera feature not currently supported in ChimeraX.
I have removed the namedRegion option of the volume command.
Documentation should be updated to remove named regions.
Might add named regions in the (distant) future. I think these were almost never used in Chimera and my current thinking is not to add them go ChimeraX. You are the first to report the problem in 5 years of ChimeraX so I suspect no one has tried to use them.
follow-up: 4 comment:4 by , 5 years ago
It appeared in many times in the "volume" page and once in "measure" but I believe all the stuff about named subregions has now been removed.
Note:
See TracTickets
for help on using tickets.
I can confirm that although "volume" allows naming the region, the region name is not recognized even by the "volume" command region option. E.g.
open 1pho
molmap strand 8
volume #2 region 10,10,10,14,15,14
volume #2 nameReg chunk
volum #2 region all
volum #2 region chunk
Error: Must specify 6 comma-separated integers, got chunk