Opened 4 years ago

Closed 4 years ago

#6011 closed enhancement (fixed)

Map fitting does not log command

Reported by: jaremko@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
When fitting in fit in map window,  there is no corresponding command that shows up in log.  This is more of a convenience thing,  but I feel it helps to learn the chimerax language.

Log:
> ui mousemode right "contour level"

> mousemode shift rightMode zoom

> set bgColor white

> graphics silhouettes true

> graphics silhouettes width 3

> hide all atoms

> style stick

Changed 0 atom styles  

> style ions sphere

Changed 0 atom styles  

> style ions sphere

Changed 0 atom styles  

> show all cartoons

> show ligand target ab

> show ions atoms

> show sidechain & (ligand | ions) :< 3.5 target ab

> color /a #55c087

> color /b #ffe255

> color /c #f6986c

> color /d #6b80bc

> color /e #aa7fba

> color /g #FFC0CB

> color /h #b2b2b2

> color /i red

> color byhetero

> lighting soft

> lighting depthCue false

> cartoon suppressBackboneDisplay false

> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  

> alias sa isolde sim stop

> alias sb isolde sim stop discardTo start

> alias m21 matchmaker #2 to #1 & sel

> alias m31 matchmaker #3 to #1 & sel

> alias m41 matchmaker #4 to #1 & sel

> alias ct ui mousemode right "contour level"

> alias zm ui mousemode right zoom

> alias cr view $*; clip off; zoom .8

UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/jaremko/Documents/cryoem/2019-12-27_x108_noATP/ResolveCryoEM_1/denmod_map.ccp4

Opened denmod_map.ccp4 as #1, grid size 101,116,169, pixel 0.84, shown at
level 1.19, step 1, values float32  

> volume #1 level 0.4626

> volume #1 level 0.104

> open
> /Users/jaremko/Documents/cryoem/2020-06-18_x108_ADP/RealSpaceRefine_20/Ref3D-38_007_for_phenix_4_real_space_refined_020.cif

Summary of feedback from opening
/Users/jaremko/Documents/cryoem/2020-06-18_x108_ADP/RealSpaceRefine_20/Ref3D-38_007_for_phenix_4_real_space_refined_020.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 219  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "1" near line 100  
Bad residue range for struct_conf "2" near line 101  
Bad residue range for struct_conf "3" near line 102  
Bad residue range for struct_conf "4" near line 103  
Bad residue range for struct_conf "5" near line 104  
16 messages similar to the above omitted  
Invalid residue range for struct_conf "22": invalid entity "B", near line 121  
Invalid residue range for struct_conf "23": invalid entity "B", near line 122  
Invalid residue range for struct_conf "24": invalid entity "B", near line 123  
Invalid residue range for struct_conf "25": invalid entity "B", near line 124  
Invalid residue range for struct_conf "26": invalid entity "B", near line 125  
44 messages similar to the above omitted  
Bad residue range for struct_conf "91" near line 190  
Bad residue range for struct_conf "92" near line 191  
Bad residue range for struct_conf "93" near line 192  
Bad residue range for struct_conf "94" near line 193  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Skipping chem_comp category: Missing column 'type' near line 17883  
Skipping chem_comp category: Missing column 'type' near line 17910  
Skipping chem_comp category: Missing column 'type' near line 18198  
  
Chain information for Ref3D-38_007_for_phenix_4_real_space_refined_020.cif #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> ui tool show "Fit in Map"

Fit molecule Ref3D-38_007_for_phenix_4_real_space_refined_020.cif (#2) to map
denmod_map.ccp4 (#1) using 16909 atoms  
average map value = 0.02451, steps = 188  
shifted from previous position = 3.65  
rotated from previous position = 12.1 degrees  
atoms outside contour = 14402, contour level = 0.104  
  
Position of Ref3D-38_007_for_phenix_4_real_space_refined_020.cif (#2) relative
to denmod_map.ccp4 (#1) coordinates:  
Matrix rotation and translation  
0.97793958 -0.17995394 0.10606958 14.35280273  
0.17944867 0.98366241 0.01436771 -30.90279314  
-0.10692219 0.00498329 0.99425490 17.49055937  
Axis -0.02245721 0.50969587 0.86006151  
Axis point 174.58420169 58.22746550 0.00000000  
Rotation angle (degrees) 12.06024449  
Shift along axis -1.03039310  
  

> preset pdb

Changed 16909 atom styles  
Changed 2 atom styles  
[Repeated 1 time(s)]Preset expands to these ChimeraX commands:

    
    
    hide all atoms
    style stick
    style ions sphere
    style ions sphere
    show all cartoons
    show ligand targ ab
    show ions atoms
    show sidechain & (ligand | ions) :< 3.5 target ab
    color /a #55c087 targ abcs; color /b #ffe255 targ abcs; color /c #f6986c targ abcs; color /d #6b80bc targ abcs; color /e #aa7fba targ abcs; color /f #00FFFF targ abcs; color /g #FFC0CB targ abcs; color /h #b2b2b2 targ abcs; color /i red targ abcs
    color byhetero
    dssp
    lighting soft
    light depthcue false
    cartoon suppressBackboneDisplay false
    graphics silhouettes true

  

> select /C:49

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

> select up

198 atoms, 201 bonds, 22 residues, 1 model selected  

> select up

4783 atoms, 4885 bonds, 585 residues, 1 model selected  

> select up

16909 atoms, 17257 bonds, 2074 residues, 1 model selected  

> select up

16909 atoms, 17257 bonds, 2074 residues, 3 models selected  

> select down

16909 atoms, 17257 bonds, 2074 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.97794,-0.17995,0.10607,15.49,0.17945,0.98366,0.014368,-43.418,-0.10692,0.0049833,0.99425,-7.3901

Fit molecule Ref3D-38_007_for_phenix_4_real_space_refined_020.cif (#2) to map
denmod_map.ccp4 (#1) using 16909 atoms  
average map value = 0.03014, steps = 80  
shifted from previous position = 1.97  
rotated from previous position = 4.63 degrees  
atoms outside contour = 13634, contour level = 0.104  
  
Position of Ref3D-38_007_for_phenix_4_real_space_refined_020.cif (#2) relative
to denmod_map.ccp4 (#1) coordinates:  
Matrix rotation and translation  
0.98329854 -0.17723115 0.04138962 24.89071529  
0.17866484 0.98332406 -0.03395108 -33.71920815  
-0.03468222 0.04077892 0.99856608 -25.89653880  
Axis 0.20114201 0.20475368 0.95792371  
Axis point 172.54446295 154.48955823 0.00000000  
Rotation angle (degrees) 10.70569402  
Shift along axis -26.70447173  
  

> ui mousemode right "contour level"

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.9833,-0.17723,0.04139,12.184,0.17866,0.98332,-0.033951,-28.194,-0.034682,0.040779,0.99857,-24.784

Fit molecule Ref3D-38_007_for_phenix_4_real_space_refined_020.cif (#2) to map
denmod_map.ccp4 (#1) using 16909 atoms  
average map value = 0.6483, steps = 108  
shifted from previous position = 7.12  
rotated from previous position = 6.52 degrees  
atoms outside contour = 3162, contour level = 0.104  
  
Position of Ref3D-38_007_for_phenix_4_real_space_refined_020.cif (#2) relative
to denmod_map.ccp4 (#1) coordinates:  
Matrix rotation and translation  
0.95841175 -0.28332498 0.03426176 32.35420613  
0.28497654 0.95655729 -0.06153471 -42.60516288  
-0.01533901 0.06873939 0.99751672 -30.98925949  
Axis 0.22263444 0.08476620 0.97120986  
Axis point 158.65320619 111.73427334 0.00000000  
Rotation angle (degrees) 17.01212080  
Shift along axis -26.50539139  
  

> ui mousemode right "contour level"

> volume #1 level 0.011

> open
> /Users/jaremko/Documents/cryoem/2019-12-27_x108_noATP/ResolveCryoEM_2/denmod_map.ccp4

Opened denmod_map.ccp4 as #3, grid size 125,140,193, pixel 0.84, shown at
level 0.969, step 1, values float32  

> hide #!2 models

> show #!2 models

> hide #!1 models

> volume #3 level 0.0481

> close session

> open
> /Users/jaremko/Documents/cryoem/2019-12-27_x108_noATP/ResolveCryoEM_2/denmod_map.ccp4
> format ccp4

Opened denmod_map.ccp4 as #1, grid size 125,140,193, pixel 0.84, shown at
level 0.969, step 1, values float32  

> volume #1 level 0.4104

> volume #1 level 0.4371

> open
> /Users/jaremko/Documents/cryoem/2020-06-18_x108_ADP/RealSpaceRefine_20/Ref3D-38_007_for_phenix_4_real_space_refined_020.cif
> format mmcif

Summary of feedback from opening
/Users/jaremko/Documents/cryoem/2020-06-18_x108_ADP/RealSpaceRefine_20/Ref3D-38_007_for_phenix_4_real_space_refined_020.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 219  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "1" near line 100  
Bad residue range for struct_conf "2" near line 101  
Bad residue range for struct_conf "3" near line 102  
Bad residue range for struct_conf "4" near line 103  
Bad residue range for struct_conf "5" near line 104  
16 messages similar to the above omitted  
Invalid residue range for struct_conf "22": invalid entity "B", near line 121  
Invalid residue range for struct_conf "23": invalid entity "B", near line 122  
Invalid residue range for struct_conf "24": invalid entity "B", near line 123  
Invalid residue range for struct_conf "25": invalid entity "B", near line 124  
Invalid residue range for struct_conf "26": invalid entity "B", near line 125  
44 messages similar to the above omitted  
Bad residue range for struct_conf "91" near line 190  
Bad residue range for struct_conf "92" near line 191  
Bad residue range for struct_conf "93" near line 192  
Bad residue range for struct_conf "94" near line 193  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Skipping chem_comp category: Missing column 'type' near line 17883  
Skipping chem_comp category: Missing column 'type' near line 17910  
Skipping chem_comp category: Missing column 'type' near line 18198  
  
Chain information for Ref3D-38_007_for_phenix_4_real_space_refined_020.cif #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> preset pdb

Changed 16909 atom styles  
Changed 2 atom styles  
[Repeated 1 time(s)]Preset expands to these ChimeraX commands:

    
    
    hide all atoms
    style stick
    style ions sphere
    style ions sphere
    show all cartoons
    show ligand targ ab
    show ions atoms
    show sidechain & (ligand | ions) :< 3.5 target ab
    color /a #55c087 targ abcs; color /b #ffe255 targ abcs; color /c #f6986c targ abcs; color /d #6b80bc targ abcs; color /e #aa7fba targ abcs; color /f #00FFFF targ abcs; color /g #FFC0CB targ abcs; color /h #b2b2b2 targ abcs; color /i red targ abcs
    color byhetero
    dssp
    lighting soft
    light depthcue false
    cartoon suppressBackboneDisplay false
    graphics silhouettes true

  

> ui mousemode right "translate selected models"

> select /B:273

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

> select up

60 atoms, 59 bonds, 7 residues, 1 model selected  

> select up

2751 atoms, 2808 bonds, 336 residues, 1 model selected  

> select up

16909 atoms, 17257 bonds, 2074 residues, 1 model selected  

> select up

16909 atoms, 17257 bonds, 2074 residues, 3 models selected  

> select down

16909 atoms, 17257 bonds, 2074 residues, 1 model selected  

> view matrix models #2,1,0,0,-18.817,0,1,0,-11.316,0,0,1,-21.54

> ui mousemode right "contour level"

> ui tool show "Fit in Map"

Fit molecule Ref3D-38_007_for_phenix_4_real_space_refined_020.cif (#2) to map
denmod_map.ccp4 (#1) using 16909 atoms  
average map value = 0.6269, steps = 152  
shifted from previous position = 1.5  
rotated from previous position = 17 degrees  
atoms outside contour = 6979, contour level = 0.43714  
  
Position of Ref3D-38_007_for_phenix_4_real_space_refined_020.cif (#2) relative
to denmod_map.ccp4 (#1) coordinates:  
Matrix rotation and translation  
0.95847449 -0.28312042 0.03419775 32.32078079  
0.28476717 0.95662301 -0.06148234 -42.60096181  
-0.01530744 0.06866765 0.99752215 -30.97766600  
Axis 0.22258886 0.08466619 0.97122903  
Axis point 158.73690127 111.71054753 0.00000000  
Rotation angle (degrees) 16.99900711  
Shift along axis -26.49902417  
  

> select clear

> open
> /Users/jaremko/Documents/cryoem/2019-12-27_x108_noATP/Refine3D/job077/run_class001.mrc

Opened run_class001.mrc as #3, grid size 384,384,384, pixel 0.84, shown at
level 0.00402, step 2, values float32  

> volume #3 step 1

> volume #3 level 0.01257

> volume #3 level 0.01622

> save /Users/jaremko/Documents/cryoem/2019-12-27_x108_noATP/ORC-ADP_fit-
> to_resolve-cryoem_2.pdb relModel #1

> volume #3 level 0.01733

> close #3

> volume #1 level 0.1378

> volume #1 level 0.1449

> close #2

> open /Users/jaremko/Documents/cryoem/2019-12-27_x108_noATP/ORC-ADP_fit-
> to_resolve-cryoem_2.pdb

Chain information for ORC-ADP_fit-to_resolve-cryoem_2.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> preset pdb

Changed 16909 atom styles  
Changed 2 atom styles  
[Repeated 1 time(s)]Preset expands to these ChimeraX commands:

    
    
    hide all atoms
    style stick
    style ions sphere
    style ions sphere
    show all cartoons
    show ligand targ ab
    show ions atoms
    show sidechain & (ligand | ions) :< 3.5 target ab
    color /a #55c087 targ abcs; color /b #ffe255 targ abcs; color /c #f6986c targ abcs; color /d #6b80bc targ abcs; color /e #aa7fba targ abcs; color /f #00FFFF targ abcs; color /g #FFC0CB targ abcs; color /h #b2b2b2 targ abcs; color /i red targ abcs
    color byhetero
    dssp
    lighting soft
    light depthcue false
    cartoon suppressBackboneDisplay false
    graphics silhouettes true

  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select #1

2 models selected  

> select /A:901@C5'

1 atom, 1 residue, 1 model selected  

> delete /A:901

> delete /A:902

> volume #1 level 0.6725

> select /E:501@C5'

1 atom, 1 residue, 1 model selected  

> delete /E:501

> select /A:760

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

> select /A:761

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

> delete /A:761

> select /A:853

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

> select up

65 atoms, 65 bonds, 8 residues, 1 model selected  

> select up

2674 atoms, 2715 bonds, 336 residues, 1 model selected  

> select down

65 atoms, 65 bonds, 8 residues, 1 model selected  

> select down

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

> select /a:1-695

1532 atoms, 1561 bonds, 3 pseudobonds, 190 residues, 2 models selected  

> volume #1 level 0.07908

> select /a:499-695

1433 atoms, 1462 bonds, 2 pseudobonds, 178 residues, 2 models selected  

> volume #1 level 0.3322

Fit molecule ORC-ADP_fit-to_resolve-cryoem_2.pdb (#2) to map denmod_map.ccp4
(#1) using 16848 atoms  
average map value = 0.6291, steps = 40  
shifted from previous position = 0.0135  
rotated from previous position = 0.0102 degrees  
atoms outside contour = 5798, contour level = 0.33224  
  
Fit molecule ORC-ADP_fit-to_resolve-cryoem_2.pdb (#2) to map denmod_map.ccp4
(#1) using 1433 atoms  
average map value = 0.4494, steps = 72  
shifted from previous position = 0.485  
rotated from previous position = 3.38 degrees  
atoms outside contour = 635, contour level = 0.33224  
  
[Repeated 1 time(s)]

> select /a:487-498,702-760

465 atoms, 466 bonds, 1 pseudobond, 60 residues, 2 models selected  

> volume #1 level 0.1435

Fit molecule ORC-ADP_fit-to_resolve-cryoem_2.pdb (#2) to map denmod_map.ccp4
(#1) using 465 atoms  
average map value = 0.2175, steps = 84  
shifted from previous position = 2.87  
rotated from previous position = 14.4 degrees  
atoms outside contour = 236, contour level = 0.1435  
  

> fitmap

Missing or invalid "atomsOrMap" argument: empty atom specifier  




OpenGL version: 4.1 ATI-4.7.101
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 1715.60.5.0.0 (iBridge: 19.16.10647.0.0,0)
      OS Loader Version: 540.60.2~89

Software:

    System Software Overview:

      System Version: macOS 12.1 (21C52)
      Kernel Version: Darwin 21.2.0
      Time since boot: 7 days 3:44

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-020
      Option ROM Version: 113-D32206U1-020
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (3)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Map fitting does not log command
Type: defect → enhancement

Reported by Matt Jaremko

comment:2 by Tom Goddard, 4 years ago

I agree it would be good if the Fit in Map tool logged the equivalent command. There are a half dozen options in that tool so it will take a page of code to handle all the options. I'll try to add this some time.

comment:3 by Tom Goddard, 4 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Made Fit in Map panel log the equivalent fitmap command. Thanks for the suggestion.

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