Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#5927 closed defect (not a bug)

Attempt to use either positions or matrix file

Reported by: jribeiro@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc: Elaine Meng
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.14393
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
When trying to open q models file there is an error "Unrecognized file sufix"
Please describe steps that led to the crash here.
Windows fatal exception: access violation

Current thread 0x00001404 (most recent call first):
  File "d:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "d:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "d:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "d:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "d:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
Startup Messages  
---  
warning | No presets found in custom preset folder D:/ChimeraX 1.2.5  
  
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 .\\\links\\\pdb\\\JAP81880.1-Alphafold.pdb

Chain information for JAP81880.1-Alphafold.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open .\\\links\\\ent\\\pdb3uv1.ent

pdb3uv1.ent title:  
Crystal structure A major allergen from dust mite [more info...]  
  
Chain information for pdb3uv1.ent #2  
---  
Chain | Description | UniProt  
A B | der F 7 allergen | A1KXH4_DERFA  
  

> mmaker #1/a to #2/a

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker pdb3uv1.ent, chain A (#2) with JAP81880.1-Alphafold.pdb, chain A
(#1), sequence alignment score = 261.9  
RMSD between 78 pruned atom pairs is 1.300 angstroms; (across all 187 pairs:
4.024)  
  

> view matrix

camera position:
0.74442,0.45361,0.48997,80.848,0.40585,0.2753,-0.87149,-120.54,-0.53021,0.84761,0.020838,-22.47  
model positions:
#1,0.80697,-0.13432,0.57511,22.326,0.12256,-0.9145,-0.38557,2.8566,0.57773,0.38163,-0.72152,-33.573,#2,1,0,0,0,0,1,0,0,0,0,1,0  
  

> view matrix\

Expected an objects specifier or a view name or a keyword  

> view matrix

camera position:
0.74442,0.45361,0.48997,80.848,0.40585,0.2753,-0.87149,-120.54,-0.53021,0.84761,0.020838,-22.47  
model positions:
#1,0.80697,-0.13432,0.57511,22.326,0.12256,-0.9145,-0.38557,2.8566,0.57773,0.38163,-0.72152,-33.573,#2,1,0,0,0,0,1,0,0,0,0,1,0  
  

> color confidence = true

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> open n:\temp\model.txt models #1

Unrecognized file suffix '.txt'  

> open n:/temp/model.txt models #1

Unrecognized file suffix '.txt'  

> toolshed show

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> ui mousemode right "rotate selected models"

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> ui tool show "Model Panel"

> toolshed show

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> ui tool show "Model Panel"

> ui tool show AlphaFold

> ui tool show "Model Panel"

> open n:\temp\model models #1

'n:\temp\model' has no suffix  

> open n:/temp/model.model models #1

Unrecognized file suffix '.model'  

> open n:/temp/model.model models #1

Unrecognized file suffix '.model'  

> open n:/temp/model #1

'n:/temp/model' has no suffix  

> open n:/temp/model.txt models #1

Unrecognized file suffix '.txt'  

> open n:/temp/model.txt models #1

Unrecognized file suffix '.txt'  

> open n:/temp/model.txt

Unrecognized file suffix '.txt'  

> save matrix "n:\\\temp\\\matrix"

Cannot determine format for 'matrix'  

> view matrix

camera position:
0.7261,0.5211,0.4486,74.629,0.44048,0.14846,-0.8854,-122.63,-0.52798,0.84049,-0.12174,-43.9  
model positions:
#1,0.80697,-0.13432,0.57511,22.326,0.12256,-0.9145,-0.38557,2.8566,0.57773,0.38163,-0.72152,-33.573,#2,1,0,0,0,0,1,0,0,0,0,1,0  
  

> save model #1/a

Cannot determine format for 'model'  

> save model #1/a "n:\\\temp\\\matrix"

Cannot determine format for 'model'  

> save model #1/a

Cannot determine format for 'model'  

> save model #1/a
> #1,0.80697,-0.13432,0.57511,22.326,0.12256,-0.9145,-0.38557,2.8566,0.57773,0.38163,-0.72152,-33.573,#2,1,0,0,0,0,1,0,0,0,0,1,0

Cannot determine format for 'model'  

> save model.txt #1/a
> #1,0.80697,-0.13432,0.57511,22.326,0.12256,-0.9145,-0.38557,2.8566,0.57773,0.38163,-0.72152,-33.573,#2,1,0,0,0,0,1,0,0,0,0,1,0

No known data format for file suffix '.txt'  

> view matrix
> mod#1,0.803979,0.048204,0.592701,2.164986,-0.220978,-0.901117,0.373038,19.548801,0.552075,-0.430888,-0.713827,-35.291908

Expected a keyword  

> save filename models
> #1/A,,0.803979,0.048204,0.592701,2.164986,-0.220978,-0.901117,0.373038,19.548801,0.552075,-0.430888,-0.713827,-35.291908

Cannot determine format for 'filename'  

> models
> #1/A,,0.803979,0.048204,0.592701,2.164986,-0.220978,-0.901117,0.373038,19.548801,0.552075,-0.430888,-0.713827,-35.291908

Unknown command: models
#1/A,,0.803979,0.048204,0.592701,2.164986,-0.220978,-0.901117,0.373038,19.548801,0.552075,-0.430888,-0.713827,-35.291908  

> close #2

> show target m

> hide #1 models

> show #1 models

> select #1

3265 atoms, 3306 bonds, 208 residues, 1 model selected  

> ~select #1

Nothing selected  

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> ave
> model.#1/A,,0.803979,0.048204,0.592701,2.164986,-0.220978,-0.901117,0.373038,19.548801,0.552075,-0.430888,-0.713827,-35.291908

Unknown command: ave
model.#1/A,,0.803979,0.048204,0.592701,2.164986,-0.220978,-0.901117,0.373038,19.548801,0.552075,-0.430888,-0.713827,-35.291908  

> save
> model.#1/A,,0.803979,0.048204,0.592701,2.164986,-0.220978,-0.901117,0.373038,19.548801,0.552075,-0.430888,-0.713827,-35.291908

No known data format for file suffix '.291908'  

> save
> model.#1/A,0.803979,0.048204,0.592701,2.164986,-0.220978,-0.901117,0.373038,19.548801,0.552075,-0.430888,-0.713827,-35.291908

No known data format for file suffix '.291908'  

> open n:\temp\model.cmx models

Unrecognized file suffix '.cmx'  


===== Log before crash end =====

Log:
Startup Messages  
---  
warning | No presets found in custom preset folder D:/ChimeraX 1.2.5  
  
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 .\\\links\\\pdb\\\JAP81880.1-Alphafold.pdb

Chain information for JAP81880.1-Alphafold.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open .\\\links\\\ent\\\pdb3uv1.ent

pdb3uv1.ent title:  
Crystal structure A major allergen from dust mite [more info...]  
  
Chain information for pdb3uv1.ent #2  
---  
Chain | Description | UniProt  
A B | der F 7 allergen | A1KXH4_DERFA  
  

> mmaker #1 to #2/a

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker pdb3uv1.ent, chain A (#2) with JAP81880.1-Alphafold.pdb, chain A
(#1), sequence alignment score = 261.9  
RMSD between 78 pruned atom pairs is 1.300 angstroms; (across all 187 pairs:
4.024)  
  

> view

> open n:\temp\model.cmx models

Unrecognized file suffix '.cmx'  






OpenGL version: 3.3 (Core Profile) Mesa 20.2.0-devel (git-a8d28e4676)
OpenGL renderer: llvmpipe (LLVM 5.0, 256 bits)
OpenGL vendor: VMware, Inc.
Manufacturer: VMware, Inc.
Model: VMware Virtual Platform
OS: Microsoft Windows Server 2016 Standard (Build 14393)
Memory: 25,769,332,736
MaxProcessMemory: 137,438,953,344
CPU: 1 Intel(R) Xeon(R) CPU E5-2660 0 @ 2.20GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    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-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-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
    comtypes: 1.1.10
    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: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    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
    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
    pywin32: 228
    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
    tables: 3.6.1
    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
    WMI: 1.5.1
File attachment: model.cmx

model.cmx​

Attachments (1)

model.cmx​ (150 bytes ) - added by jribeiro@… 4 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (6)

by jribeiro@…, 4 years ago

Attachment: model.cmx​ added

Added by email2trac

comment:1 by Eric Pettersen, 4 years ago

Cc: Elaine Meng added
Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Attempt to use either positions or matrix file

Reported by Jose Ribeiro

comment:2 by Tom Goddard, 4 years ago

Resolution: → not a bug
Status: assigned → closed

I don't understand what you are trying to do. If you are trying to save the position matrices of some models then that is described in the ChimeraX documentation here

​https://www.cgl.ucsf.edu/chimerax/docs/user/formats/positions.html

and an example using it would be

save ~/Desktop/docked.positions model #1
open ~/Desktop/docked.positions model #1

The file type is recognized by the ".positions" file name suffix. You could use a different suffix and add the format option but I don't recommend that.

You seem to be trying to save the position matrix of a chain #1/A but chains do not have separate matrices, only whole models do. If you have docked just part of a model chain A and want to save it you would need to save all the coordinates, for example, "save docked.cif model #1". In fact it is a pretty weird use case where you want to just save the matrices. Normally you just save a new PDB (*.pdb) or mmCIF file (*.cif) if you reposition a model. Or you just save a whole ChimeraX session (*.cxs) if your future use is just going to be within ChimeraX.

in reply to:  4 comment:3 by jribeiro@…, 4 years ago 

Hi,

Thank you for your quick response. I found it useful to learn of the suffix for the position files. Perhaps that could be included in the help file

https://www.cgl.ucsf.edu/chimerax/docs/user/formats/positions.html

I now advanced to another error, and I filed another bug report.

What I am trying to do is to import a position file from the dali program into chimerax and check whether the dali position differs from the mm product from chimerax.

Thanks,

Jose



Jose Ribeiro

Head,
Section of Vector Biology
Laboratory of Malaria and Vector Research
National Institute of Allergy and Infectious Diseases

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Friday, January 14, 2022 5:47 PM
Cc: goddard@cgl.ucsf.edu; Ribeiro, Jose (NIH/NIAID) [E] <jribeiro@niaid.nih.gov>; meng@cgl.ucsf.edu
Subject: [EXTERNAL] Re: [ChimeraX] #5927: Attempt to use either positions or matrix file

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.


#5927: Attempt to use either positions or matrix file
---------------------------------+-------------------------
          Reporter:  jribeiro@…  |      Owner:  Tom Goddard
              Type:  defect      |     Status:  closed
          Priority:  normal      |  Milestone:
         Component:  Graphics    |    Version:
        Resolution:  not a bug   |   Keywords:
        Blocked By:              |   Blocking:
Notify when closed:              |   Platform:  all
           Project:  ChimeraX    |
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Changes (by Tom Goddard):

 * status:  assigned => closed
 * resolution:   => not a bug


Comment:

 I don't understand what you are trying to do.  If you are trying to save  the position matrices of some models then that is described in the  ChimeraX documentation here

 https://www.cgl.ucsf.edu/chimerax/docs/user/formats/positions.html

 and an example using it would be

 save ~/Desktop/docked.positions model #1  open ~/Desktop/docked.positions model #1

 The file type is recognized by the ".positions" file name suffix.  You  could use a different suffix and add the format option but I don't  recommend that.

 You seem to be trying to save the position matrix of a chain #1/A but  chains do not have separate matrices, only whole models do.  If you have  docked just part of a model chain A and want to save it you would need to  save all the coordinates, for example, "save docked.cif model #1".  In  fact it is a pretty weird use case where you want to just save the  matrices.  Normally you just save a new PDB (*.pdb) or mmCIF file (*.cif)  if you reposition a model.  Or you just save a whole ChimeraX session
 (*.cxs) if your future use is just going to be within ChimeraX.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5927#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:4 by Tom Goddard, 4 years ago

Ok. I'll take a look at the next bug report!

The filename suffix ".positions" is the very first thing the current documentation page says

"A ChimeraX positions file (format positions, filename suffix .positions) contains..."

Sometimes we put command examples in the documentation and maybe we could add an example in this case. Example commands are always easier than reading very detailed descriptions or looking at general syntax notations for the commands.

in reply to:  6 comment:5 by Elaine Meng, 4 years ago 

Hi Jose,
The filename suffix is mentioned in the first sentence of the help:

"A ChimeraX positions file (format positions, filename suffix .positions) contains one line per model,"

<https://www.cgl.ucsf.edu/chimerax/docs/user/formats/positions.html>

I understand that sometimes it is easy for the eye to skip over when reading something, though!
Best,
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco
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