[Chimera-users] Batch mode for Chimera

James Starlight jmsstarlight at gmail.com
Fri Sep 1 01:23:08 PDT 2017


now the errors of the execution of the script using headless chimera:

Opening rmsf_visu_AT1_dry_apo.2rep.step7_1.pdb...
The following problems occurred while reading PDB file for
rmsf_visu_AT1_dry_apo.2rep.step7_1.pdb
warning:  Ignored bad PDB record found on line 2

Opened rmsf_visu_AT1_dry_apo.2rep.step7_1.pdb containing 1 model, 903
atoms, and 301 residues
Rendering high resolution image...
./run.sh: line 113: 14479 Segmentation fault      (core dumped)
chimera_batch $pdb "${temp}"/script_${name}.cmd


the same with a pow-ray render

Opened rmsf_visu_AT1_wat_Na.3rep.step7_1.pdb containing 1 model, 903
atoms, and 301 residues
Generating POV-Ray data file
Exporting POV-Ray data to
/home/gleb/Desktop/Scripts/MegaAnalysis/output/plots/rmsf/rmsf_AT1_wat_Na.3rep.pov
Ignoring CHIMERA environment variable
Parse error at line 1:
 no element found


here is my script:

preset apply publication 2
rangecolor bfactor 2 blue 30 red 50 yellow
copy file /home/gleb/Desktop/Scripts/MegaAnalysis/output/plots/rmsf/AT1_wat_apo.3rep.png
png width 800 height 600


I have made the same images in chimera GUI and it worked very well.

Is it possible to run same script using in chimera-gui but from batch mode?

2017-08-31 22:04 GMT+02:00 Greg Couch <gregc at cgl.ucsf.edu>:
> You must have the given the "key" argument to the rangecolor command.  That
> option tries to display the Color Key tool which want you to use the mouse
> to position the color key in the graphics window.  That is not possible in
> batch mode.  You'll need to add the color key afterwards with an image
> editor if you need it.
>
>     HTH,
>
>     Greg
>
>
>
> On 08/31/2017 01:00 AM, James Starlight wrote:
>>
>> Thanks Eric!
>>
>> Everything works fine with the exception of the copy command. On the
>> rendering stage I have:
>>
>>
>> Opened AT1_dry_apo.1rep.step7_1.pdb containing 1 model, 57791 atoms,
>> and 12661 residues
>> Traceback (most recent call last):
>>    File "/home/gleb/.local/UCSF-Chimera64-batch/share/chimeraInit.py",
>> line 683, in init
>>      chimera.openModels.open(a, prefixableType=1)
>>    File
>> "/home/gleb/.local/UCSF-Chimera64-batch/share/chimera/__init__.py",
>> line 1951, in open
>>      models = func(filename, *args, **kw)
>>    File
>> "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/ChimeraExtension.py",
>> line 31, in func
>>      processCommandFile(fileName)
>>    File
>> "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/midas_text.py",
>> line 108, in processCommandFile
>>      _processFile(f, emulateRead, filename)
>>    File
>> "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/midas_text.py",
>> line 143, in _processFile
>>      if makeCommand(line):
>>    File
>> "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/midas_text.py",
>> line 69, in makeCommand
>>      f(c, args)
>>    File
>> "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/midas_text.py",
>> line 1786, in doRangeColor
>>      showKey=key)
>>    File "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/__init__.py",
>> line 2526, in rangeColor
>>      from Ilabel.gui import IlabelDialog
>>    File "/home/gleb/.local/UCSF-Chimera64-batch/share/Ilabel/gui.py",
>> line 13, in <module>
>>      from chimera import tkgui, chimage, CLOSE_SESSION
>>    File "/home/gleb/.local/UCSF-Chimera64-batch/share/chimera/tkgui.py",
>> line 74, in <module>
>>      import Togl
>> ImportError: No module named Togl
>>
>> Error while processing
>>
>> /home/gleb/Desktop/Scripts/MegaAnalysis/temp/script_AT1_dry_apo.1rep.step7_1.pdb.cmd:
>> ImportError: No module named Togl
>>
>>    File "/home/gleb/.local/UCSF-Chimera64-batch/share/chimera/tkgui.py",
>> line 74, in <module>
>>      import Togl
>>
>> See reply log for Python traceback.
>>
>> I have found that it is due to some conflict in PYTHONPATH from my
>> bash since I am running Chimera directly from BASH. The people also
>> wrote that Its related to setting transparency-  which was not a case
>> there - I did not set in my script. Anyway how to fix it?
>>
>> Thanks you!
>>
>> James
>>
>> 2017-08-30 22:54 GMT+02:00 Eric Pettersen <pett at cgl.ucsf.edu>:
>>>
>>> Hi James,
>>> First, if you want to save images without showing the Chimera GUI then
>>> you
>>> have to use the “headless” version of Chimera, available on the download
>>> page.  To do the other things you want, just put the equivalent commands
>>> in
>>> a file that ends in “.cmd” and just add that file to your invocation of
>>> Chimera, e.g.:
>>>
>>> chimera $pdb script.cmd
>>>
>>> The easiest way to handle the image file name is probably to used a fixed
>>> name in the Chimera “copy” command, and then in your bash script move
>>> that
>>> file to the final name you want.  Also, "preset” is the command to apply
>>> presets — “help preset” in Chimera for more info.
>>>
>>> Hope this helps.
>>>
>>> —Eric
>>>
>>>
>>> Eric Pettersen
>>> UCSF Computer Graphics Lab
>>>
>>>
>>> On Aug 30, 2017, at 8:40 AM, James Starlight <jmsstarlight at gmail.com>
>>> wrote:
>>>
>>> Dear Chimera Users!
>>>
>>> My simple bash script loops the folder with the pdbs and open it in
>>> Chimera
>>>
>>> for pdb in ${output}/xtc_proc/*.pdb ; do
>>> name=$(basename "$pdb")
>>> echo "I am sending ${name} to Chimera!"
>>> chimera $pdb
>>> done
>>>
>>> My question - can I use with chimera some batch file which will
>>> apply the following commands to each of the loaded pdbs without
>>> opening of Chimera GUI:
>>>
>>> 1- Apply "publications-2" preset
>>>
>>> 2 - rangecolor bfactor key 2 blue 30 red 50 yellow # color pdb
>>> according to b-factor provided in the pdb file
>>>
>>> 3- make a screen-shot of the colored cartoon figure in the selected
>>> output folder.
>>>
>>>
>>> I thanks so much for the example of batch file and the syntax accepted
>>> by chimera from the linux shell.
>>>
>>> James
>>> _______________________________________________
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