[Chimera-users] Batch mode for Chimera

Greg Couch gregc at cgl.ucsf.edu
Thu Aug 31 13:04:04 PDT 2017


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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