Re: [Chimera-users] Batch mode for Chimera

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 :

...

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 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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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