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