[Chimera-users] Visualisation in Headless Chimera

Elaine Meng meng at cgl.ucsf.edu
Thu Mar 28 14:08:03 PDT 2019

Eric’s idea for incorporating the color key if it’s the same in all your final images gave me a different crazy idea, but it might be slightly tricky to do on the headless system:

(1) using the GUI version of Chimera, save an image of nothing but the white background with the color key on it, using the same image size as you plan to make your structure images on the headless machine

(2) in Chimera preferences (still in the Chimera GUI), category: Background, set Background method: image, and use for the Background image: the file you saved in step #1, and then save preferences.  Quit from the GUI Chimera.

(3) the harder part: copy the image file to the headless machine, and edit the Chimera preferences file on that machine (you can look at the preferences file on the GUI machine as a guide to how to edit it) to use an image for the background, and to give the correct pathname for the image file on the headless machine.

The default location of the preferences file (actually named “preferences”) is in a .chimera subdirectory of the user’s home directory.


> On Mar 28, 2019, at 1:48 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> If your key is the same for all your images, there is a trick you can use.  Use the regular Chimera graphical interface to draw the color key (Tools→Utilities→Color Key) positioned and looking the way you want with no other models open, then save an image.  When saving the image, make sure to tick the “Transparent background” option in the Save-Image dialog (and make sure the image is the same size as your pipeline images).  Then there are many possible image-processing programs you can use to superimpose that key on the images you are getting from your pipeline.
> —Eric
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
>> On Mar 28, 2019, at 9:49 AM, James Starlight <jmsstarlight at gmail.com> wrote:
>> Thank you so much, Elaine!
>> Yes, indeed, I have tested it's a problem in set silhouettes command
>> which cause headless-chimera to crush.
>> the same is for the "preset" command.
>> And the problem is on the step of the rendering of the image
>> Rendering high resolution image...
>> ./structure.sh : ligne 70 :  3515 Erreur de segmentation  (core
>> dumped) chimera-batch ${pdb} ${temp}/chimera.${pdb_name}.com
>> and here is my script
>> set bgcol white
>> set silhouette
>> ~set depth
>> ribscale licorice
>> ribrep edged strand
>> #light options
>> light contrast 0.4
>> light reflectivity 0.9
>> #structure pre-processing
>> ksdssp
>> #use this commands to re-orient PDB
>> turn x 90 center view
>> #turn y 20 center view
>> turn z -80 center view
>> move z -15
>> # make visualisation of b-factors
>> rangecolor bfactor 2 blue 30 red 50 yellow
>> # make a png immage
>> copy file ./B-factors_EvXynTS_apo_340K.png png width 800 height 600
>> Finally I just have checked it also in chimera-gui, everything works
>> fine with the same commands!
>> чт, 28 мар. 2019 г. в 17:31, Elaine Meng <meng at cgl.ucsf.edu>:
>>> Hi James,
>>> (1) The black outlines are silhouettes, so if silhouettes cause the problem there is no way around it.  The preset also does some other things, however, so you could doublecheck just using the “set silhouettes” command instead of “preset.”
>>> The image you attached is from the ribbon styles tutorial. The tutorial shows the commands you would need to make that image.
>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ribstyles.html>
>>> Image description is "smooth ribbons, default lighting except decreased contrast and reflectivity”
>>> …corresponding to the  the first two “set” commands in that tutorial (white background and black silhouettes) and the last two commands (lighting contrast and reflectivity).
>>> (2) The “key” command option only enables interactive placement of a color key by hand using the GUI.  Sorry, there is no option to place the color key directly, without human intervention.
>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html>
>>> Best,
>>> Elaine
>>> -----
>>> Elaine C. Meng, Ph.D.
>>> UCSF Chimera(X) team
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>>> On Mar 28, 2019, at 4:11 AM, James Starlight <jmsstarlight at gmail.com> wrote:
>>>> Dear Chimera users!
>>>> I am using headless version of Chimera inside of my Bash script to
>>>> prepare images of the pdbs. Normally I provide a pdb file with a
>>>> script in loop to obrain images automatically
>>>> Here are some of my questions related to the visualisation:
>>>> 1) I have a problem with the "preset apply publication 1"
>>>> notably Chimera is crushed when I use #set silhouette option
>>>> Is it possible to make "a black border of a selected thickness" for
>>>> all of the elements of secondary structure of my proteins via some
>>>> another command?
>>>> Actually in terms of the cartoon's style (but not a colour) I would
>>>> like to obtain something like was shown here
>>>> https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ribstyles-contrast3-reflect5.png
>>>> 2) I am using "rangecolor bfactor 2 blue 30 red 50 yellow" option to
>>>> colour the structure according to the B-factor information provided in
>>>> the given PDB.
>>>> The problem is when I provide "key" option for it to place a colour
>>>> diagram on the resulted picture I ontain a crush in headless version.
>>>> Do some other methods exist for the placement of the colour legend for
>>>> the B-factor colouring which could be used in the headless version?
>>>> Thank you for help in avance!
>>>> James

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