Handle pymol via CUI.

I often use Pymol to visualize PDB files.
Recently I want to merge some PDB files in one Pymol session file from CUI.
Because I run the task as batch. So I searched API document and tried it.
At first I need launch pymol in silent mode ( no GUI ).
And then load pdb files.
Next I set color of each object by b factor as spectrum.
Finally save object as pymol session file and closed pymol.
Every thing worked well.

Following code and sample files are pushed my repo.


import pymol
from pymol import cmd
cmd.spectrum('b', 'blue_white_red','1atp', 0, 100)
cmd.spectrum('b', 'yellow_cyan_blue','1atp2', 0, 100)
cmd.spectrum('b', 'green_magenta','1atp3', 0, 100)

Published by iwatobipen

I'm medicinal chemist in mid size of pharmaceutical company. I love chemoinfo, cording, organic synthesis, my family.

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