Hi,
I do not provide a full solution...
I suggest
* try every particular step in pymol, in the command window
* if one step is successful, then put it (finally everything) into a file
* use python commands (not pymol; e.g. cmd.color("blue", "lig_01"))
* run the file either using "run python.file.py" in pymol; in this case
you can set "argumuments" as regular python variables before running
"run ..."
* run the file from the shell "pymol -c python.file.py -- arg1 arg_i
view1.pkl
* if you have several poses in the vina output, I suggest to split them
(vina_split) convert to pdb (e.g. openbabel) and then load them
individually into pymol in a for cycle
* before saving png, try/test "ray x, y"; later this can be set in the
"png" command
* READ the documentation
* use GOOGLE; e.g. "pymol find polar contacts"
You can save your view:
pickle.dump(cmd.get_view(), open(fname, 'wb'))
Load it back:
cmd.set_view(pickle.load(open(fname, 'rb')))
On 4/29/20 6:29 PM, leifepeter...@sbcglobal.net wrote:
I have two receptors and their active sites for which I need to draw
about 70 separate ligand-active site images (.png). Both active sites
are saved in session files (.pse) based on 3D coordinates from pdbqt
files after prepping for Vina docking. The ligand 3D coordinates are
based on *_out.pdbqt files from docking with Vina.
After opening a .pse file to show the surface of the active site, the
following automated steps are needed:
1. Open a ligand docking output file, ligandname_out.pdbqt, and
automatically orient the active site (the site coordinates jump a
little as soon as each ligand docking output file is opened). So
the same active site orientation is needed so images are consistent.
2. Adjust the brightness level (mouse thumbwheel) so that each saved
image has a consistent look.
3. On the ligand, removes valence.
4. Change the color of the ligand using ColoràElementsàGreen (carbon)
5. On the ligand, FindàPolar contactsàTo any atom (is there away to
get counts of H-bonds)
6. Save PNG using ligand name.
(need to also programmatically hit Return after code is pasted into
command line)
Once I get something that works after pasting the code for the above 6
steps into the command line, and discover that the image is saved, I
can then write my own code to clone the commands, and substitute all
the ligand file names.
Certainly, someone has already written code to autodraw a docked
ligand (from Vina) sitting in an active site?
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