Re: [PyMOL] Script for drawing docked ligand-active site pics

[Tamas H. <bio...@gm...>]

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, lei...@sb... 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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