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 Color-->Elements-->Green (carbon) 5. On the ligand, Find-->Polar contacts-->To 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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