Thanks, I was able to resolve the issue by placing refresh before the png command, and not using sleep. Sleep used anywhere before or after png caused a one-ligand lag in the ligand in the image and the ligand name for the next ligand. Refresh resulted in very fast image generation and IO to disk, without the time delay. Sleep mixed up ligands and image having the wrong ligand-specific filename.
From: Tamas Hegedus <biohege...@gmail.com> Sent: Wednesday, April 29, 2020 10:40 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Wait for processing to complete before invoking new commands Something is fishy... as I do not expect this to happen. I have never experienced this problem. I made different types of mistakes resulting in such a phenomenon. * using a for loop and in the command, loading the ligand, I did not inserted the loop variable into the file name (e.g. I used lig_1.pdb instead of "lig_%i.pdb" % ix) * it was not with vina (difficult to imagine this situation), but once I generated a set of pdb files with the same coordinates On the other hand: https://pymolwiki.org/index.php/Sync On 4/30/20 5:09 AM, leifepeter...@sbcglobal.net <mailto:leifepeter...@sbcglobal.net> wrote: I am writing png images for many docked ligands but all the png files have the same image - even though the file names are different for the ligand_out.pdbqt files. So PyMol is getting ahead of itself and quickly looping through all the code and dumping the same image but with different files names since the image buffer never caught up. Thus, I will need to programatically wait for each png to be generated, and once the png command is finished, I can move to the next ligand. What command can be used to instruct PyMol to finish its processing before taking on new commands, either that or e.g. 5 sec pause? I will need to use this command right after the png command. _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
_______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
