Thank you very much Jared! Could you tell me if you have some cool present for the surface representations ?
For example I am using the following script to visualize the surface of the protein around the ligand binding site: cmd.show('surface', 'polymer within 15 of complex* and not polymer') cmd.set('surface_color','marine','polymer') cmd.set('transparency', '0.4') cmd.hide('cartoon', 'all') cmd.png('image.png',width=${image},height=${image},dpi=50,ray=1) It produces a good looking image but the surface looks monotone. How could I improve its representation using some preset?? Cheers, Enrico вт, 11 янв. 2022 г. в 15:58, Jared Sampson <jared.samp...@columbia.edu>: > > Hi Enrico - > > If you want to reproduce GUI actions programmatically, you can see what > happens under the hood for most things by opening a log file: > > log_open log.pml > > then perform the desired action and the Python API version of the > corresponding command will be written to the log file. For example, for the > ligand sites > cartoon action menu item, this would be: > > preset.ligand_cartoon("myobject",_self=cmd) > > If you want to use this in a script I think you'll also have to do: > > from pymol import preset > > Hope that helps. > > Cheers, > Jared > > > On Tue, Jan 11, 2022 at 5:21 AM Enrico Martinez <jmsstarli...@gmail.com> > wrote: >> >> Dear Pymol Users! >> Is it possible to visualize protein-ligand interactions (which >> normally is achieved in GUI via a - > present -> ligand sites >> using some combination of the pymol commands, which could be scripted >> using cmd. syntax ? >> I've found this explanation >> https://pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts >> but did not understand quite well how it works. >> I would be grateful for the example of the commands which show the >> polar contacts (I am mostly interested in hydrogen bonds) in my pymol >> session without calling each time the GUI menu. >> Many thanks in advance! >> Enrico >> >> >> _______________________________________________ >> 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