Have you tried setting ray_trace_mode? Info here: https://pymolwiki.org/index.php/Ray
------------------------------ *Saurabh Gayali* / Post Doctoral Fellow saurabh.gay...@gmail.com / +91 8800412916 *CSIR-IGIB* <http://example.com/>New Delhi, India [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> 21/01/22, 10:10:28 am On Thu, Jan 20, 2022 at 11:02 PM Enrico Martinez <jmsstarli...@gmail.com> wrote: > Dear Pymol Users! > I've faced the problem of saving a PNG image without ray using the png > command in non-gui mode. First if I do it in pymol gui > #cmd.png('test.png',width=800,height=800,ray=0) > .. it produces fine image (without ray) > > However if I execute the same command inside of my bash sript: > > $pymol -c -d " > from pymol import cmd > from pymol import preset > cmd.load('my_pdb.pdb') > cmd.show('surface', 'my_pdb and polymer') > cmd.set('surface_color', 'default', 'my_pdb and polymer') > cmd.set('transparency', '0.8', 'my_pdb and polymer') > cmd.save('${vizu}/${output}_${lig_name}_rep${i}.pse') > > cmd.png('${vizu}/${output}_${lig_name}_interact_rep${i}.png',width=${image},height=${image},ray=0) > " > > Eventually It produces the correct pymol session but on the PNG image > I do not see any cartoon representation (only transparent surface) of > my protein. I did some tests and found that using non-gui mode (like > in the script shown above) pymol always sets the ray flag to ray=1 > even if it is disabled in my script. Is there any way to disable ray > (ray=0) in my script besides setting it in the cmd.png? > 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 >
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