yep, it is not possible actually to switch off the Ray using no-gui mode in
pymol ( i've just read another topic on this case). BTW I found that the
problem of the disappearing of carton is mor related to the transparency,
since it had already been set for the surface as well. In the case when I
set it both for cartoon and surface, the cartoon diagram is lost :-)
here is my script:
cmd.set('transparency_mode','1')
cmd.set('transparency', '0.7', '${output}* and polymer')
cmd.set('cartoon_transparency', '0.3', '${output}* and polymer')пт, 21 янв. 2022 г. в 05:40, Saurabh Gayali <saurabh.gay...@gmail.com>: > 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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