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
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