I've just found the list of the presets:
https://pymolwiki.org/index.php/Preset
so a new question is still about preset.ligand_cartoon.
It works well, but shows me too much information. Is it possible to
limit the set of the identified residues e.g. to indicating only the
residues involved in the hydrogen bonds/ salt bridges?
Thank you in advance!
Enrico
вт, 11 янв. 2022 г. в 18:10, Enrico Martinez <jmsstarli...@gmail.com>:
>
> 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
> >>
> >>
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