Re: [PyMOL] Visualisation of protein-ligand interactions using cmd

[Enrico M. <jms...@gm...>]

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 <jar...@co...>:
>
> 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 <jms...@gm...> 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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