Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

[James S. <jms...@gm...>]

By the way

in some papers I've seen  2D schematic diagrams of the protein-ligand
interactions.
The exapmle of such maps could be found here
http://ars.els-cdn.com.sci-hub.org/content/image/1-s2.0-S0005273610001707-gr4.jpg

 Could you tell me examples of software wich could produce such maps?


Thanks

James

2012/6/15 James Starlight <jms...@gm...>

> Thomas, thanks this works perfect.
>
>
> Jason,  I've tested  this script on my system ( this is the membrane
> protein inserted in the bilayer surrounded by two water layers ( up and
> down ). During simulation individual water mollecules move into the protein
> interiour ( in that case protein like a water pore althought it's the
> receptor ) so I want to visualise only that buried water.
>
> I've tried to do it via find_buried_waters script both via ASA as well as
> in case when I've used small cutoffs ( 0.1) but the script selected too
> many waters ( e.g virtually all waters from up and down layers have been
> selected ). How I could specify this selection more carefully ?
>
> find_buried_waters 1, 0.1
>
>
> James
>
>
> 2012/6/12 Thomas Holder <sp...@us...>
>
>> This will show them in the same slot in group mode.
>>>
>>
>> sorry, not "group mode" but "grid mode" of course.
>>
>>
>> --
>> Thomas Holder
>> MPI for Developmental Biology
>> Spemannstr. 35
>> D-72076 Tübingen
>>
>
>