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

Dear James.

I found the hollow script and/or Castp quite useful for this. There exist also 
a program called surfplot, from Roman Laskowski again. It is integrated in the 
pdbsum interface and creates ther surfaces. You may look there for examples. 
Another possibility is Voidoo from Uppsala. 

By the way, there are already comments about the internal waters from the 
pose-view group?

Best Regards 

Christian

Am Donnerstag 28 Juni 2012 07:53:31 schrieb James Starlight:
> I've obtained accademical licence on LigProt and I found that this
> softwatre is most handfull in the 2d analysis of protein-ligand
> interactions. Is it possible to integrate it into pymol  what have been
> done in case of Pose view ? )
> 
> By the way does anybody know any another intresting software or pymol
> modules for the analysis of protein-ligand interactions. In particular I'd
> like to obtain 3d surfaces of vdw as well as electrosctatics profiles of
> the active sites of my proteins as well as analysing of H-bonds ?
> 
> 
> James
> 
> 2012/6/26 James Starlight <jms...@gm...>
> 
> > I'm still waiting for accademical license on lig prot. By the way it's
> > very strange that PoseView have not been accompanied with 'internal water
> > detector' ;) i've sent  the letter to developers with this question and
> > hope they can help
> >
> > James
> >
> > 2012/6/26 Thomas Holder <sp...@us...>
> >
> >> Hi James,
> >>
> >> hm, looks like PoseView ignores all water molecules :(
> >>
> >> Have you tried LigPlot? It has a "-w" option to include waters.
> >>
> >> Cheers,
> >>  Thomas
> >>
> >> On 06/26/2012 05:11 PM, James Starlight wrote:
> >>> Thomas,
> >>> Its really great )
> >>> Could you tell me if you find a possible way to take into account
> >>> burried water from the protein interiour in the Pose View
> >>> protein-ligand interaction 2D plots ?
> >>> Most of my proteins consist of such internal water ( like a het atoms
> >>> in the protein.pdb ) but pose view didnt take this mollecules into
> >>> account so the final plot lack of many crussial h_bonds between ligand
> >>> and protein itself.
> >>> James
> >>> 2012/6/26 Thomas Holder <sp...@us...
> >>> <mailto:speleo3@users.**sourceforge.net
> >>> <sp...@us...>>>
> >>>
> >>>
> >>>
> >>>    Hi all,
> >>>
> >>>    I thought it would be nice to run such tools directly from PyMOL. So
> >>>    there is a PoseView wrapper on the PyMOLWiki now:
> >>>
> >>>   
> >>> http://pymolwiki.org/index.**php/PoseView<http://pymolwiki.org/index.ph
> >>>p/PoseView>
> >>>
> >>>    A LigPlot wrapper may follow...
> >>>
> >>>    Cheers,
> >>>       Thomas
> >>>
> >>>    On 06/26/2012 10:13 AM, James Starlight wrote:
> >>>     > Christian,
> >>>     > Also I've found the same software- pose view (in that article
> >>>
> >>>    I've also
> >>>
> >>>     > found link on it). Its very friendly but I've noticed some erorrs
> >>>
> >>>    during
> >>>
> >>>     > representation of the non-covalent contacts partly in case of the
> >>>
> >>> vdw
> >>>
> >>>     > interactions ( e,g i've change cutof from 0.8 to 1.2 nm for vdw
> >>>
> >>>    but some
> >>>
> >>>     > crussial interactions could not be visualized)
> >>>     > And the main disadvantage of that software is that it does not
> >>>
> >>>    take into
> >>>
> >>>     > account burrial water and it's h-bond networks within protein.
> >>>     > I've ordered free license on the lig prot and hope that this
> >>>
> >>> software
> >>>
> >>>     > will be better ;)
> >>>     > James
> >>>     > 2012/6/26 Christian Roth
> >>>     > <chr...@bb...-**leipzig.de<chr...@bb...-leipz
> >>>     >ig.de>
> >>>
> >>>   
> >>> <mailto:christian.roth@bbz.**uni-leipzig.de<chr...@bb...-leip
> >>>zig.de>
> >>>
> >>>     > <mailto:christian.roth@bbz.**uni-leipzig.de<chr...@bb...
> >>>     >i-leipzig.de>
> >>>
> >>>   
> >>> <mailto:christian.roth@bbz.**uni-leipzig.de<chr...@bb...-leip
> >>>zig.de>
> >>>
> >>>     >     Hi James,
> >>>     >
> >>>     >     LigPlot is free for academic users. You just have to verify
> >>>
> >>>    that you
> >>>
> >>>     >     are a
> >>>     >     academic user. MOE does a simimlar representiation but is
> >>>
> >>>    definitely
> >>>
> >>>     >     not free.
> >>>     >
> >>>     >     Christian
> >>
> >> --
> >> Thomas Holder
> >> MPI for Developmental Biology
> >> Spemannstr. 35
> >> D-72076 Tübingen
> 


-- 
Christian Roth
Institut für Bioanalytische Chemie
Biotechnologisch-Biomedizinisches Zentrum
Fakultät für Chemie und Mineralogie
Universität Leipzig
Deutscher Platz 5
04103 Leipzig
Telefon: +49 (0)341 97 31316
Fax: +49 (0)341 97 31319