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

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

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.php/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 <christian.roth@bbz.uni-**leipzig.de<chr...@bb...>
>>>    <mailto:christian.roth@bbz.**uni-leipzig.de<chr...@bb...>
>>> >
>>>     > <mailto:christian.roth@bbz.**uni-leipzig.de<chr...@bb...>
>>>
>>>    <mailto:christian.roth@bbz.**uni-leipzig.de<chr...@bb...>
>>> >>>
>>>     >
>>>     >     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
>>
>
>