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 <spel...@users.sourceforge.net>
> 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 <spel...@users.sourceforge.net
>> <mailto:speleo3@users.**sourceforge.net <spel...@users.sourceforge.net>>>
>>
>>
>>
>> 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.r...@bbz.uni-**leipzig.de<christian.r...@bbz.uni-leipzig.de>
>>
>> <mailto:christian.roth@bbz.**uni-leipzig.de<christian.r...@bbz.uni-leipzig.de>
>> >
>> >
>> <mailto:christian.roth@bbz.**uni-leipzig.de<christian.r...@bbz.uni-leipzig.de>
>>
>>
>> <mailto:christian.roth@bbz.**uni-leipzig.de<christian.r...@bbz.uni-leipzig.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
>
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