From: James S. <jms...@gm...> - 2012-06-26 18:23:03
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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: >> >> " rel="nofollow">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 <chr...@bb...-**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 > |