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
> Hi James,
>
> hm, looks lik
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
>
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 did
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
A LigPlot wrapper may follow...
Cheers,
Thomas
On 06/26/2012 10:13 AM, James Starlight wrote:
> Christian,
> Also I've foun
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
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
--
Live Security Virtual Conference
Exclusi
