Re: [rDock-list-def] Visualizing cavities

[Szilveszter J. <szi...@gm...>]

I prefer pymol, and isomesh works like dream, thank you!
Cheers:
Szilva

On Wed, May 14, 2014 at 4:24 PM, Sergio Ruiz Carmona
<sru...@gm...> wrote:
> Hi Szilva,
>
> We have never used the rDock GUI, so I can't help you in this aspect.
> What we do for viewing a cavity is to generate a grid with "-d" flag when
> running rbcavity and open it with pymol, for instance.
> A typical command would look like this:
>
>> rbcavity -was -d -r PRMFILE.prm
>
>
> That will generate two files: PRMFILE.as and PRMFILE_cav1.grd.
> Then, what we do is to open in pymol the receptor and the generated grd file
> and create a mesh (isovalue of 0.99) with the grid data as follows:
>
>> isomesh cavity, PRMFILE_cav1, 0.99
>
>
> Hope it helps!
> Sergio Ruiz
>
> PS: Thanks Marko for your reply!
>
>
> 2014-05-14 15:45 GMT+02:00 Szilveszter Juhos <szi...@gm...>:
>>
>> Hi All,
>>
>> Is there an easy way of visualizing the cavities (*.as) crated by
>> rbcavity? Tried to run the rDock GUI from the York webpage but got
>> only NPE when trying to run.
>>
>> Cheers:
>> Szilva
>>
>>
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>
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