[Chimera-users] Visualizing negative volume as in CastP

[Neelen, Christopher]

Hi Elaine,

Thank you very much !

Best,

Chris

-----Ursprüngliche Nachricht-----
Von: Elaine Meng <meng at cgl.ucsf.edu> 
Gesendet: Mittwoch, 23. November 2022 17:50
An: Neelen, Christopher <Christopher.Neelen-2 at vetmed.uni-giessen.de>
Cc: chimera-users at cgl.ucsf.edu
Betreff: Re: [Chimera-users] Visualizing negative volume as in CastP

Hi Chris,
If you mean that CastP shows enclosed blobs which are different surfaces than the patches of molecular surface shown by Chimera, sorry no, Chimera does not show those other blob surfaces (I believe they are not included in the CastP data that Chimera reads).   Alternatives to display closed surfaces of pocket volumes might be showing results from the 3Vee server or MOLEonline server in Chimera.
<http://3vee.molmovdb.org/>
<https://mole.upol.cz/>

Recently we also added the ability to show MOLEonline results to ChimeraX version 1.5 and higher:
<https://www.rbvi.ucsf.edu/chimerax/features.html#mole-channels>

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 23, 2022, at 4:47 AM, Neelen, Christopher via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello everyone,
>  
> I am trying to visualize cavities from a protein I am currently working on. Therefore I calculated the cavities volume using CastP. I then import the obtained files into chimera. Unfortunately CastP visualizes the cavities as a negative volume of the solvent accessible area. Chimera on the other hand only shows the surface. So is there a way to also visualize the negative volume in Chimara just like in CastP ?
>  
> Thanks in advance!
>  
> All the best,
>  
> Chris