[chimera-dev] VolumeEraser

[Elaine Meng]

Hi Alex,
The Surfnet results are just surfaces in Chimera without associated volume data.  
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfnet/surfnet.html>
That is, they are just the hollow “skins” without data values inside and outside, and Chimera “volume” tools such as Volume Eraser don’t apply.  Chimera uses the term volume data for 3D grids of values, typically maps of electron density or electrostatic potential.

Some other approaches for studying pocket void space are mentioned in this recent post to chimera-users at cgl.ucsf.edu:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-May/010993.html>

I can’t think of any Chimera-only approach to intersect 3D shapes.  There is volume data addition, subtraction, and masking with surfaces (see commands “vop add/subtract” and “mask”), but in that case you would need to have some volume data by Chimera’s definition.  The Voss Volume Voxelator site mentioned in the post above does create volume data to fill pockets in proteins, but I don’t know if it would work with such subsequent manipulations in Chimera.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html>

I hope this clarifies,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

P.S.  the chimera-users address mentioned above is probably better for general usage questions; chimera-dev is for programming-related questions

On May 6, 2015, at 8:18 AM, yes sir <fileslave at hotmail.com> wrote:

> Dear Sirs,
> I recently started using chimera, please apologise my lack of knowledge. 
> In order to erase a surfnet volume I am trying to use the Erase volume module, but it doesn't work. Are the surfnet objects available to be used in VolumeEraser functions? Is there another way to study volume intersections?
> If you know, please point out the article which describes the procedure for this kind of volume calculation.
> 
> Best regards,
> Alex