[Chimera-users] Selecting from a surface area

Conrad Huang conrad at cgl.ucsf.edu
Mon Jun 26 09:55:47 PDT 2006

Miguel Ortiz-Lombardia wrote:
> Hash: SHA1
> Hi,
> I'd like to pick an area of a (msms) surface (like with a "lasso" tool)
> and from that area, select the atoms/residues from which it is built.
> I haven't found anything like this in the documentation, so I'm afraid
> it's not possible. Or is it?
> Best regards,
> Miguel

I'm afraid that is not currently possible.  To make this work, we would 
need to modify the surface rendering graphics code.  However, since we 
are in the midst of replacing the molecular surface computation code, we 
are holding off other changes to the surface code.

The current molecular surface computation code in Chimera is the MSMS 
library from Michel Sanner.  We are replacing it for a couple different 
reasons: (1) MSMS fails to generate surfaces for some molecular 
structures, and (2) we want additional capabilities in our surface 
computations (e.g., solvent _accessible_ surface as well as solvent 
_excluded_ surface, surface area, cavity detection, etc.).  As part of 
the replacement process, we are planning to integrate the multiple types 
of surfaces (isosurfaces from volume rendering, low-resolution surfaces 
from multiscale modeling, and molecular surfaces) into a single type. 
This is desirable because there are currently different tools for 
manipulating different types of surfaces.  By integrating them into a 
single type, we can make these tools work across surfaces generated via 
different means.

So, the bottom line is that we hope to have something for you later this 


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