[IMP-dev] Volume calculation for an elongated protein in IMP?

[Seung Joong Kim <sjkim@salilab.org>]

Hi all,

  It seems to me that the current volume calculation in IMP EM module 
is based on a globular protein/complex shape (assuming 1.2 cubic 
angstrom per dalton), not applicable to an elongated protein such as 
Amelogenin.  I compared UCSF chimera and it reported ~half size volume 
for the same density map and threshold.  I don't know in detail how 
Chimera calculates volume for the density map of an elongated protein, 
but it would be great if we can add this function (or any other method 
that we can trust for an elongated /extended protein) to IMP.  Any 
suggestions?  Thanks!
- SJ

--
Seung Joong Kim, Ph.D.

Postdoctoral Scholar, Andrej Sali group
Department of Bioengineering and Therapeutic Sciences
University of California at San Francisco (UCSF)
1-217-649-2147