hi SJ:

Yes the volume calculation assumes the protein is globular. The way the function works is getting approximated volume from mass and then finding a threshold of a EM density map that meets the predicted volume (this function was contributed by Ben S). To make the functionality usable for elongated ones, we need a function to predict volume from mass from elongated proteins. We currently do not have one and I am sure sure how to calculate volume from mass for elongated proteins - maybe someone else knows?

Keren.

On Aug 9, 2011, at 9:25 PM, Seung Joong Kim wrote:

> 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