VMD-L Mailing List

From: BRAULIO FAVIÁN VALDEBENITO MATURANA (bvaldebenito09_at_alumnos.utalca.cl)
Date: Thu May 26 2011 - 12:41:48 CDT

Dear all,

We're working on a Tcl/Tk script whose function is to determine both surface and internal cavities of a given protein. In order to achieve that, we've been thinking in the "volmap" function as stated by John Stone in reply to "cavity/pocket representation" on May 2nd, 2006 (it can be seen here: http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/6885.html), but instead of a graphical output, we need the analytical data too.

Well, regarding the output of the "volmap" command, which is a file with .dx extension, we would like to know if there is any way to use the information on that file so that we can "substract" from the entire map the volume occupied by the actual molecule, thus letting the volume of any possible cavities.

Thanks in advance!
Braulio.