For all the gentoo guys out there: I wrote an ebuild for msms. Any Bugs and suggestions should be reported to me for further improvement.
Robert Campbell schrieb: > Dear Buz, > > On Fri, 04 Jan 2008 15:43:41 -0500, Buz Barstow <b...@mac.com> > wrote: > > >> Dear all, >> >> I'd like to very accurately calculate the volume of a selection in >> pymol, or with tools that are callable by pymol? Could anyone suggest >> a program or algorithm? >> > > MSMS will calculate areas and volumes. I have written a python script that > you can run from within PyMOL to call msms. You can find it > (msms_pymol.py) at my scripts web page: > > http://pldserver1.biochem.queensu.ca/~rlc/work/pymol > > It does not use the pdb_to_xyzrn script supplied with msms -- that > conversion is now built in to the python script. > > After "running" the script to load it, then you can do: > > calc_msms_area object_name > > with options for changing the selection for calculating the area, the probe > radius and density. > > Because I was most interested in the calculation of surface areas, > including buried surface areas, the initial MSMS calculation is only run on > the complete object. That is what volume will be reported. > > For example, to calculate the surface area of chain A of a protein that is > buried by chain B, first create two objects: > > create protein_A, protein & chain A > create protein_B, protein & chain B > > Then run: > > calc_msms_area protein_A,protein_A within 4. of protein_B,probe=1.4 > > This will therefore report the volume of all of protein_A, but for the > surface areas, only the part of A that is buried by B. > > Cheers, > Rob > ------------------------------------------------------------------- ------------------------------------------------------------------- Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Bärbel Brumme-Bothe Geschäftsführung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Dr. Sebastian M. Schmidt ------------------------------------------------------------------- -------------------------------------------------------------------
inherit eutils DESCRIPTION="This allows you to run msms as a standalone application. A wrapped version of the library comes with MGLTools" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/MSMSRELEASE/REL2.6.1/msms_i86Linux2_2.6.1.tar.gz"; HOMEPAGE="http://mgltools.scripps.edu"; RESTRICT="primaryuri" LICENSE="academical free" SLOT="0" KEYWORDS="~x86" IUSE="" RDEPEND="" DEPEND="${RDEPEND}" src_install() { insinto /usr/lib/msms/ doins atmtypenumbers exeinto /usr/lib/msms/ doexe pdb_to_xyzr pdb_to_yzrn msms.i86Linux2.2.6.1 dosym /usr/lib/msms/pdb_to_xyzr /bin/pdb_to_xyzr dosym /usr/lib/msms/pdb_to_xyzrn /bin/pdb_to_xyzrn dosym /usr/lib/msms/msms.i86Linux2.2.6.1 /usr/bin/msms dodoc README ReleaseNotes doman msms.1 }
