VMD can generate a surface for a given structure. To accomplish that it needs either MSMS or SURF, which is build in, but slower. So adding a the useflag MSMS would make the "Drawing Methods" feature complete. There is a ready to use ebuild written by Justin Lecher (jlec) http://bugs.gentoo.org/show_bug.cgi?id=209161 Please find attached a diff for the current "vmd-1.8.7.ebuild". Cheers Bjoern Olausson Reproducible: Always
Created attachment 210521 [details, diff] vmd-1.8.7.ebuild.diff
Thanks! Let's see if Justin can come up with a working ebuild for msms and then we can have vmd use it as well. cheers, Markus
The problem is, that msms as wrapped version of the msms-lib is only provided as binary version. The msmslib itself is provided as source and there is a working ebuild in the overlay. @Bjoern, perhaps you can ask upstream to provide a source download for the wrapper, too.
@Justin: Okay, now I am kinda confused... why would we need the wrapped version? And by the way, I found a nice plugin "MultiMSMS VMD plugin" - The MultiMSMS VMD plugin caches the Solvent Excluded Surface computed by MSMS to speedup the animation of a sequence of frames. http://personal.cscs.ch/~mvalle/ChemViz/multimsms.html For VMD we just need the MSMS C library. MGLTools (AutoDockTools etc.) need the wrapped version... As much as I understand it. But I found neither the source for the MSMS C library nor for the wrapped version. So before I go and ask Michel Sanner I would like to get things sorted. Cheers Bjoern
sci-libs/msms contains the c lib, which is in sci overlay, and the wrapped version is in my personal overlay for ancient reasons.
Okay, the msms ebuild from science overlay is not what we need. Wee need this: # Copyright 1999-2008 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ inherit eutils DL_URI="http://mgltools.scripps.edu/downloads/tars/releases/MSMSRELEASE/" DESCRIPTION="msms is a wrapped version of the library comes with MGLTools" SRC_URI="x86? ( ${DL_URI}REL${PV}/msms_i86Linux2_${PV}.tar.gz ) amd64? ( ${DL_URI}REL${PV}/msms_i86_64Linux2_${PV}.tar.gz )" HOMEPAGE="http://mgltools.scripps.edu" RESTRICT="mirror" LICENSE="mgltools" SLOT="0" KEYWORDS="-* ~x86 ~amd64" IUSE="static" src_unpack(){ unpack ${A} epatch "${FILESDIR}"/atmtypenumbers.patch } src_install() { insinto /opt/msms/ doins atmtypenumbers sed -i 's:nawk:gawk:g' {pdb_to_xyzr,pdb_to_xyzrn} exeinto /opt/msms/ doexe pdb_to_xyzr pdb_to_xyzrn case "${ARCH}" in x86) doexe msms.i86Linux2.2.6.1 dosym ../../opt/msms/msms.i86Linux2.2.6.1 /usr/bin/msms;; amd64) use !static && doexe msms.x86_64Linux2.2.6.1 && \ dosym ../../opt/msms/msms.x86_64Linux2.2.6.1 /usr/bin/msms use static && doexe msms.x86_64Linux2.2.6.1.staticgcc &&\ dosym ../../opt/msms/msms.x86_64Linux2.2.6.1.staticgcc /usr/bin/msms;; *) die || "${Arch} not supported";; esac dosym ../../opt/msms/pdb_to_xyzr /usr/bin/pdb_to_xyzr dosym ../../opt/msms/pdb_to_xyzrn /usr/bin/pdb_to_xyzrn dodoc README ReleaseNotes doman msms.1 } ${FILESDIR}"/atmtypenumbers.patch --- pdb_to_xyzr.orig 2008-04-17 15:40:07.000000000 +0200 +++ pdb_to_xyzr 2008-04-17 15:40:27.000000000 +0200 @@ -31,7 +31,7 @@ nawk 'BEGIN{ # read radius table and patterns from supplied file npats=0 - numfile = "./atmtypenumbers" + numfile = "/opt/msms/atmtypenumbers" while ((getline < numfile) > 0) { if(NF==0||substr($1,1,1)=="#") continue; if($1=="radius") { And I will ask if they can relese http://mgltools.scripps.edu/downloads#msms as source. Cheers Bjoern
DESCRIPTION="msms is a wrapped version of the library comes with MGLTools" ;)
Sometimes I just should ... take a nap :-) But no response so far. Cheers Bjoern
Added msms and povray use flags
