1 files changed, 1057 insertions, 344 deletions

diff --git a/science/vmd/pkg-plist b/science/vmd/pkg-plist
index b78504ff706c..daff3ee26865 100644
--- a/science/vmd/pkg-plist
+++ b/science/vmd/pkg-plist
@@ -1,14 +1,16 @@
 bin/vmd
+lib/vmd/.vmdrc
+lib/vmd/.vmdsensors
 lib/vmd/Announcement
 lib/vmd/LICENSE
 lib/vmd/README
-lib/vmd/.vmdrc
-lib/vmd/.vmdsensors
 lib/vmd/doc/ug.pdf
-lib/vmd/plugins/%%VMD_ARCH%%/bin/catdcd4.0/catdcd
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/avsplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/babelplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/basissetplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/bgfplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/binposplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/biomoccaplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/brixplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/carplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/ccp4plugin.so
@@ -19,6 +21,7 @@ lib/vmd/plugins/%%VMD_ARCH%%/molfile/cubeplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/dcdplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/dlpolyplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/dsn6plugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/dtrplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/dxplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/edmplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/fs4plugin.so
@@ -27,16 +30,20 @@ lib/vmd/plugins/%%VMD_ARCH%%/molfile/graspplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/grdplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/gridplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/gromacsplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/jsplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/lammpsplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/libmolfile_plugin.a
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/libmolfile_plugin.h
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/maeffplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/mapplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/mdfplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/mol2plugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/moldenplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/msmsplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/namdbinplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/parm7plugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/parmplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/pbeqplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/pdbplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/phiplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/pltplugin.so
@@ -44,43 +51,146 @@ lib/vmd/plugins/%%VMD_ARCH%%/molfile/pqrplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/psfplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/raster3dplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/rst7plugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/situsplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/spiderplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/stlplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/tinkerplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/webpdbplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/uhbdplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/vaspchgcarplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/vaspoutcarplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/vaspparchgplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/vaspposcarplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/vaspxdatcarplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/vaspxmlplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/vtfplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/xbgfplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/xsfplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/xyzplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/pmepot1.0/libpmepot.so
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/pmepot1.0/pkgIndex.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/pmepot1.0/pmepot.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/pmepot1.0/pmepot_gui.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen1.3/libpsfgen.so
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen1.3/pkgIndex.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen1.3/ug.pdf
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/hesstrans1.0/hessTest.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/hesstrans1.0/hesstrans.so
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/hesstrans1.0/hesstrans.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/hesstrans1.0/pkgIndex.tcl
+lib/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so
+lib/vmd/plugins/LINUX/tcl/intersurf1.1/color_func.tcl
+lib/vmd/plugins/LINUX/tcl/intersurf1.1/intersurf_gui.tcl
+lib/vmd/plugins/LINUX/tcl/intersurf1.1/license.txt
+lib/vmd/plugins/LINUX/tcl/intersurf1.1/nicostuf.tcl
+lib/vmd/plugins/LINUX/tcl/intersurf1.1/pkgIndex.tcl
+lib/vmd/plugins/WIN32/tcl/intersurf1.1/bin/intersurf.dll
+lib/vmd/plugins/WIN32/tcl/intersurf1.1/color_func.tcl
+lib/vmd/plugins/WIN32/tcl/intersurf1.1/intersurf_gui.tcl
+lib/vmd/plugins/WIN32/tcl/intersurf1.1/license.txt
+lib/vmd/plugins/WIN32/tcl/intersurf1.1/nicostuf.tcl
+lib/vmd/plugins/WIN32/tcl/intersurf1.1/pkgIndex.tcl
 lib/vmd/plugins/include/molfile_plugin.h
+lib/vmd/plugins/include/vmdconio.h
 lib/vmd/plugins/include/vmdplugin.h
-lib/vmd/plugins/noarch/tcl/apbsrun1.0/apbsrun.tcl
-lib/vmd/plugins/noarch/tcl/apbsrun1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/apbsrun1.0/radii.dat
-lib/vmd/plugins/noarch/tcl/autoimd1.4/autoimd-api.tcl
-lib/vmd/plugins/noarch/tcl/autoimd1.4/autoimd-gui.tcl
-lib/vmd/plugins/noarch/tcl/autoimd1.4/autoimd-settings.tcl
-lib/vmd/plugins/noarch/tcl/autoimd1.4/autoimd-template.namd
-lib/vmd/plugins/noarch/tcl/autoimd1.4/autoimd.tcl
-lib/vmd/plugins/noarch/tcl/autoimd1.4/namdrun.tcl
-lib/vmd/plugins/noarch/tcl/autoimd1.4/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/autoimd1.4/ug.pdf
-lib/vmd/plugins/noarch/tcl/autoionize1.1/autoionize.tcl
-lib/vmd/plugins/noarch/tcl/autoionize1.1/ions.top
-lib/vmd/plugins/noarch/tcl/autoionize1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/apbsrun1.3/apbsrun.tcl
+lib/vmd/plugins/noarch/tcl/apbsrun1.3/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/apbsrun1.3/radii.dat
+lib/vmd/plugins/noarch/tcl/atomedit1.0/atomedit.tcl
+lib/vmd/plugins/noarch/tcl/atomedit1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/autoimd1.6/autoimd-api.tcl
+lib/vmd/plugins/noarch/tcl/autoimd1.6/autoimd-gui.tcl
+lib/vmd/plugins/noarch/tcl/autoimd1.6/autoimd-settings.tcl
+lib/vmd/plugins/noarch/tcl/autoimd1.6/autoimd-template.namd
+lib/vmd/plugins/noarch/tcl/autoimd1.6/autoimd.tcl
+lib/vmd/plugins/noarch/tcl/autoimd1.6/namdrun.tcl
+lib/vmd/plugins/noarch/tcl/autoimd1.6/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/autoimd1.6/ug.pdf
+lib/vmd/plugins/noarch/tcl/autoionize1.2/autoionize.tcl
+lib/vmd/plugins/noarch/tcl/autoionize1.2/autoionizegui.tcl
+lib/vmd/plugins/noarch/tcl/autoionize1.2/ions.top
+lib/vmd/plugins/noarch/tcl/autoionize1.2/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/bignum1.0/bignum.tcl
+lib/vmd/plugins/noarch/tcl/bignum1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/biocore1.1/biocore.tcl
+lib/vmd/plugins/noarch/tcl/biocore1.1/biocoreHelper.tcl
+lib/vmd/plugins/noarch/tcl/biocore1.1/biocorechat.tcl
+lib/vmd/plugins/noarch/tcl/biocore1.1/biocorelogin.tcl
+lib/vmd/plugins/noarch/tcl/biocore1.1/biocorepubsync.tcl
+lib/vmd/plugins/noarch/tcl/biocore1.1/biocoreutil.tcl
+lib/vmd/plugins/noarch/tcl/biocore1.1/locked.gif
+lib/vmd/plugins/noarch/tcl/biocore1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/biocore1.1/unlocked.gif
+lib/vmd/plugins/noarch/tcl/blast1.1/blast.tcl
+lib/vmd/plugins/noarch/tcl/blast1.1/blast_resultviewer.tcl
+lib/vmd/plugins/noarch/tcl/blast1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/cgtools1.0/cggui.tcl
+lib/vmd/plugins/noarch/tcl/cgtools1.0/cgnetworking.tcl
+lib/vmd/plugins/noarch/tcl/cgtools1.0/cgtools.tcl
+lib/vmd/plugins/noarch/tcl/cgtools1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/cgtools1.0/protein.cgc
+lib/vmd/plugins/noarch/tcl/cgtools1.0/rbcg-2007.par
+lib/vmd/plugins/noarch/tcl/cgtools1.0/rbcg-2007.top
+lib/vmd/plugins/noarch/tcl/cgtools1.0/water.cgc
 lib/vmd/plugins/noarch/tcl/cliptool1.0/cliptool.tcl
 lib/vmd/plugins/noarch/tcl/cliptool1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/clonerep1.1/clonerep.tcl
+lib/vmd/plugins/noarch/tcl/clonerep1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/colorscalebar1.2/colorscalebar.tcl
+lib/vmd/plugins/noarch/tcl/colorscalebar1.2/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/contactmap1.1/contactmap.tcl
 lib/vmd/plugins/noarch/tcl/contactmap1.1/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/exectool1.0/exectool.tcl
-lib/vmd/plugins/noarch/tcl/exectool1.0/jobmanager.tcl
-lib/vmd/plugins/noarch/tcl/exectool1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/dataimport1.0/dataimport.tcl
+lib/vmd/plugins/noarch/tcl/dataimport1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/demomaster1.0/demomaster.tcl
+lib/vmd/plugins/noarch/tcl/demomaster1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/dipwatch1.2/dipwatch.tcl
+lib/vmd/plugins/noarch/tcl/dipwatch1.2/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/dowser1.0/dowser.tcl
+lib/vmd/plugins/noarch/tcl/dowser1.0/dowser_gui.tcl
+lib/vmd/plugins/noarch/tcl/dowser1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/exectool1.2/exectool.tcl
+lib/vmd/plugins/noarch/tcl/exectool1.2/jobmanager.tcl
+lib/vmd/plugins/noarch/tcl/exectool1.2/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/extendedpdb1.0/extendedpdb.tcl
+lib/vmd/plugins/noarch/tcl/extendedpdb1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/gofrgui1.1/gofrgui.tcl
+lib/vmd/plugins/noarch/tcl/gofrgui1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/hbonds1.1/hbonds.tcl
+lib/vmd/plugins/noarch/tcl/hbonds1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/idatm0.1/idatm.tcl
+lib/vmd/plugins/noarch/tcl/idatm0.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/ilstools1.2/acetylene.xyz
+lib/vmd/plugins/noarch/tcl/ilstools1.2/carbondioxide.xyz
+lib/vmd/plugins/noarch/tcl/ilstools1.2/carbonmonoxide.xyz
+lib/vmd/plugins/noarch/tcl/ilstools1.2/ethene.xyz
+lib/vmd/plugins/noarch/tcl/ilstools1.2/hydrogen.xyz
+lib/vmd/plugins/noarch/tcl/ilstools1.2/ilstools.tcl
+lib/vmd/plugins/noarch/tcl/ilstools1.2/methane.xyz
+lib/vmd/plugins/noarch/tcl/ilstools1.2/nitricoxide.xyz
+lib/vmd/plugins/noarch/tcl/ilstools1.2/nitrogen.xyz
+lib/vmd/plugins/noarch/tcl/ilstools1.2/nitrogendioxide.xyz
+lib/vmd/plugins/noarch/tcl/ilstools1.2/nitrousoxide.xyz
+lib/vmd/plugins/noarch/tcl/ilstools1.2/oxygen.xyz
+lib/vmd/plugins/noarch/tcl/ilstools1.2/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/imdmenu1.0/imdmenu.tcl
 lib/vmd/plugins/noarch/tcl/imdmenu1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/inorganicbuilder.tcl
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/CVS/Entries
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/CVS/Repository
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/CVS/Root
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/asio2.inp
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/asio2.pdb
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/asio2.top
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/au.pdb
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/au.top
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/graphite.pdb
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/graphite.top
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/quartz_alpha.pdb
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/quartz_alpha.top
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/si.pdb
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/si.top
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/si3n4.inp
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/si3n4.pdb
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/si3n4.top
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/sio2.inp
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/sio2.pdb
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/sio2.top
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/irspecgui1.1/irspecgui.tcl
+lib/vmd/plugins/noarch/tcl/irspecgui1.1/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/membrane1.0/membrane.tcl
 lib/vmd/plugins/noarch/tcl/membrane1.0/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/membrane1.0/popc_box.pdb
@@ -88,59 +198,404 @@ lib/vmd/plugins/noarch/tcl/membrane1.0/popc_box.psf
 lib/vmd/plugins/noarch/tcl/membrane1.0/pope_box.pdb
 lib/vmd/plugins/noarch/tcl/membrane1.0/pope_box.psf
 lib/vmd/plugins/noarch/tcl/membrane1.0/top_all27_prot_lipid.inp
+lib/vmd/plugins/noarch/tcl/mergestructs1.0/mergestructs.tcl
+lib/vmd/plugins/noarch/tcl/mergestructs1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/ATOMTYPE_OPLS.DEF
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/CVS/Entries
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/CVS/Repository
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/CVS/Root
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/ALA.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/ARG.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/ASN.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/ASP.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/CVS/Entries
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/CVS/Repository
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/CVS/Root
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/CYS.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/GLN.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/GLU.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/GLY-end.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/GLY.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/HIS.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/HSE.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/ILE.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/LEU.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/LYS.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/MET.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/PHE.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/PRO.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/SER.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/THR.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/TRP.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/TYR.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/VAL.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/basemol/CVS/Entries
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/basemol/CVS/Repository
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/basemol/CVS/Root
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/basemol/acetone.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/basemol/ammonia.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/basemol/basefrag.mdb
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/basemol/benzene.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/basemol/benzene.pdb
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/basemol/butane.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/basemol/cyclobutane.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/basemol/cyclohexane.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/basemol/cyclopentane.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/basemol/cyclopropane.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/basemol/furan.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/basemol/isoprene.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/basemol/methane.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/basemol/naphthalene.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/basemol/thf.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/basemol/thiophene.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/basemol/water.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/convert_xbgf_to_frags.tcl
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/fragments/CVS/Entries
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/fragments/CVS/Repository
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/fragments/CVS/Root
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/fragments/amino.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/fragments/butyl.mfrag
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+lib/vmd/scripts/tk8.5/demos/textpeer.tcl
+lib/vmd/scripts/tk8.5/demos/timer
+lib/vmd/scripts/tk8.5/demos/toolbar.tcl
+lib/vmd/scripts/tk8.5/demos/tree.tcl
+lib/vmd/scripts/tk8.5/demos/ttkbut.tcl
+lib/vmd/scripts/tk8.5/demos/ttkmenu.tcl
+lib/vmd/scripts/tk8.5/demos/ttknote.tcl
+lib/vmd/scripts/tk8.5/demos/ttkpane.tcl
+lib/vmd/scripts/tk8.5/demos/ttkprogress.tcl
+lib/vmd/scripts/tk8.5/demos/twind.tcl
+lib/vmd/scripts/tk8.5/demos/unicodeout.tcl
+lib/vmd/scripts/tk8.5/demos/vscale.tcl
+lib/vmd/scripts/tk8.5/demos/widget
+lib/vmd/scripts/tk8.5/dialog.tcl
+lib/vmd/scripts/tk8.5/entry.tcl
+lib/vmd/scripts/tk8.5/focus.tcl
+lib/vmd/scripts/tk8.5/images/README
+lib/vmd/scripts/tk8.5/images/logo.eps
+lib/vmd/scripts/tk8.5/images/logo100.gif
+lib/vmd/scripts/tk8.5/images/logo64.gif
+lib/vmd/scripts/tk8.5/images/logoLarge.gif
+lib/vmd/scripts/tk8.5/images/logoMed.gif
+lib/vmd/scripts/tk8.5/images/pwrdLogo.eps
+lib/vmd/scripts/tk8.5/images/pwrdLogo100.gif
+lib/vmd/scripts/tk8.5/images/pwrdLogo150.gif
+lib/vmd/scripts/tk8.5/images/pwrdLogo175.gif
+lib/vmd/scripts/tk8.5/images/pwrdLogo200.gif
+lib/vmd/scripts/tk8.5/images/pwrdLogo75.gif
+lib/vmd/scripts/tk8.5/images/tai-ku.gif
+lib/vmd/scripts/tk8.5/listbox.tcl
+lib/vmd/scripts/tk8.5/menu.tcl
+lib/vmd/scripts/tk8.5/mkpsenc.tcl
+lib/vmd/scripts/tk8.5/msgbox.tcl
+lib/vmd/scripts/tk8.5/msgs/cs.msg
+lib/vmd/scripts/tk8.5/msgs/da.msg
+lib/vmd/scripts/tk8.5/msgs/de.msg
+lib/vmd/scripts/tk8.5/msgs/el.msg
+lib/vmd/scripts/tk8.5/msgs/en.msg
+lib/vmd/scripts/tk8.5/msgs/en_gb.msg
+lib/vmd/scripts/tk8.5/msgs/eo.msg
+lib/vmd/scripts/tk8.5/msgs/es.msg
+lib/vmd/scripts/tk8.5/msgs/fr.msg
+lib/vmd/scripts/tk8.5/msgs/hu.msg
+lib/vmd/scripts/tk8.5/msgs/it.msg
+lib/vmd/scripts/tk8.5/msgs/nl.msg
+lib/vmd/scripts/tk8.5/msgs/pl.msg
+lib/vmd/scripts/tk8.5/msgs/pt.msg
+lib/vmd/scripts/tk8.5/msgs/ru.msg
+lib/vmd/scripts/tk8.5/msgs/sv.msg
+lib/vmd/scripts/tk8.5/obsolete.tcl
+lib/vmd/scripts/tk8.5/optMenu.tcl
+lib/vmd/scripts/tk8.5/palette.tcl
+lib/vmd/scripts/tk8.5/panedwindow.tcl
+lib/vmd/scripts/tk8.5/prolog.ps
+lib/vmd/scripts/tk8.5/safetk.tcl
+lib/vmd/scripts/tk8.5/scale.tcl
+lib/vmd/scripts/tk8.5/scrlbar.tcl
+lib/vmd/scripts/tk8.5/spinbox.tcl
+lib/vmd/scripts/tk8.5/tclIndex
+lib/vmd/scripts/tk8.5/tearoff.tcl
+lib/vmd/scripts/tk8.5/text.tcl
+lib/vmd/scripts/tk8.5/tk.tcl
+lib/vmd/scripts/tk8.5/tkAppInit.c
+lib/vmd/scripts/tk8.5/tkfbox.tcl
+lib/vmd/scripts/tk8.5/ttk/altTheme.tcl
+lib/vmd/scripts/tk8.5/ttk/aquaTheme.tcl
+lib/vmd/scripts/tk8.5/ttk/button.tcl
+lib/vmd/scripts/tk8.5/ttk/clamTheme.tcl
+lib/vmd/scripts/tk8.5/ttk/classicTheme.tcl
+lib/vmd/scripts/tk8.5/ttk/combobox.tcl
+lib/vmd/scripts/tk8.5/ttk/cursors.tcl
+lib/vmd/scripts/tk8.5/ttk/defaults.tcl
+lib/vmd/scripts/tk8.5/ttk/entry.tcl
+lib/vmd/scripts/tk8.5/ttk/fonts.tcl
+lib/vmd/scripts/tk8.5/ttk/menubutton.tcl
+lib/vmd/scripts/tk8.5/ttk/notebook.tcl
+lib/vmd/scripts/tk8.5/ttk/panedwindow.tcl
+lib/vmd/scripts/tk8.5/ttk/progress.tcl
+lib/vmd/scripts/tk8.5/ttk/scale.tcl
+lib/vmd/scripts/tk8.5/ttk/scrollbar.tcl
+lib/vmd/scripts/tk8.5/ttk/sizegrip.tcl
+lib/vmd/scripts/tk8.5/ttk/treeview.tcl
+lib/vmd/scripts/tk8.5/ttk/ttk.tcl
+lib/vmd/scripts/tk8.5/ttk/utils.tcl
+lib/vmd/scripts/tk8.5/ttk/winTheme.tcl
+lib/vmd/scripts/tk8.5/ttk/xpTheme.tcl
+lib/vmd/scripts/tk8.5/unsupported.tcl
+lib/vmd/scripts/tk8.5/xmfbox.tcl
 lib/vmd/scripts/vmd/CVS/Entries
 lib/vmd/scripts/vmd/CVS/Repository
 lib/vmd/scripts/vmd/CVS/Root
 lib/vmd/scripts/vmd/README.chemical2vmd
 lib/vmd/scripts/vmd/atomselect.tcl
-lib/vmd/scripts/vmd/atomselmacros.tcl
+lib/vmd/scripts/vmd/atomselmacros.dat
 lib/vmd/scripts/vmd/biocore.tcl
 lib/vmd/scripts/vmd/chemical2vmd
 lib/vmd/scripts/vmd/colordefs.dat
 lib/vmd/scripts/vmd/draw.tcl
 lib/vmd/scripts/vmd/graphlabels.tcl
 lib/vmd/scripts/vmd/hotkeys.tcl
+lib/vmd/scripts/vmd/loadplugins.tcl
 lib/vmd/scripts/vmd/logfile.tcl
+lib/vmd/scripts/vmd/materials.dat
 lib/vmd/scripts/vmd/openURL.tcl
 lib/vmd/scripts/vmd/restypes.dat
 lib/vmd/scripts/vmd/save_state.tcl
@@ -404,57 +1032,142 @@ lib/vmd/stride_%%VMD_ARCH%%
 lib/vmd/surf_%%VMD_ARCH%%
 lib/vmd/tachyon_%%VMD_ARCH%%
 lib/vmd/vmd_%%VMD_ARCH%%
-@dirrm lib/vmd/shaders/CVS
-@dirrm lib/vmd/shaders
-@dirrm lib/vmd/scripts/vmd/CVS
-@dirrm lib/vmd/scripts/vmd
-@dirrm lib/vmd/scripts/tk8.4/msgs
-@dirrm lib/vmd/scripts/tk8.4/images
-@dirrm lib/vmd/scripts/tk8.4/demos/images
-@dirrm lib/vmd/scripts/tk8.4/demos
-@dirrm lib/vmd/scripts/tk8.4
-@dirrm lib/vmd/scripts/tcl8.4/tcltest2.2
-@dirrm lib/vmd/scripts/tcl8.4/opt0.4
-@dirrm lib/vmd/scripts/tcl8.4/msgcat1.3
-@dirrm lib/vmd/scripts/tcl8.4/http2.4
-@dirrm lib/vmd/scripts/tcl8.4/http1.0
-@dirrm lib/vmd/scripts/tcl8.4/encoding
-@dirrm lib/vmd/scripts/tcl8.4
-@dirrm lib/vmd/scripts/python
-@dirrm lib/vmd/scripts/CVS
-@dirrm lib/vmd/scripts
-@dirrm lib/vmd/plugins/noarch/tcl/zoomseq1.0
-@dirrm lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/CVS
-@dirrm lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs
-@dirrm lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/CVS
-@dirrm lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3
-@dirrm lib/vmd/plugins/noarch/tcl/vmdtkcon1.0
-@dirrm lib/vmd/plugins/noarch/tcl/vmdmovie1.2
-@dirrm lib/vmd/plugins/noarch/tcl/viewmaster2.1
-@dirrm lib/vmd/plugins/noarch/tcl/timeline1.0
-@dirrm lib/vmd/plugins/noarch/tcl/solvate1.2
-@dirrm lib/vmd/plugins/noarch/tcl/rmsd1.0
-@dirrm lib/vmd/plugins/noarch/tcl/ramaplot1.0
-@dirrm lib/vmd/plugins/noarch/tcl/pdbtool1.0
-@dirrm lib/vmd/plugins/noarch/tcl/navigate1.0
-@dirrm lib/vmd/plugins/noarch/tcl/membrane1.0
-@dirrm lib/vmd/plugins/noarch/tcl/imdmenu1.0
-@dirrm lib/vmd/plugins/noarch/tcl/exectool1.0
-@dirrm lib/vmd/plugins/noarch/tcl/contactmap1.1
+lib/vmd/vmd_completion.dat
+
+@dirrm lib/vmd/doc
+@dirrm lib/vmd/plugins/%%VMD_ARCH%%/molfile
+@dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl/hesstrans1.0
+@dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl
+@dirrm lib/vmd/plugins/%%VMD_ARCH%%
+@dirrm lib/vmd/plugins/LINUX/tcl/intersurf1.1/bin
+@dirrm lib/vmd/plugins/LINUX/tcl/intersurf1.1
+@dirrm lib/vmd/plugins/LINUX/tcl
+@dirrm lib/vmd/plugins/LINUX
+@dirrm lib/vmd/plugins/WIN32/tcl/intersurf1.1/bin
+@dirrm lib/vmd/plugins/WIN32/tcl/intersurf1.1
+@dirrm lib/vmd/plugins/WIN32/tcl
+@dirrm lib/vmd/plugins/WIN32
+@dirrm lib/vmd/plugins/include
+@dirrm lib/vmd/plugins/noarch/tcl/apbsrun1.3
+@dirrm lib/vmd/plugins/noarch/tcl/atomedit1.0
+@dirrm lib/vmd/plugins/noarch/tcl/autoimd1.6
+@dirrm lib/vmd/plugins/noarch/tcl/autoionize1.2
+@dirrm lib/vmd/plugins/noarch/tcl/bignum1.0
+@dirrm lib/vmd/plugins/noarch/tcl/biocore1.1
+@dirrm lib/vmd/plugins/noarch/tcl/blast1.1
+@dirrm lib/vmd/plugins/noarch/tcl/cgtools1.0
 @dirrm lib/vmd/plugins/noarch/tcl/cliptool1.0
-@dirrm lib/vmd/plugins/noarch/tcl/autoionize1.1
-@dirrm lib/vmd/plugins/noarch/tcl/autoimd1.4
-@dirrm lib/vmd/plugins/noarch/tcl/apbsrun1.0
+@dirrm lib/vmd/plugins/noarch/tcl/clonerep1.1
+@dirrm lib/vmd/plugins/noarch/tcl/colorscalebar1.2
+@dirrm lib/vmd/plugins/noarch/tcl/contactmap1.1
+@dirrm lib/vmd/plugins/noarch/tcl/dataimport1.0
+@dirrm lib/vmd/plugins/noarch/tcl/demomaster1.0
+@dirrm lib/vmd/plugins/noarch/tcl/dipwatch1.2
+@dirrm lib/vmd/plugins/noarch/tcl/dowser1.0
+@dirrm lib/vmd/plugins/noarch/tcl/exectool1.2
+@dirrm lib/vmd/plugins/noarch/tcl/extendedpdb1.0
+@dirrm lib/vmd/plugins/noarch/tcl/gofrgui1.1
+@dirrm lib/vmd/plugins/noarch/tcl/hbonds1.1
+@dirrm lib/vmd/plugins/noarch/tcl/idatm0.1
+@dirrm lib/vmd/plugins/noarch/tcl/ilstools1.2
+@dirrm lib/vmd/plugins/noarch/tcl/imdmenu1.0
+@dirrm lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/CVS
+@dirrm lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials
+@dirrm lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1
+@dirrm lib/vmd/plugins/noarch/tcl/irspecgui1.1
+@dirrm lib/vmd/plugins/noarch/tcl/membrane1.0
+@dirrm lib/vmd/plugins/noarch/tcl/mergestructs1.0
+@dirrm lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/CVS
+@dirrm lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids/CVS
+@dirrm lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/amino_acids
+@dirrm lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/basemol/CVS
+@dirrm lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/basemol
+@dirrm lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/fragments/CVS
+@dirrm lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/fragments
+@dirrm lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/nucleic_acids/CVS
+@dirrm lib/vmd/plugins/noarch/tcl/molefacture1.1/lib/nucleic_acids
+@dirrm lib/vmd/plugins/noarch/tcl/molefacture1.1/lib
+@dirrm lib/vmd/plugins/noarch/tcl/molefacture1.1
+@dirrm lib/vmd/plugins/noarch/tcl/moltoptools0.1
+@dirrm lib/vmd/plugins/noarch/tcl/multimolanim1.0
+@dirrm lib/vmd/plugins/noarch/tcl/multiplot1.4
+@dirrm lib/vmd/plugins/noarch/tcl/multiseq2.1
+@dirrm lib/vmd/plugins/noarch/tcl/multiseqdialog1.1
+@dirrm lib/vmd/plugins/noarch/tcl/multitext1.0
+@dirrm lib/vmd/plugins/noarch/tcl/namdenergy1.2
+@dirrm lib/vmd/plugins/noarch/tcl/namdgui1.2
+@dirrm lib/vmd/plugins/noarch/tcl/namdplot1.0
+@dirrm lib/vmd/plugins/noarch/tcl/namdserver1.1
+@dirrm lib/vmd/plugins/noarch/tcl/nanotube1.0
+@dirrm lib/vmd/plugins/noarch/tcl/navfly1.0
+@dirrm lib/vmd/plugins/noarch/tcl/navigate1.0
+@dirrm lib/vmd/plugins/noarch/tcl/optimization1.0
+@dirrm lib/vmd/plugins/noarch/tcl/palettetool1.0
+@dirrm lib/vmd/plugins/noarch/tcl/paratool1.4
+@dirrm lib/vmd/plugins/noarch/tcl/pbctools2.5
+@dirrm lib/vmd/plugins/noarch/tcl/pdbtool1.0
+@dirrm lib/vmd/plugins/noarch/tcl/phylotree1.1
+@dirrm lib/vmd/plugins/noarch/tcl/psipred1.1
+@dirrm lib/vmd/plugins/noarch/tcl/qmtool1.1
+@dirrm lib/vmd/plugins/noarch/tcl/ramaplot1.1
+@dirrm lib/vmd/plugins/noarch/tcl/readcharmmpar1.1
+@dirrm lib/vmd/plugins/noarch/tcl/readcharmmtop1.0
+@dirrm lib/vmd/plugins/noarch/tcl/resptool1.1
+@dirrm lib/vmd/plugins/noarch/tcl/rmsd1.0
+@dirrm lib/vmd/plugins/noarch/tcl/rmsdtt2.0
+@dirrm lib/vmd/plugins/noarch/tcl/rnaview1.0
+@dirrm lib/vmd/plugins/noarch/tcl/ruler1.0
+@dirrm lib/vmd/plugins/noarch/tcl/runante0.1
+@dirrm lib/vmd/plugins/noarch/tcl/saltbr1.0
+@dirrm lib/vmd/plugins/noarch/tcl/seqdata1.1
+@dirrm lib/vmd/plugins/noarch/tcl/seqedit1.1/blosum
+@dirrm lib/vmd/plugins/noarch/tcl/seqedit1.1
+@dirrm lib/vmd/plugins/noarch/tcl/solvate1.3
+@dirrm lib/vmd/plugins/noarch/tcl/ssrestraints1.0
+@dirrm lib/vmd/plugins/noarch/tcl/stingtool1.0
+@dirrm lib/vmd/plugins/noarch/tcl/symmetrytool1.2
+@dirrm lib/vmd/plugins/noarch/tcl/timeline2.0
+@dirrm lib/vmd/plugins/noarch/tcl/topotools1.0
+@dirrm lib/vmd/plugins/noarch/tcl/trunctraj1.5/toppar/non_charmm
+@dirrm lib/vmd/plugins/noarch/tcl/trunctraj1.5/toppar/stream
+@dirrm lib/vmd/plugins/noarch/tcl/trunctraj1.5/toppar
+@dirrm lib/vmd/plugins/noarch/tcl/trunctraj1.5
+@dirrm lib/vmd/plugins/noarch/tcl/utilities1.0
+@dirrm lib/vmd/plugins/noarch/tcl/vdna2.0
+@dirrm lib/vmd/plugins/noarch/tcl/viewmaster2.2
+@dirrm lib/vmd/plugins/noarch/tcl/vmdmovie1.7
+@dirrm lib/vmd/plugins/noarch/tcl/vmdtkcon1.1/tkcon-2.3/CVS
+@dirrm lib/vmd/plugins/noarch/tcl/vmdtkcon1.1/tkcon-2.3/docs/CVS
+@dirrm lib/vmd/plugins/noarch/tcl/vmdtkcon1.1/tkcon-2.3/docs
+@dirrm lib/vmd/plugins/noarch/tcl/vmdtkcon1.1/tkcon-2.3
+@dirrm lib/vmd/plugins/noarch/tcl/vmdtkcon1.1
+@dirrm lib/vmd/plugins/noarch/tcl/volmapgui1.1
+@dirrm lib/vmd/plugins/noarch/tcl/zoomseq1.1
 @dirrm lib/vmd/plugins/noarch/tcl
 @dirrm lib/vmd/plugins/noarch
-@dirrm lib/vmd/plugins/include
-@dirrm lib/vmd/plugins/%%VMD_ARCH%%/bin/catdcd4.0
-@dirrm lib/vmd/plugins/%%VMD_ARCH%%/bin
-@dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen1.3
-@dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl/pmepot1.0
-@dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl
-@dirrm lib/vmd/plugins/%%VMD_ARCH%%/molfile
-@dirrm lib/vmd/plugins/%%VMD_ARCH%%
 @dirrm lib/vmd/plugins
-@dirrm lib/vmd/doc
+@dirrm lib/vmd/scripts/CVS
+@dirrm lib/vmd/scripts/python
+@dirrm lib/vmd/scripts/tcl8.5/encoding
+@dirrm lib/vmd/scripts/tcl8.5/http1.0
+@dirrm lib/vmd/scripts/tcl8.5/msgs
+@dirrm lib/vmd/scripts/tcl8.5/opt0.4
+@exec mkdir -p %D/lib/vmd/scripts/tcl8/8.3
+@dirrm lib/vmd/scripts/tcl8/8.3
+@dirrm lib/vmd/scripts/tcl8/8.4/platform
+@dirrm lib/vmd/scripts/tcl8/8.4
+@dirrm lib/vmd/scripts/tcl8/8.5
+@dirrm lib/vmd/scripts/tcl8
+@dirrm lib/vmd/scripts/tcl8.5
+@dirrm lib/vmd/scripts/tk8.5/demos/images
+@dirrm lib/vmd/scripts/tk8.5/demos
+@dirrm lib/vmd/scripts/tk8.5/images
+@dirrm lib/vmd/scripts/tk8.5/msgs
+@dirrm lib/vmd/scripts/tk8.5/ttk
+@dirrm lib/vmd/scripts/tk8.5
+@dirrm lib/vmd/scripts/vmd/CVS
+@dirrm lib/vmd/scripts/vmd
+@dirrm lib/vmd/scripts
+@dirrm lib/vmd/shaders/CVS
+@dirrm lib/vmd/shaders
 @dirrm lib/vmd