1 files changed, 273 insertions, 232 deletions

diff --git a/science/vmd/pkg-plist b/science/vmd/pkg-plist
index 6018c05ac527..b78504ff706c 100644
--- a/science/vmd/pkg-plist
+++ b/science/vmd/pkg-plist
@@ -1,40 +1,164 @@
 bin/vmd
-lib/vmd/doc/ug.pdf
 lib/vmd/Announcement
-lib/vmd/README
 lib/vmd/LICENSE
-lib/vmd/vmd_%%VMD_ARCH%%
-lib/vmd/surf_%%VMD_ARCH%%
-lib/vmd/stride_%%VMD_ARCH%%
-lib/vmd/tachyon_%%VMD_ARCH%%
-lib/vmd/scripts/CVS/Root
-lib/vmd/scripts/CVS/Repository
+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/binposplugin.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
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/corplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/cpmdplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/crdplugin.so
+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/dxplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/edmplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/fs4plugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/gamessplugin.so
+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/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/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/namdbinplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/parm7plugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/parmplugin.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
+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/stlplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/tinkerplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/webpdbplugin.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/include/molfile_plugin.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/cliptool1.0/cliptool.tcl
+lib/vmd/plugins/noarch/tcl/cliptool1.0/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/imdmenu1.0/imdmenu.tcl
+lib/vmd/plugins/noarch/tcl/imdmenu1.0/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
+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/navigate1.0/navigate.tcl
+lib/vmd/plugins/noarch/tcl/navigate1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/pdbtool1.0/pdbtool.tcl
+lib/vmd/plugins/noarch/tcl/pdbtool1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/ramaplot1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/ramaplot1.0/ramaplot.tcl
+lib/vmd/plugins/noarch/tcl/rmsd1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/rmsd1.0/rmsd.tcl
+lib/vmd/plugins/noarch/tcl/solvate1.2/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/solvate1.2/solvate.tcl
+lib/vmd/plugins/noarch/tcl/solvate1.2/wat.pdb
+lib/vmd/plugins/noarch/tcl/solvate1.2/wat.psf
+lib/vmd/plugins/noarch/tcl/solvate1.2/wat.top
+lib/vmd/plugins/noarch/tcl/timeline1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/timeline1.0/timeline.tcl
+lib/vmd/plugins/noarch/tcl/viewmaster2.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/viewmaster2.1/viewmaster.tcl
+lib/vmd/plugins/noarch/tcl/vmdmovie1.2/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/vmdmovie1.2/vmdmovie.tcl
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/README
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/CVS/Entries
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/CVS/Repository
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/CVS/Root
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/ChangeLog
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/README.txt
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/CVS/Entries
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/CVS/Repository
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/CVS/Root
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/bindings.html
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/changes.txt
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/demopic.gif
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/dump.html
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/idebug.html
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/index.html
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/license.terms
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/limits.html
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/nontcl.html
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/observe.html
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/perl.txt
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/plugin.html
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/procs.html
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/purpose.html
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/start.html
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/style.css
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/tkcon.html
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/todo.html
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/index.html
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/tkcon.tcl
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-modified.tcl
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/vmdtkcon.tcl
+lib/vmd/plugins/noarch/tcl/zoomseq1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/zoomseq1.0/zoomseq.tcl
 lib/vmd/scripts/CVS/Entries
-lib/vmd/scripts/vmd/CVS/Root
-lib/vmd/scripts/vmd/CVS/Repository
-lib/vmd/scripts/vmd/CVS/Entries
-lib/vmd/scripts/vmd/README.chemical2vmd
-lib/vmd/scripts/vmd/save_state.tcl
-lib/vmd/scripts/vmd/atomselect.tcl
-lib/vmd/scripts/vmd/tclIndex
-lib/vmd/scripts/vmd/chemical2vmd
-lib/vmd/scripts/vmd/draw.tcl
-lib/vmd/scripts/vmd/vmdinit.tcl
-lib/vmd/scripts/vmd/vectors.tcl
-lib/vmd/scripts/vmd/graphlabels.tcl
-lib/vmd/scripts/vmd/hotkeys.tcl
-lib/vmd/scripts/vmd/openURL.tcl
-lib/vmd/scripts/vmd/atomselmacros.tcl
-lib/vmd/scripts/vmd/biocore.tcl
-lib/vmd/scripts/vmd/logfile.tcl
-lib/vmd/scripts/vmd/www.tcl
+lib/vmd/scripts/CVS/Repository
+lib/vmd/scripts/CVS/Root
 lib/vmd/scripts/README
-lib/vmd/scripts/tcl8.4/http2.4/http.tcl
-lib/vmd/scripts/tcl8.4/http2.4/pkgIndex.tcl
-lib/vmd/scripts/tcl8.4/http1.0/http.tcl
-lib/vmd/scripts/tcl8.4/http1.0/pkgIndex.tcl
-lib/vmd/scripts/tcl8.4/opt0.4/optparse.tcl
-lib/vmd/scripts/tcl8.4/opt0.4/pkgIndex.tcl
+lib/vmd/scripts/python/AtomSel.py
+lib/vmd/scripts/python/Label.py
+lib/vmd/scripts/python/Material.py
+lib/vmd/scripts/python/Molecule.py
+lib/vmd/scripts/python/Tkinter.py
+lib/vmd/scripts/python/VMD.py
+lib/vmd/scripts/python/startvmd.py
+lib/vmd/scripts/python/testMolecule.py
+lib/vmd/scripts/python/testdisplay.py
+lib/vmd/scripts/tcl
+lib/vmd/scripts/tcl8.0
+lib/vmd/scripts/tk
+lib/vmd/scripts/tk8.0
+lib/vmd/scripts/tcl8.4/auto.tcl
 lib/vmd/scripts/tcl8.4/encoding/ascii.enc
 lib/vmd/scripts/tcl8.4/encoding/big5.enc
 lib/vmd/scripts/tcl8.4/encoding/cp1250.enc
@@ -82,7 +206,6 @@ lib/vmd/scripts/tcl8.4/encoding/iso8859-10.enc
 lib/vmd/scripts/tcl8.4/encoding/iso8859-13.enc
 lib/vmd/scripts/tcl8.4/encoding/iso8859-14.enc
 lib/vmd/scripts/tcl8.4/encoding/iso8859-15.enc
-lib/vmd/scripts/tcl8.4/encoding/jis0201.enc
 lib/vmd/scripts/tcl8.4/encoding/iso8859-16.enc
 lib/vmd/scripts/tcl8.4/encoding/iso8859-2.enc
 lib/vmd/scripts/tcl8.4/encoding/iso8859-3.enc
@@ -92,6 +215,7 @@ lib/vmd/scripts/tcl8.4/encoding/iso8859-6.enc
 lib/vmd/scripts/tcl8.4/encoding/iso8859-7.enc
 lib/vmd/scripts/tcl8.4/encoding/iso8859-8.enc
 lib/vmd/scripts/tcl8.4/encoding/iso8859-9.enc
+lib/vmd/scripts/tcl8.4/encoding/jis0201.enc
 lib/vmd/scripts/tcl8.4/encoding/jis0208.enc
 lib/vmd/scripts/tcl8.4/encoding/jis0212.enc
 lib/vmd/scripts/tcl8.4/encoding/koi8-r.enc
@@ -112,85 +236,32 @@ lib/vmd/scripts/tcl8.4/encoding/macUkraine.enc
 lib/vmd/scripts/tcl8.4/encoding/shiftjis.enc
 lib/vmd/scripts/tcl8.4/encoding/symbol.enc
 lib/vmd/scripts/tcl8.4/encoding/tis-620.enc
-lib/vmd/scripts/tcl8.4/msgcat1.3/msgcat.tcl
-lib/vmd/scripts/tcl8.4/msgcat1.3/pkgIndex.tcl
-lib/vmd/scripts/tcl8.4/tcltest2.2/pkgIndex.tcl
-lib/vmd/scripts/tcl8.4/tcltest2.2/tcltest.tcl
-lib/vmd/scripts/tcl8.4/auto.tcl
 lib/vmd/scripts/tcl8.4/history.tcl
+lib/vmd/scripts/tcl8.4/http1.0/http.tcl
+lib/vmd/scripts/tcl8.4/http1.0/pkgIndex.tcl
+lib/vmd/scripts/tcl8.4/http2.4/http.tcl
+lib/vmd/scripts/tcl8.4/http2.4/pkgIndex.tcl
 lib/vmd/scripts/tcl8.4/init.tcl
+lib/vmd/scripts/tcl8.4/ldAix
 lib/vmd/scripts/tcl8.4/ldAout.tcl
+lib/vmd/scripts/tcl8.4/msgcat1.3/msgcat.tcl
+lib/vmd/scripts/tcl8.4/msgcat1.3/pkgIndex.tcl
+lib/vmd/scripts/tcl8.4/opt0.4/optparse.tcl
+lib/vmd/scripts/tcl8.4/opt0.4/pkgIndex.tcl
 lib/vmd/scripts/tcl8.4/package.tcl
 lib/vmd/scripts/tcl8.4/parray.tcl
 lib/vmd/scripts/tcl8.4/safe.tcl
-lib/vmd/scripts/tcl8.4/word.tcl
-lib/vmd/scripts/tcl8.4/tclIndex
 lib/vmd/scripts/tcl8.4/tclAppInit.c
-lib/vmd/scripts/tcl8.4/ldAix
-lib/vmd/scripts/tk8.4/images/README
-lib/vmd/scripts/tk8.4/images/logo.eps
-lib/vmd/scripts/tk8.4/images/logo100.gif
-lib/vmd/scripts/tk8.4/images/logo64.gif
-lib/vmd/scripts/tk8.4/images/logoLarge.gif
-lib/vmd/scripts/tk8.4/images/logoMed.gif
-lib/vmd/scripts/tk8.4/images/pwrdLogo.eps
-lib/vmd/scripts/tk8.4/images/pwrdLogo100.gif
-lib/vmd/scripts/tk8.4/images/pwrdLogo150.gif
-lib/vmd/scripts/tk8.4/images/pwrdLogo175.gif
-lib/vmd/scripts/tk8.4/images/pwrdLogo200.gif
-lib/vmd/scripts/tk8.4/images/pwrdLogo75.gif
-lib/vmd/scripts/tk8.4/images/tai-ku.gif
-lib/vmd/scripts/tk8.4/msgs/cs.msg
-lib/vmd/scripts/tk8.4/msgs/de.msg
-lib/vmd/scripts/tk8.4/msgs/el.msg
-lib/vmd/scripts/tk8.4/msgs/en.msg
-lib/vmd/scripts/tk8.4/msgs/en_gb.msg
-lib/vmd/scripts/tk8.4/msgs/es.msg
-lib/vmd/scripts/tk8.4/msgs/fr.msg
-lib/vmd/scripts/tk8.4/msgs/it.msg
-lib/vmd/scripts/tk8.4/msgs/nl.msg
-lib/vmd/scripts/tk8.4/msgs/ru.msg
+lib/vmd/scripts/tcl8.4/tclIndex
+lib/vmd/scripts/tcl8.4/tcltest2.2/pkgIndex.tcl
+lib/vmd/scripts/tcl8.4/tcltest2.2/tcltest.tcl
+lib/vmd/scripts/tcl8.4/word.tcl
 lib/vmd/scripts/tk8.4/bgerror.tcl
 lib/vmd/scripts/tk8.4/button.tcl
 lib/vmd/scripts/tk8.4/choosedir.tcl
 lib/vmd/scripts/tk8.4/clrpick.tcl
 lib/vmd/scripts/tk8.4/comdlg.tcl
 lib/vmd/scripts/tk8.4/console.tcl
-lib/vmd/scripts/tk8.4/dialog.tcl
-lib/vmd/scripts/tk8.4/entry.tcl
-lib/vmd/scripts/tk8.4/focus.tcl
-lib/vmd/scripts/tk8.4/listbox.tcl
-lib/vmd/scripts/tk8.4/menu.tcl
-lib/vmd/scripts/tk8.4/mkpsenc.tcl
-lib/vmd/scripts/tk8.4/msgbox.tcl
-lib/vmd/scripts/tk8.4/obsolete.tcl
-lib/vmd/scripts/tk8.4/optMenu.tcl
-lib/vmd/scripts/tk8.4/palette.tcl
-lib/vmd/scripts/tk8.4/panedwindow.tcl
-lib/vmd/scripts/tk8.4/safetk.tcl
-lib/vmd/scripts/tk8.4/scale.tcl
-lib/vmd/scripts/tk8.4/scrlbar.tcl
-lib/vmd/scripts/tk8.4/spinbox.tcl
-lib/vmd/scripts/tk8.4/tearoff.tcl
-lib/vmd/scripts/tk8.4/text.tcl
-lib/vmd/scripts/tk8.4/tk.tcl
-lib/vmd/scripts/tk8.4/tkfbox.tcl
-lib/vmd/scripts/tk8.4/unsupported.tcl
-lib/vmd/scripts/tk8.4/xmfbox.tcl
-lib/vmd/scripts/tk8.4/prolog.ps
-lib/vmd/scripts/tk8.4/tclIndex
-lib/vmd/scripts/tk8.4/tkAppInit.c
-lib/vmd/scripts/tk8.4/demos/images/earth.gif
-lib/vmd/scripts/tk8.4/demos/images/earthris.gif
-lib/vmd/scripts/tk8.4/demos/images/face.bmp
-lib/vmd/scripts/tk8.4/demos/images/flagdown.bmp
-lib/vmd/scripts/tk8.4/demos/images/flagup.bmp
-lib/vmd/scripts/tk8.4/demos/images/gray25.bmp
-lib/vmd/scripts/tk8.4/demos/images/letters.bmp
-lib/vmd/scripts/tk8.4/demos/images/noletter.bmp
-lib/vmd/scripts/tk8.4/demos/images/pattern.bmp
-lib/vmd/scripts/tk8.4/demos/images/tcllogo.gif
-lib/vmd/scripts/tk8.4/demos/images/teapot.ppm
 lib/vmd/scripts/tk8.4/demos/README
 lib/vmd/scripts/tk8.4/demos/arrow.tcl
 lib/vmd/scripts/tk8.4/demos/bind.tcl
@@ -215,6 +286,17 @@ lib/vmd/scripts/tk8.4/demos/hscale.tcl
 lib/vmd/scripts/tk8.4/demos/icon.tcl
 lib/vmd/scripts/tk8.4/demos/image1.tcl
 lib/vmd/scripts/tk8.4/demos/image2.tcl
+lib/vmd/scripts/tk8.4/demos/images/earth.gif
+lib/vmd/scripts/tk8.4/demos/images/earthris.gif
+lib/vmd/scripts/tk8.4/demos/images/face.bmp
+lib/vmd/scripts/tk8.4/demos/images/flagdown.bmp
+lib/vmd/scripts/tk8.4/demos/images/flagup.bmp
+lib/vmd/scripts/tk8.4/demos/images/gray25.bmp
+lib/vmd/scripts/tk8.4/demos/images/letters.bmp
+lib/vmd/scripts/tk8.4/demos/images/noletter.bmp
+lib/vmd/scripts/tk8.4/demos/images/pattern.bmp
+lib/vmd/scripts/tk8.4/demos/images/tcllogo.gif
+lib/vmd/scripts/tk8.4/demos/images/teapot.ppm
 lib/vmd/scripts/tk8.4/demos/items.tcl
 lib/vmd/scripts/tk8.4/demos/ixset
 lib/vmd/scripts/tk8.4/demos/label.tcl
@@ -244,132 +326,86 @@ lib/vmd/scripts/tk8.4/demos/timer
 lib/vmd/scripts/tk8.4/demos/twind.tcl
 lib/vmd/scripts/tk8.4/demos/vscale.tcl
 lib/vmd/scripts/tk8.4/demos/widget
-lib/vmd/scripts/python/AtomSel.py
-lib/vmd/scripts/python/Label.py
-lib/vmd/scripts/python/Material.py
-lib/vmd/scripts/python/Molecule.py
-lib/vmd/scripts/python/VMD.py
-lib/vmd/scripts/python/startvmd.py
-lib/vmd/scripts/python/testMolecule.py
-lib/vmd/scripts/python/testdisplay.py
-lib/vmd/plugins/include/vmdplugin.h
-lib/vmd/plugins/include/molfile_plugin.h
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/cpmdplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/psfplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/pdbplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/dcdplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/babelplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/gromacsplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/parmplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/crdplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/namdbinplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/binposplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/webpdbplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/graspplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/stlplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/cubeplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/edmplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/ccp4plugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/dsn6plugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/brixplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/pltplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/parm7plugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/raster3dplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/rst7plugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/xyzplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/corplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/moldenplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/phiplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/grdplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/dxplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/mapplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/avsplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/fs4plugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/libmolfile_plugin.a
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/libmolfile_plugin.h
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen1.3/libpsfgen.so
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen1.3/ug.pdf
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen1.3/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/autoionize1.0/ions.top
-lib/vmd/plugins/noarch/tcl/autoionize1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/autoionize1.0/autoionize.tcl
-lib/vmd/plugins/noarch/tcl/solvate1.2/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/solvate1.2/solvate.tcl
-lib/vmd/plugins/noarch/tcl/solvate1.2/wat.psf
-lib/vmd/plugins/noarch/tcl/solvate1.2/wat.pdb
-lib/vmd/plugins/noarch/tcl/solvate1.2/wat.top
-lib/vmd/plugins/noarch/tcl/autoimd1.3/ug.pdf
-lib/vmd/plugins/noarch/tcl/autoimd1.3/template.namd
-lib/vmd/plugins/noarch/tcl/autoimd1.3/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/autoimd1.3/autoimd-local.tcl
-lib/vmd/plugins/noarch/tcl/autoimd1.3/autoimd.tcl
-lib/vmd/plugins/noarch/tcl/namdrun0.1/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/namdrun0.1/namdrun.tcl
-lib/vmd/plugins/noarch/tcl/jmvexport1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/jmvexport1.0/jmvexport.tcl
-lib/vmd/plugins/noarch/tcl/vmdmovie1.1/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/vmdmovie1.1/vmdmovie.tcl
-lib/vmd/plugins/noarch/tcl/aligntool1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/aligntool1.0/cealign.tcl
-lib/vmd/plugins/noarch/tcl/aligntool1.0/aligntool.tcl
-lib/vmd/plugins/noarch/tcl/contactmap1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/contactmap1.0/contactmap.tcl
-lib/vmd/plugins/noarch/tcl/timeline1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/timeline1.0/timeline.tcl
-lib/vmd/plugins/noarch/tcl/ramaplot1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/ramaplot1.0/ramaplot.tcl
-lib/vmd/plugins/noarch/tcl/rmsd1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/rmsd1.0/rmsd.tcl
-lib/vmd/plugins/noarch/tcl/membrane1.0/popc_box.psf
-lib/vmd/plugins/noarch/tcl/membrane1.0/pope_box.psf
-lib/vmd/plugins/noarch/tcl/membrane1.0/pope_box.pdb
-lib/vmd/plugins/noarch/tcl/membrane1.0/top_all27_prot_lipid.inp
-lib/vmd/plugins/noarch/tcl/membrane1.0/popc_box.pdb
-lib/vmd/plugins/noarch/tcl/membrane1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/membrane1.0/membrane.tcl
-lib/vmd/plugins/noarch/tcl/zoomseq1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/zoomseq1.0/zoomseq.tcl
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/CVS/Root
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/CVS/Repository
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/CVS/Entries
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/bindings.html
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/changes.txt
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/demopic.gif
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/dump.html
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/idebug.html
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/index.html
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/license.terms
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/limits.html
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/style.css
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/observe.html
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/perl.txt
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/plugin.html
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/procs.html
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/purpose.html
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/start.html
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/tkcon.html
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/todo.html
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/nontcl.html
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/CVS/Root
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/CVS/Repository
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/CVS/Entries
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/ChangeLog
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/README.txt
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/index.html
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/tkcon.tcl
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-modified.tcl
-lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/vmdtkcon.tcl
-lib/vmd/plugins/noarch/tcl/imdmenu1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/imdmenu1.0/imdmenu.tcl
-lib/vmd/plugins/noarch/tcl/pdbtool1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/pdbtool1.0/pdbtool.tcl
-lib/vmd/.vmdsensors
-lib/vmd/.vmdrc
-lib/vmd/scripts/tcl
-lib/vmd/scripts/tcl8.0
-lib/vmd/scripts/tk
-lib/vmd/scripts/tk8.0
+lib/vmd/scripts/tk8.4/dialog.tcl
+lib/vmd/scripts/tk8.4/entry.tcl
+lib/vmd/scripts/tk8.4/focus.tcl
+lib/vmd/scripts/tk8.4/images/README
+lib/vmd/scripts/tk8.4/images/logo.eps
+lib/vmd/scripts/tk8.4/images/logo100.gif
+lib/vmd/scripts/tk8.4/images/logo64.gif
+lib/vmd/scripts/tk8.4/images/logoLarge.gif
+lib/vmd/scripts/tk8.4/images/logoMed.gif
+lib/vmd/scripts/tk8.4/images/pwrdLogo.eps
+lib/vmd/scripts/tk8.4/images/pwrdLogo100.gif
+lib/vmd/scripts/tk8.4/images/pwrdLogo150.gif
+lib/vmd/scripts/tk8.4/images/pwrdLogo175.gif
+lib/vmd/scripts/tk8.4/images/pwrdLogo200.gif
+lib/vmd/scripts/tk8.4/images/pwrdLogo75.gif
+lib/vmd/scripts/tk8.4/images/tai-ku.gif
+lib/vmd/scripts/tk8.4/listbox.tcl
+lib/vmd/scripts/tk8.4/menu.tcl
+lib/vmd/scripts/tk8.4/mkpsenc.tcl
+lib/vmd/scripts/tk8.4/msgbox.tcl
+lib/vmd/scripts/tk8.4/msgs/cs.msg
+lib/vmd/scripts/tk8.4/msgs/de.msg
+lib/vmd/scripts/tk8.4/msgs/el.msg
+lib/vmd/scripts/tk8.4/msgs/en.msg
+lib/vmd/scripts/tk8.4/msgs/en_gb.msg
+lib/vmd/scripts/tk8.4/msgs/es.msg
+lib/vmd/scripts/tk8.4/msgs/fr.msg
+lib/vmd/scripts/tk8.4/msgs/it.msg
+lib/vmd/scripts/tk8.4/msgs/nl.msg
+lib/vmd/scripts/tk8.4/msgs/ru.msg
+lib/vmd/scripts/tk8.4/obsolete.tcl
+lib/vmd/scripts/tk8.4/optMenu.tcl
+lib/vmd/scripts/tk8.4/palette.tcl
+lib/vmd/scripts/tk8.4/panedwindow.tcl
+lib/vmd/scripts/tk8.4/prolog.ps
+lib/vmd/scripts/tk8.4/safetk.tcl
+lib/vmd/scripts/tk8.4/scale.tcl
+lib/vmd/scripts/tk8.4/scrlbar.tcl
+lib/vmd/scripts/tk8.4/spinbox.tcl
+lib/vmd/scripts/tk8.4/tclIndex
+lib/vmd/scripts/tk8.4/tearoff.tcl
+lib/vmd/scripts/tk8.4/text.tcl
+lib/vmd/scripts/tk8.4/tk.tcl
+lib/vmd/scripts/tk8.4/tkAppInit.c
+lib/vmd/scripts/tk8.4/tkfbox.tcl
+lib/vmd/scripts/tk8.4/unsupported.tcl
+lib/vmd/scripts/tk8.4/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/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/logfile.tcl
+lib/vmd/scripts/vmd/openURL.tcl
+lib/vmd/scripts/vmd/restypes.dat
+lib/vmd/scripts/vmd/save_state.tcl
+lib/vmd/scripts/vmd/tclIndex
+lib/vmd/scripts/vmd/vectors.tcl
+lib/vmd/scripts/vmd/vmdinit.tcl
+lib/vmd/scripts/vmd/www.tcl
+lib/vmd/shaders/CVS/Entries
+lib/vmd/shaders/CVS/Repository
+lib/vmd/shaders/CVS/Root
+lib/vmd/shaders/vmd.frag
+lib/vmd/shaders/vmd.vert
+lib/vmd/shaders/vmdsphere.frag
+lib/vmd/shaders/vmdsphere.vert
+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
@@ -393,24 +429,29 @@ lib/vmd/scripts/tk8.0
 @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/vmdmovie1.1
+@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/namdrun0.1
+@dirrm lib/vmd/plugins/noarch/tcl/navigate1.0
 @dirrm lib/vmd/plugins/noarch/tcl/membrane1.0
-@dirrm lib/vmd/plugins/noarch/tcl/jmvexport1.0
 @dirrm lib/vmd/plugins/noarch/tcl/imdmenu1.0
-@dirrm lib/vmd/plugins/noarch/tcl/contactmap1.0
-@dirrm lib/vmd/plugins/noarch/tcl/autoionize1.0
-@dirrm lib/vmd/plugins/noarch/tcl/autoimd1.3
-@dirrm lib/vmd/plugins/noarch/tcl/aligntool1.0
+@dirrm lib/vmd/plugins/noarch/tcl/exectool1.0
+@dirrm lib/vmd/plugins/noarch/tcl/contactmap1.1
+@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
 @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%%