reverted vmd-1.8.7-config.patch

(Portage version: 2.2_rc67/cvs/Linux x86_64)

2 files changed, 15 insertions, 965 deletions

diff --git a/sci-chemistry/vmd/files/vmd-1.8.7-config.patch b/sci-chemistry/vmd/files/vmd-1.8.7-config.patch
index 57d1bd9f6376..7850e9f32b6b 100644
--- a/sci-chemistry/vmd/files/vmd-1.8.7-config.patch
+++ b/sci-chemistry/vmd/files/vmd-1.8.7-config.patch
@@ -1,923 +1,6 @@
-diff --git a/plugins/Makefile b/plugins/Makefile
-index e2e5e5e..f2eabaf 100755
---- a/plugins/Makefile
-+++ b/plugins/Makefile
-@@ -4,7 +4,6 @@
- ## Theoretical and Computational Biophysics Group
- ##
- 
--.SILENT:
- 
- default: make-arch-help
- 
-diff --git a/plugins/Makefile.newmultiseq b/plugins/Makefile.newmultiseq
-index c271b44..d00522c 100644
---- a/plugins/Makefile.newmultiseq
-+++ b/plugins/Makefile.newmultiseq
-@@ -4,7 +4,6 @@
- ## Theoretical and Computational Biophysics Group
- ##
- 
--.SILENT:
- 
- default: make-arch-help
- 
-diff --git a/plugins/Makefile.orig b/plugins/Makefile.orig
-index e6406fd..6208576 100644
---- a/plugins/Makefile.orig
-+++ b/plugins/Makefile.orig
-@@ -4,7 +4,6 @@
- ## Theoretical and Computational Biophysics Group
- ##
- 
--.SILENT:
- 
- default: make-arch-help
- 
-diff --git a/plugins/Makefile.rej b/plugins/Makefile.rej
-index 1b6ea67..d13aca1 100644
---- a/plugins/Makefile.rej
-+++ b/plugins/Makefile.rej
-@@ -3,7 +3,6 @@
-   # Makefile for molecule file readers
-   # $Id: vmd-1.8.7-config.patch,v 1.3 2010/05/18 07:22:51 jlec Exp $
-   
--- .SILENT:
-   
-   .SUFFIXES:
-   
-@@ -17,7 +16,6 @@
-   # Makefile for molecule file readers
-   # $Id: vmd-1.8.7-config.patch,v 1.3 2010/05/18 07:22:51 jlec Exp $
-   
--+ .SILENT:
-   
-   .SUFFIXES:
-   
-diff --git a/plugins/aligntool/Makefile b/plugins/aligntool/Makefile
-index 8155a6d..e4df74c 100644
---- a/plugins/aligntool/Makefile
-+++ b/plugins/aligntool/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = aligntool.tcl cealign.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/apbsrun/Makefile b/plugins/apbsrun/Makefile
-index aca0b4e..b86ee59 100644
---- a/plugins/apbsrun/Makefile
-+++ b/plugins/apbsrun/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = apbsrun.tcl pkgIndex.tcl radii.dat
- VMVERSION = 1.3
-diff --git a/plugins/atomedit/Makefile b/plugins/atomedit/Makefile
-index 558606c..05d7f90 100644
---- a/plugins/atomedit/Makefile
-+++ b/plugins/atomedit/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = atomedit.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/autoimd/Makefile b/plugins/autoimd/Makefile
-index 9d432e4..7f0a802 100644
---- a/plugins/autoimd/Makefile
-+++ b/plugins/autoimd/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- AUTOIMDFILES = autoimd.tcl autoimd-settings.tcl autoimd-api.tcl autoimd-gui.tcl pkgIndex.tcl autoimd-template.namd doc/ug.pdf namdrun.tcl
- AUTOIMDVERSION = 1.6
-diff --git a/plugins/autoionize/Makefile b/plugins/autoionize/Makefile
-index c74ad01..b392d3f 100644
---- a/plugins/autoionize/Makefile
-+++ b/plugins/autoionize/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = autoionize.tcl autoionizegui.tcl pkgIndex.tcl ions.top
- VMVERSION = 1.2
-diff --git a/plugins/bignum/Makefile b/plugins/bignum/Makefile
-index 9c90f17..c35322d 100644
---- a/plugins/bignum/Makefile
-+++ b/plugins/bignum/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = bignum.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/biocore/Makefile b/plugins/biocore/Makefile
-index 887b592..d2919dd 100644
---- a/plugins/biocore/Makefile
-+++ b/plugins/biocore/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = biocore.tcl biocorechat.tcl biocorelogin.tcl biocorepubsync.tcl pkgIndex.tcl locked.gif unlocked.gif biocoreHelper.tcl biocoreutil.tcl
- 
-diff --git a/plugins/catdcd/Makefile b/plugins/catdcd/Makefile
-index 7a8f0f8..ce75e33 100644
---- a/plugins/catdcd/Makefile
-+++ b/plugins/catdcd/Makefile
-@@ -1,6 +1,5 @@
- # Makefile for catdcd
- 
--.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/cgtools/Makefile b/plugins/cgtools/Makefile
-index adca18b..84bf723 100644
---- a/plugins/cgtools/Makefile
-+++ b/plugins/cgtools/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = cggui.tcl cgtools.tcl cgnetworking.tcl pkgIndex.tcl \
-           protein.cgc water.cgc rbcg-2007.par rbcg-2007.top
-diff --git a/plugins/cionize/.#Makefile.specialbuilds.1.1 b/plugins/cionize/.#Makefile.specialbuilds.1.1
-index 4672932..181ba85 100644
---- a/plugins/cionize/.#Makefile.specialbuilds.1.1
-+++ b/plugins/cionize/.#Makefile.specialbuilds.1.1
-@@ -1,6 +1,5 @@
- # Makefile for cionize
- 
--#.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/cionize/Makefile b/plugins/cionize/Makefile
-index c5fe136..f24fe29 100644
---- a/plugins/cionize/Makefile
-+++ b/plugins/cionize/Makefile
-@@ -1,6 +1,5 @@
- # Makefile for cionize
- 
--#.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/cionize/Makefile.mine b/plugins/cionize/Makefile.mine
-index 5ee841a..1588837 100644
---- a/plugins/cionize/Makefile.mine
-+++ b/plugins/cionize/Makefile.mine
-@@ -1,6 +1,5 @@
- # Makefile for cionize
- 
--#.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/cionize/Makefile.mine.old b/plugins/cionize/Makefile.mine.old
-index 48714b6..0dc4085 100644
---- a/plugins/cionize/Makefile.mine.old
-+++ b/plugins/cionize/Makefile.mine.old
-@@ -1,6 +1,5 @@
- # Makefile for cionize
- 
--#.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/cionize/Makefile.specialbuilds b/plugins/cionize/Makefile.specialbuilds
-index a529758..f85bcfe 100644
---- a/plugins/cionize/Makefile.specialbuilds
-+++ b/plugins/cionize/Makefile.specialbuilds
-@@ -1,6 +1,5 @@
- # Makefile for cionize
- 
--#.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/cionize/mcudahacks/Makefile.specialbuilds b/plugins/cionize/mcudahacks/Makefile.specialbuilds
-index e93cad2..dc7b632 100644
---- a/plugins/cionize/mcudahacks/Makefile.specialbuilds
-+++ b/plugins/cionize/mcudahacks/Makefile.specialbuilds
-@@ -1,6 +1,5 @@
- # Makefile for cionize
- 
--#.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/cliptool/Makefile b/plugins/cliptool/Makefile
-index 9c41370..679abbe 100644
---- a/plugins/cliptool/Makefile
-+++ b/plugins/cliptool/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = cliptool.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/clonerep/Makefile b/plugins/clonerep/Makefile
-index e8a4949..e101e56 100755
---- a/plugins/clonerep/Makefile
-+++ b/plugins/clonerep/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = clonerep.tcl pkgIndex.tcl
- VMVERSION = 1.1
-diff --git a/plugins/clustalw/Makefile b/plugins/clustalw/Makefile
-index 6329f64..265bb85 100644
---- a/plugins/clustalw/Makefile
-+++ b/plugins/clustalw/Makefile
-@@ -1,6 +1,5 @@
- # Makefile for clustalw
- 
--.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/cluster/Makefile b/plugins/cluster/Makefile
-index 99d347e..a083e57 100644
---- a/plugins/cluster/Makefile
-+++ b/plugins/cluster/Makefile
-@@ -1,6 +1,5 @@
- # Makefile for psfgen
- 
--.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/colorscalebar/Makefile b/plugins/colorscalebar/Makefile
-index 1413898..f58074a 100644
---- a/plugins/colorscalebar/Makefile
-+++ b/plugins/colorscalebar/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = colorscalebar.tcl pkgIndex.tcl
- VMVERSION = 1.2
-diff --git a/plugins/contactmap/Makefile b/plugins/contactmap/Makefile
-index 36f6b18..3336e41 100644
---- a/plugins/contactmap/Makefile
-+++ b/plugins/contactmap/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = contactmap.tcl pkgIndex.tcl
- VMVERSION = 1.1
-diff --git a/plugins/dataimport/Makefile b/plugins/dataimport/Makefile
-index e63ebca..71b59fb 100644
---- a/plugins/dataimport/Makefile
-+++ b/plugins/dataimport/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = dataimport.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/demomaster/Makefile b/plugins/demomaster/Makefile
-index 6264d76..27a3d20 100644
---- a/plugins/demomaster/Makefile
-+++ b/plugins/demomaster/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = demomaster.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/dipwatch/Makefile b/plugins/dipwatch/Makefile
-index 7d36042..4af35c7 100755
---- a/plugins/dipwatch/Makefile
-+++ b/plugins/dipwatch/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = dipwatch.tcl pkgIndex.tcl
- VMVERSION = 1.2
-diff --git a/plugins/doc/Makefile b/plugins/doc/Makefile
-index ed1ce9d..07ff534 100644
---- a/plugins/doc/Makefile
-+++ b/plugins/doc/Makefile
-@@ -1,7 +1,6 @@
- #
- # Plugin documentation Makefile
- #
--.SILENT:
- 
- ECHO            = echo
- DELETEDIR       = rm -rf
-diff --git a/plugins/dowser/Makefile b/plugins/dowser/Makefile
-index 1795db3..d00cacc 100644
---- a/plugins/dowser/Makefile
-+++ b/plugins/dowser/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = dowser.tcl dowser_gui.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/exectool/Makefile b/plugins/exectool/Makefile
-index afa024d..6ba1889 100644
---- a/plugins/exectool/Makefile
-+++ b/plugins/exectool/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = exectool.tcl jobmanager.tcl pkgIndex.tcl
- VMVERSION = 1.2
-diff --git a/plugins/extendedpdb/Makefile b/plugins/extendedpdb/Makefile
-index 9061aa1..5a5fb8f 100644
---- a/plugins/extendedpdb/Makefile
-+++ b/plugins/extendedpdb/Makefile
-@@ -1,4 +1,3 @@
--#.SILENT:
- 
- VMFILES = extendedpdb.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/fmtool/Makefile b/plugins/fmtool/Makefile
-index 76a9e69..a3f320d 100644
---- a/plugins/fmtool/Makefile
-+++ b/plugins/fmtool/Makefile
-@@ -1,6 +1,5 @@
- # Makefile for fmtool
- 
--.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/gofrgui/Makefile b/plugins/gofrgui/Makefile
-index e192f02..7251884 100644
---- a/plugins/gofrgui/Makefile
-+++ b/plugins/gofrgui/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = gofrgui.tcl pkgIndex.tcl
- VMVERSION = 1.1
-diff --git a/plugins/hbonds/Makefile b/plugins/hbonds/Makefile
-index 6bee92d..45f1fe3 100644
---- a/plugins/hbonds/Makefile
-+++ b/plugins/hbonds/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = hbonds.tcl pkgIndex.tcl
- VMVERSION = 1.1
-diff --git a/plugins/idatm/Makefile b/plugins/idatm/Makefile
-index e23ca1c..4280b6a 100644
---- a/plugins/idatm/Makefile
-+++ b/plugins/idatm/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = idatm.tcl pkgIndex.tcl
- VMVERSION = 0.1
-diff --git a/plugins/ilstools/Makefile b/plugins/ilstools/Makefile
-index e145c30..7cc9d1b 100644
---- a/plugins/ilstools/Makefile
-+++ b/plugins/ilstools/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- COPYFILES = ilstools.tcl pkgIndex.tcl oxygen.xyz nitricoxide.xyz \
-             carbonmonoxide.xyz carbondioxide.xyz ethene.xyz methane.xyz \
-diff --git a/plugins/imdmenu/Makefile b/plugins/imdmenu/Makefile
-index dca0e25..277f386 100644
---- a/plugins/imdmenu/Makefile
-+++ b/plugins/imdmenu/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- IMDMENUFILES = imdmenu.tcl pkgIndex.tcl
- IMDMENUVERSION = 1.0
-diff --git a/plugins/inorganicbuilder/Makefile b/plugins/inorganicbuilder/Makefile
-index 8e0439a..4af2b0f 100755
---- a/plugins/inorganicbuilder/Makefile
-+++ b/plugins/inorganicbuilder/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = inorganicbuilder.tcl pkgIndex.tcl
- VMVERSION = 0.1
-diff --git a/plugins/irspecgui/Makefile b/plugins/irspecgui/Makefile
-index 754ebc8..e86b09a 100755
---- a/plugins/irspecgui/Makefile
-+++ b/plugins/irspecgui/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = irspecgui.tcl pkgIndex.tcl
- VMVERSION = 1.1
-diff --git a/plugins/jmvexport/Makefile b/plugins/jmvexport/Makefile
-index 7f45260..9eb996b 100644
---- a/plugins/jmvexport/Makefile
-+++ b/plugins/jmvexport/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = jmvexport.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/libbiokit/Makefile b/plugins/libbiokit/Makefile
-index 7a66d08..ba709a7 100644
---- a/plugins/libbiokit/Makefile
-+++ b/plugins/libbiokit/Makefile
-@@ -1,6 +1,5 @@
- # Makefile for libbiokit
- 
--.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/membrane/Makefile b/plugins/membrane/Makefile
-index f92c426..38a9c06 100644
---- a/plugins/membrane/Makefile
-+++ b/plugins/membrane/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = membrane.tcl pkgIndex.tcl \
- 	popc_box.pdb popc_box.psf \
-diff --git a/plugins/mergestructs/Makefile b/plugins/mergestructs/Makefile
-index d6a4225..66ba9b2 100644
---- a/plugins/mergestructs/Makefile
-+++ b/plugins/mergestructs/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = mergestructs.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/molefacture/Makefile b/plugins/molefacture/Makefile
-index 96e70dc..8d10ef4 100644
---- a/plugins/molefacture/Makefile
-+++ b/plugins/molefacture/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = molefacture.tcl molefacture_builder.tcl \
- 	molefacture_edit.tcl molefacture_geometry.tcl molefacture_gui.tcl \
-diff --git a/plugins/molfile_plugin/Makefile b/plugins/molfile_plugin/Makefile
-index 18fb6dc..f17bdda 100644
---- a/plugins/molfile_plugin/Makefile
-+++ b/plugins/molfile_plugin/Makefile
-@@ -1,7 +1,6 @@
- # Makefile for molecule file readers
- # $Id: vmd-1.8.7-config.patch,v 1.3 2010/05/18 07:22:51 jlec Exp $
- 
--.SILENT:
- 
- .SUFFIXES:
- 
-diff --git a/plugins/molfile_plugin/src/cifplugin/Makefile b/plugins/molfile_plugin/src/cifplugin/Makefile
-index 1dfa768..88f4b7b 100644
---- a/plugins/molfile_plugin/src/cifplugin/Makefile
-+++ b/plugins/molfile_plugin/src/cifplugin/Makefile
-@@ -1,6 +1,5 @@
- # Makefile for molecule file readers
- 
--.SILENT:
- 
- .SUFFIXES:
- 
-diff --git a/plugins/moltoptools/Makefile b/plugins/moltoptools/Makefile
-index 3599cb7..8d80ec2 100644
---- a/plugins/moltoptools/Makefile
-+++ b/plugins/moltoptools/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = moltoptools.tcl pkgIndex.tcl
- VMVERSION = 0.1
-diff --git a/plugins/multimolanim/Makefile b/plugins/multimolanim/Makefile
-index 09b4cb1..39b3139 100755
---- a/plugins/multimolanim/Makefile
-+++ b/plugins/multimolanim/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = multimolanim.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/multiplot/Makefile b/plugins/multiplot/Makefile
-index 520bf3e..a5b7bc5 100644
---- a/plugins/multiplot/Makefile
-+++ b/plugins/multiplot/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = multiplot.tcl pkgIndex.tcl
- VMVERSION = 1.4
-diff --git a/plugins/multitext/Makefile b/plugins/multitext/Makefile
-index cc98bde..453c0da 100644
---- a/plugins/multitext/Makefile
-+++ b/plugins/multitext/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = multitext.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/namdenergy/Makefile b/plugins/namdenergy/Makefile
-index 9d4c11c..229f6cc 100644
---- a/plugins/namdenergy/Makefile
-+++ b/plugins/namdenergy/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = namdenergy.tcl pkgIndex.tcl
- VMVERSION = 1.2
-diff --git a/plugins/namdgui/Makefile b/plugins/namdgui/Makefile
-index 2e25b19..c03d87b 100644
---- a/plugins/namdgui/Makefile
-+++ b/plugins/namdgui/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = namdgui.tcl namdgui_tclforces.tcl pkgIndex.tcl
- VMVERSION = 1.2
-diff --git a/plugins/namdplot/Makefile b/plugins/namdplot/Makefile
-index e155387..88969e6 100644
---- a/plugins/namdplot/Makefile
-+++ b/plugins/namdplot/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = namdplot.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/namdserver/Makefile b/plugins/namdserver/Makefile
-index 378d203..84dcb24 100644
---- a/plugins/namdserver/Makefile
-+++ b/plugins/namdserver/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = namdserver.tcl pkgIndex.tcl
- VMVERSION = 1.1
-diff --git a/plugins/nanotube/Makefile b/plugins/nanotube/Makefile
-index 6662cd5..deaf55c 100644
---- a/plugins/nanotube/Makefile
-+++ b/plugins/nanotube/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = nanotube.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/navfly/Makefile b/plugins/navfly/Makefile
-index 82d913b..0194be8 100644
---- a/plugins/navfly/Makefile
-+++ b/plugins/navfly/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = navfly.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/navigate/Makefile b/plugins/navigate/Makefile
-index 6d48c3e..cf18738 100644
---- a/plugins/navigate/Makefile
-+++ b/plugins/navigate/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- COPYFILES = navigate.tcl pkgIndex.tcl
- DIR = $(PLUGINDIR)/noarch/tcl/navigate1.0
-diff --git a/plugins/nlenergy/Makefile b/plugins/nlenergy/Makefile
-index 8c028ca..3c295fd 100644
---- a/plugins/nlenergy/Makefile
-+++ b/plugins/nlenergy/Makefile
-@@ -1,6 +1,5 @@
- # Makefile for nlenergy
- 
--.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/optimization/Makefile b/plugins/optimization/Makefile
-index e38a9dc..4188e7f 100644
---- a/plugins/optimization/Makefile
-+++ b/plugins/optimization/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = optimization.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/palettetool/Makefile b/plugins/palettetool/Makefile
-index 6317657..166d423 100644
---- a/plugins/palettetool/Makefile
-+++ b/plugins/palettetool/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = palettetool.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/paratool/Makefile b/plugins/paratool/Makefile
-index 8f24cc1..cbf1618 100644
---- a/plugins/paratool/Makefile
-+++ b/plugins/paratool/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = paratool.tcl paratool_atomedit.tcl paratool_aux.tcl \
-           paratool_respcharges.tcl paratool_charmmcharges.tcl \
-diff --git a/plugins/pbctools/Makefile b/plugins/pbctools/Makefile
-index 164c456..bcf6851 100755
---- a/plugins/pbctools/Makefile
-+++ b/plugins/pbctools/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = pbcbox.tcl pbcgui.tcl pbcjoin.tcl pbcset.tcl pbctools.tcl \
- 	pbcunwrap.tcl pbcwrap.tcl pkgIndex.tcl
-diff --git a/plugins/pdbtool/Makefile b/plugins/pdbtool/Makefile
-index c05579d..3f120c5 100644
---- a/plugins/pdbtool/Makefile
-+++ b/plugins/pdbtool/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = pdbtool.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/pmepot/Makefile b/plugins/pmepot/Makefile
-index 1858d13..fa6ac36 100644
---- a/plugins/pmepot/Makefile
-+++ b/plugins/pmepot/Makefile
-@@ -1,6 +1,5 @@
- # Makefile for PME potential library
- 
--.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/psfgen/Makefile b/plugins/psfgen/Makefile
-index d9c7c85..0d9b80e 100644
---- a/plugins/psfgen/Makefile
-+++ b/plugins/psfgen/Makefile
-@@ -1,6 +1,5 @@
- # Makefile for psfgen
- 
--.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/psfgen/Makefile.pluginio b/plugins/psfgen/Makefile.pluginio
-index 29444f2..28a6213 100644
---- a/plugins/psfgen/Makefile.pluginio
-+++ b/plugins/psfgen/Makefile.pluginio
-@@ -5,7 +5,6 @@
- #     them itself, but at the moment this is a good short-term development
- #     path until we write something better.
- 
--.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/qmtool/Makefile b/plugins/qmtool/Makefile
-index a8aafff..2a45307 100644
---- a/plugins/qmtool/Makefile
-+++ b/plugins/qmtool/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = qmtool.tcl qmtool_analysis.tcl qmtool_atomedit.tcl \
-           qmtool_aux.tcl qmtool_charges.tcl qmtool_intcoor.tcl \
-diff --git a/plugins/ramaplot/Makefile b/plugins/ramaplot/Makefile
-index 29a1f23..be6e86a 100644
---- a/plugins/ramaplot/Makefile
-+++ b/plugins/ramaplot/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- FILES = ramaplot.tcl pkgIndex.tcl
- VERSION = 1.1
-diff --git a/plugins/readcharmmpar/Makefile b/plugins/readcharmmpar/Makefile
-index fffb98e..d257edd 100644
---- a/plugins/readcharmmpar/Makefile
-+++ b/plugins/readcharmmpar/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = readcharmmpar.tcl par_all27_prot_lipid_na.inp pkgIndex.tcl par_amber2charmm.inp
- VMVERSION = 1.1
-diff --git a/plugins/readcharmmtop/Makefile b/plugins/readcharmmtop/Makefile
-index 88c7ab5..c8cb771 100644
---- a/plugins/readcharmmtop/Makefile
-+++ b/plugins/readcharmmtop/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = readcharmmtop.tcl pkgIndex.tcl top_all27_prot_lipid_na.inp top_all27_hybrid.inp top_amber2charmm.inp
- VMVERSION = 1.0
-diff --git a/plugins/resptool/Makefile b/plugins/resptool/Makefile
-index 1f20b70..80e01eb 100644
---- a/plugins/resptool/Makefile
-+++ b/plugins/resptool/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = resptool.tcl pkgIndex.tcl
- VMVERSION = 1.1
-diff --git a/plugins/rmsd/Makefile b/plugins/rmsd/Makefile
-index 23df59b..c328322 100644
---- a/plugins/rmsd/Makefile
-+++ b/plugins/rmsd/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = rmsd.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/rmsdtt/Makefile b/plugins/rmsdtt/Makefile
-index c914531..62b14fd 100644
---- a/plugins/rmsdtt/Makefile
-+++ b/plugins/rmsdtt/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = rmsdtt.tcl pkgIndex.tcl
- VMVERSION = 2.0
-diff --git a/plugins/rnaview/Makefile b/plugins/rnaview/Makefile
-index f020ca0..9ab6914 100644
---- a/plugins/rnaview/Makefile
-+++ b/plugins/rnaview/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = rnaview.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/ruler/Makefile b/plugins/ruler/Makefile
-index 146cc4c..a7864d1 100644
---- a/plugins/ruler/Makefile
-+++ b/plugins/ruler/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = ruler.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/runante/Makefile b/plugins/runante/Makefile
-index 0410d50..a8fbe81 100644
---- a/plugins/runante/Makefile
-+++ b/plugins/runante/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = runante.tcl pkgIndex.tcl
- VMVERSION = 0.1
-diff --git a/plugins/saltbr/Makefile b/plugins/saltbr/Makefile
-index 7e4234a..f5358e2 100644
---- a/plugins/saltbr/Makefile
-+++ b/plugins/saltbr/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = saltbr.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/solvate/Makefile b/plugins/solvate/Makefile
-index b1c5d92..7dfcd9b 100644
---- a/plugins/solvate/Makefile
-+++ b/plugins/solvate/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- SOLVFILES = wat.top wat.pdb wat.psf solvate.tcl pkgIndex.tcl
- SOLVVERSION = 1.3
-diff --git a/plugins/ssrestraints/Makefile b/plugins/ssrestraints/Makefile
-index 81b79d8..dca38e7 100644
---- a/plugins/ssrestraints/Makefile
-+++ b/plugins/ssrestraints/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = ssrestraints.tcl ssrestraints_stride.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/stamp/Makefile b/plugins/stamp/Makefile
-index f0fb515..715be81 100644
---- a/plugins/stamp/Makefile
-+++ b/plugins/stamp/Makefile
-@@ -1,6 +1,5 @@
- # Makefile for stamp
- 
--.SILENT:
- 
- .SUFFIXES: 
- 
-diff --git a/plugins/stingtool/Makefile b/plugins/stingtool/Makefile
-index d7b84fe..477a97c 100644
---- a/plugins/stingtool/Makefile
-+++ b/plugins/stingtool/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = stingtool.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/symmetrytool/Makefile b/plugins/symmetrytool/Makefile
-index 43adc25..6898a43 100644
---- a/plugins/symmetrytool/Makefile
-+++ b/plugins/symmetrytool/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = symmetry.tcl pkgIndex.tcl
- VMVERSION = 1.2
-diff --git a/plugins/textview/Makefile b/plugins/textview/Makefile
-index 5e35a4a..ba98391 100644
---- a/plugins/textview/Makefile
-+++ b/plugins/textview/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = textview.tcl pkgIndex.tcl
- VMVERSION = 1.1
-diff --git a/plugins/timeline/Makefile b/plugins/timeline/Makefile
-index 3b9e7ac..a09c572 100644
---- a/plugins/timeline/Makefile
-+++ b/plugins/timeline/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = timeline.tcl pkgIndex.tcl
- VMVERSION = 2.0
-diff --git a/plugins/topotools/Makefile b/plugins/topotools/Makefile
-index a8af827..beb4b54 100644
---- a/plugins/topotools/Makefile
-+++ b/plugins/topotools/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = pkgIndex.tcl README topotools.tcl topoatoms.tcl \
- 	topobonds.tcl topoangles.tcl topodihedrals.tcl topoimpropers.tcl \
-diff --git a/plugins/trunctraj/Makefile b/plugins/trunctraj/Makefile
-index 624b3e6..991b4e1 100644
---- a/plugins/trunctraj/Makefile
-+++ b/plugins/trunctraj/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = trunctraj.tcl pkgIndex.tcl
- VMVERSION = 1.5
-diff --git a/plugins/updater/Makefile b/plugins/updater/Makefile
-index 4e29538..3122421 100644
---- a/plugins/updater/Makefile
-+++ b/plugins/updater/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = updater.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/utilities/Makefile b/plugins/utilities/Makefile
-index df1ccf4..c18c048 100644
---- a/plugins/utilities/Makefile
-+++ b/plugins/utilities/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = utilities.tcl pkgIndex.tcl
- VMVERSION = 1.0
-diff --git a/plugins/vdna/Makefile b/plugins/vdna/Makefile
-index f994198..dd2d57b 100644
---- a/plugins/vdna/Makefile
-+++ b/plugins/vdna/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = vdna.tcl pkgIndex.tcl
- VMVERSION = 2.0
-diff --git a/plugins/viewmaster/Makefile b/plugins/viewmaster/Makefile
-index c5d1625..8d25c7e 100644
---- a/plugins/viewmaster/Makefile
-+++ b/plugins/viewmaster/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = viewmaster.tcl pkgIndex.tcl
- VMVERSION = 2.2
-diff --git a/plugins/vmdmovie/Makefile b/plugins/vmdmovie/Makefile
-index 10af8e2..cacc294 100644
---- a/plugins/vmdmovie/Makefile
-+++ b/plugins/vmdmovie/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = vmdmovie.tcl pkgIndex.tcl
- VMVERSION = 1.7
-diff --git a/plugins/vmdtkcon/Makefile b/plugins/vmdtkcon/Makefile
-index 5f6a05d..04de94f 100644
---- a/plugins/vmdtkcon/Makefile
-+++ b/plugins/vmdtkcon/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- TKCONFILES = vmdtkcon.tcl tkcon-modified.tcl pkgIndex.tcl tkcon-2.3 README
- DIR = $(PLUGINDIR)/noarch/tcl/vmdtkcon1.1
-diff --git a/plugins/volmapgui/Makefile b/plugins/volmapgui/Makefile
-index 9ece112..57ec111 100644
---- a/plugins/volmapgui/Makefile
-+++ b/plugins/volmapgui/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- COPYFILES = volmapgui.tcl pkgIndex.tcl
- DIR = $(PLUGINDIR)/noarch/tcl/volmapgui1.1
-diff --git a/plugins/zoomseq/Makefile b/plugins/zoomseq/Makefile
-index aa95b41..66ee516 100644
---- a/plugins/zoomseq/Makefile
-+++ b/plugins/zoomseq/Makefile
-@@ -1,4 +1,3 @@
--.SILENT:
- 
- VMFILES = zoomseq.tcl pkgIndex.tcl
- VMVERSION = 1.1
-diff --git a/vmd-1.8.7/configure b/vmd-1.8.7/configure
-index f01944a..051e04a 100755
---- a/vmd-1.8.7/configure
-+++ b/vmd-1.8.7/configure
+diff -Naur vmd-1.8.7/configure vmd-1.8.7.new/configure
+--- vmd-1.8.7/configure	2009-08-01 03:19:34.000000000 -0400
++++ vmd-1.8.7.new/configure	2009-08-07 09:12:43.000000000 -0400
 @@ -13,10 +13,10 @@
  $install_name = "vmd";
  
@@ -931,7 +14,7 @@ index f01944a..051e04a 100755
  
  
  # optionally override hard-coded defaults above with environment variables
-@@ -128,29 +128,6 @@ if ($ENV{VMDINSTALLLIBRARYDIR}) {
+@@ -128,29 +128,6 @@
  # Configure script code begins here
  ############################################################################
  
@@ -961,7 +44,7 @@ index f01944a..051e04a 100755
  #################### Parse command line options   ###########
  # list of allowed architectures
  @archlist=('IRIX6', 'IRIX6_64', 'FREEBSD', 'HPUX11', 'AIX4', 'AIX5', 'AIX5_64', 'AIX6_64', 'LINUX', 'LINUXALPHA', 'LINUXAMD64', 'LINUXIA64', 'LINUXPPC', 'LINUXPPC64', 'MACOSX', 'MACOSXX86', 'MACOSXX86_64', 'TRU64', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'SOLARISX86_64', 'WIN32', 'WIN64');
-@@ -435,7 +412,7 @@ chop($arch_no_math_float);
+@@ -435,7 +412,7 @@
  
  ################ Plugin options
  #
@@ -970,7 +53,7 @@ index f01944a..051e04a 100755
  $plugin_include = "-I$plugin_dir/include";
  $plugin_library = "";
  $plugin_libs    = "";
-@@ -448,7 +425,7 @@ $plugin_defines = "";
+@@ -448,7 +425,7 @@
  @plugin_extra   = ();
  
  if ($config_staticplugin) {
@@ -979,7 +62,7 @@ index f01944a..051e04a 100755
    $plugin_include .= " -I$molfile_dir";
    $plugin_library .= " -L$molfile_dir";
    $plugin_libs    .= " -lmolfile_plugin";
-@@ -550,8 +527,8 @@ $fltkopengl_defines     = "-DVMDOPENGL -DVMDFLTKOPENGL -DVMDGRAPHICS";
+@@ -550,8 +527,8 @@
  ################ FLTK GUI
  $fltk_defines     = "-DVMDGUI -DVMDFLTK";
  $fltk_dir         = "$vmd_library_dir/fltk";
@@ -990,7 +73,7 @@ index f01944a..051e04a 100755
  $fltk_libs        = "-lfltk -lX11";
  #@fltk_cc          = ('forms_ui.c');
  @fltk_cu          = ();
-@@ -612,8 +589,8 @@ $tcl_include      = "-I$stock_tcl_include_dir";
+@@ -612,8 +589,8 @@
  if ($config_tk) { $tcl_include .= " -I$stock_tk_include_dir"; }
  $tcl_library      = "-L$stock_tcl_library_dir";
  if ($config_tk) { $tcl_library .= " -L$stock_tk_library_dir"; }
@@ -1001,7 +84,7 @@ index f01944a..051e04a 100755
  
  @tcl_cc           = ();
  @tcl_cu           = ();
-@@ -938,8 +915,8 @@ $cuda_libs        = "-Wl,-rpath -Wl,\$\$ORIGIN/ -lcudart";
+@@ -938,8 +915,8 @@
  #######################
  $netcdf_defines     = "";
  $netcdf_dir         = "$vmd_library_dir/netcdf";
@@ -1012,7 +95,7 @@ index f01944a..051e04a 100755
  $netcdf_libs        = "-lnetcdf";
  @netcdf_cc          = ();
  @netcdf_cu          = ();
-@@ -1007,9 +984,9 @@ $pthreads_libs     = "-lpthread";
+@@ -1007,9 +984,9 @@
  $python_defines     = "-DVMDPYTHON";
  $python_dir         = "$vmd_library_dir/python";
  $numpy_dir          = "$vmd_library_dir/numpy";
@@ -1025,7 +108,7 @@ index f01944a..051e04a 100755
  @python_h           = ('PythonTextInterp.h',
                         'VMDTkinterMenu.h',
  		       'py_commands.h',
-@@ -1621,8 +1598,8 @@ if ($config_arch eq "LINUX") {
+@@ -1621,8 +1598,8 @@
  
      # XFree 4.0 Direct Rendering Interface and GLX 
      $opengl_dir         = "/usr/X11R6";
@@ -1036,7 +119,7 @@ index f01944a..051e04a 100755
      $opengl_libs        = "-lGL -lGLU"; 
      # $opengl_libs      = "-L/usr/X11R6/lib -lGL -lGLU -lXext -lX11";
  
-@@ -1650,15 +1627,15 @@ if ($config_arch eq "LINUX") {
+@@ -1650,15 +1627,15 @@
        $arch_lopts       .= "-i-static ";
      } else {
        # compling with GCC
@@ -1049,44 +132,11 @@ index f01944a..051e04a 100755
 +      $arch_shld        = "gentoo-g++ -shared";
        $arch_shlibname   = "so";
        $arch_shcppopts   = "-fPIC";
--      $arch_shldopts    = "";
+       $arch_shldopts    = "";
 -      $arch_opt_flag    = "-m32 -fno-for-scope -Wno-deprecated -Wall -O3";
 -      $arch_copts       = "-m32 -Wall -O3";
-+      $arch_shldopts    = "gentoo-ldflags";
 +      $arch_opt_flag    = "gentoo-cflags";
 +      $arch_copts       = "gentoo-cflags";
  
        if ($config_static) {
          $arch_lopts       = "-static";
-@@ -1768,7 +1745,7 @@ if ($config_arch eq "LINUXAMD64") {
-       $arch_template_repository = "foobar";
-       $arch_shlibname   = "so";
-       $arch_shcppopts   = "-fPIC";
--      $arch_shldopts    = "";
-+      $arch_shldopts    = "gentoo-ldflags";
- 
-       if ($config_static) {
-         # link everything statically (this won't work due to libGL issues)
-@@ -2804,8 +2781,7 @@ install:
- 	-\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "$install_library_dir"
- 	\$(CD) $vmd_bin_dir ; \\
- 	if [ -f run_vmd_tmp ]; then \$(DELETE) run_vmd_tmp; fi ; \\
--	if [ ! -x "/bin/csh" ]; then \\
--		\$(ECHO) "Info: /bin/csh shell not found, installing Bourne shell startup script instead" ; \\
-+	if [ -x "/bin/bash" ]; then \\
- 		\$(ECHO) '#!/bin/sh' >> run_vmd_tmp ; \\
- 		\$(ECHO) 'defaultvmddir="$install_library_dir"' >> run_vmd_tmp ; \\
- 		\$(ECHO) 'vmdbasename=vmd' >> run_vmd_tmp ; \\
-diff --git a/vmd-1.8.7/src/Makefile b/vmd-1.8.7/src/Makefile
-index 971a8c1..fe4c635 100755
---- a/vmd-1.8.7/src/Makefile
-+++ b/vmd-1.8.7/src/Makefile
-@@ -432,7 +432,7 @@ vmd_WIN32: y.tab.h $(VMD_OBJS)
- 	if [ ! -r ./ ]; then \
- 	  ln -s ../src/ ./ ; \
- 	fi; \
--	$(CCPP) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ; 
-+	$(CCPP) $(LDFLAGS) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ; 
- 	$(COMPILERC) $(RCFLAGS)
- 
- install:
diff --git a/sci-chemistry/vmd/vmd-1.8.7-r1.ebuild b/sci-chemistry/vmd/vmd-1.8.7-r1.ebuild
index 0d228694d500..8a1e54c4ea5d 100644
--- a/sci-chemistry/vmd/vmd-1.8.7-r1.ebuild
+++ b/sci-chemistry/vmd/vmd-1.8.7-r1.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/vmd-1.8.7-r1.ebuild,v 1.1 2010/05/18 07:22:51 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/vmd-1.8.7-r1.ebuild,v 1.2 2010/05/18 08:06:48 jlec Exp $
 
 EAPI="3"
 
@@ -46,7 +46,7 @@ QA_DT_HASH_amd64="usr/lib64/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
 QA_DT_HASH_x86="usr/lib/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
 
 pkg_nofetch() {
-	elog "Please download ${SRC_URI} from"
+	elog "Please download ${A} from"
 	elog "${VMD_DOWNLOAD}"
 	elog "after agreeing to the license and then move it to "
 	elog "${DISTDIR}"