Swiss-PdbViewer is an application that provides a user friendly interface

allowing to analyse several proteins at the same time. The proteins can be
superimposed in order to deduce structural alignments and compare their
active sites or any other relevant parts. Amino acid mutations, H-bonds,
angles and distances between atoms are easy to obtain thanks to the
intuitive graphic and menu interface.

Moreover, Swiss-PdbViewer is tightly linked to Swiss-Model, an automated
homology modelling server developped at Glaxo Welcome Experimental Research
in Geneva. Working with these two programs greatly reduces the amount of work
necessary to generate models, as it is possible to thread a protein primary
sequence onto a 3D template and get an immediate feedback of how well the
threaded protein will be accepted by the reference structure before
submitting a request to build missing loops and refine sidechain packing.

Swiss-PdbViewer can also read electron density maps, and provides various
tools to build into the density. In addition, various modelling tools are
integrated and command files for popular energy minimisation packages can be
generated.

Finally, as a special bonus, POV-Ray scenes can be generated from the
current view in order to make stunning ray-traced quality images.

WWW:  http://www.expasy.ch/spdbv/

PR:		33902
Submitted by:	chuynh@biolateral.com.au

2 files changed, 138 insertions, 0 deletions

diff --git a/biology/spdbv/files/patch-aa b/biology/spdbv/files/patch-aa
new file mode 100644
index 000000000000..125c1dd245b8
--- /dev/null
+++ b/biology/spdbv/files/patch-aa
@@ -0,0 +1,118 @@
+--- install.sh.orig	Mon Dec  4 21:31:45 2000
++++ install.sh	Thu Dec 20 10:15:42 2001
+@@ -7,10 +7,9 @@
+ SPDBVNEEDOSbis="Linux"
+ 
+ SPDBVUSERDIR="$HOME"
+-SPDBVSHAREDIR="/usr/share"
+ SPDBVDIR="SPDBV"
+ SPDBVSTUFF="_stuff_"
+-SPDBVDEST=""
++SPDBVDEST="${PREFIX}"
+ SPDBVOSVERSION=`uname -r`
+ SPDBVOS=`uname -s`
+ if [ $SPDBVOS = IRIX64 ]; then
+@@ -27,20 +26,8 @@
+     echo "Will install the shared files in $SPDBVDEST."
+     if [  -d $SPDBVDEST/$SPDBVDIR ]; then
+         echo "Shared files are already installed on this system."
+-        echo "Delete old files and reinstall (Y/N)?"
+-        read INP
+-        if [ $INP = "Y" -o $INP = "y" ]; then
+-            echo " "
+-            echo "will reinstall"
+-	    if [ -w $SPDBVDEST/$SPDBVDIR ]; then
+-		rm -r $SPDBVDEST/$SPDBVDIR
+-	    else
+-	        echo "Could not delete shared files."
+-		abort
+-	    fi
+-        else
+-            abort
+-        fi
++        echo " "
++        echo "will reinstall"
+     fi
+     mkdir $SPDBVDEST/$SPDBVDIR #2> /dev/null
+     if [ ! -d $SPDBVDEST/$SPDBVDIR ]; then
+@@ -64,11 +51,11 @@
+     chmod ugo+rx $SPDBVDEST/$SPDBVDIR/bin/spdbv.sh
+ 
+     #try to make link from /usr/bin/spdbv to ./spdbv.sh
+-    if [ ! -w /usr/bin/ ]; then
++    if [ ! -w ${SPDBVDEST}/bin/ ]; then
+        echo " "
+-       echo "Can't make a link from /usr/bin/spdbv to spdbv.sh"
++       echo "Can't make a link from ${SPDBVDEST}/bin/spdbv to spdbv.sh"
+     else
+-       ln -sf $SPDBVDEST/$SPDBVDIR/bin/spdbv.sh /usr/bin/spdbv
++       ln -sf $SPDBVDEST/$SPDBVDIR/bin/spdbv.sh ${SPDBVDEST}/bin/spdbv
+     fi
+ }
+ 
+@@ -82,65 +69,18 @@
+    echo " Installation script for Release $SPDBVVERSION ($SPDBVNEEDOS)"
+    echo " " 
+    echo " " 
+-   echo " Please follow the instructions below."
+-   echo " "
+-   echo "Where do you want me to install the files:"
+-   echo "globally in /usr/share/SPDBV  ->  G"
+-   echo "or just locally in ~/SPDBV    ->  L"
+-   echo "something different           ->  O"
+-   echo "(G/L/O)?"
+-   read DEST
+-
+-   SPDBVDEST=""
+-   if [ $DEST = "G" -o $DEST = "g" ]; then
+-       SPDBVDEST=$SPDBVSHAREDIR
+-   elif [ $DEST = "L" -o $DEST = "l" ]; then
+-       SPDBVDEST=$SPDBVUSERDIR
+-   elif [ $DEST = "O" -o $DEST = "o" ]; then
+-       echo "enter target Path where to install directory SPDBV:"
+-       read SPDBVDEST
+-   fi
+-
+-   if [ -z $SPDBVDEST ]; then
+-       echo ""
+-       echo "$SPDBVDEST is not a valid answer. 1"
+-       echo ""
+-       echo "continue .. hit any key"
+-       read DEST
+-       mainmenu
+-   fi
+-   if [ ! '(' -d $SPDBVDEST ')' ]; then
+-       echo ""
+-       echo "$SPDBVDEST is not a valid answer. 2"
+-       echo ""
+-       echo "continue .. hit any key"
+-       read DEST
+-       mainmenu
+-   fi
+ 
+    makesharedinst
+ 
+-#   clear
+-
+    echo " "
+    echo " SPDBV - Swiss PDB Viewer" 
+    echo " Installation script for Release $SPDBVVERSION ($SPDBVNEEDOS)"
+    echo " "
+    echo "Installation completed."
+-   echo "Start your copy of SPDBV with the script $SPDBVDEST/$SPDBVDIR/bin/spdbv.sh"
+    echo ""
+    echo "ENJOY SPDBV!"
+    exit
+ }
+-
+-# test for the right os
+-if [ $SPDBVOS != $SPDBVNEEDOS ]; then
+-  if [ $SPDBVOS != $SPDBVNEEDOSbis ]; then 
+-    echo "SPDBV $SPDBVVERSION ($SPDBVNEEDOS) is intended to run on hardware under $SPDBVNEEDOS."
+-    abort
+-    exit
+-  fi
+-fi
+ 
+ # start up the mainmenu
+ mainmenu 
diff --git a/biology/spdbv/files/patch-ab b/biology/spdbv/files/patch-ab
new file mode 100644
index 000000000000..48bb1215f83d
--- /dev/null
+++ b/biology/spdbv/files/patch-ab
@@ -0,0 +1,20 @@
+--- SPDBV/bin/spdbv-orig.sh.orig	Thu Dec 20 10:11:25 2001
++++ SPDBV/bin/spdbv-orig.sh	Thu Dec 20 10:26:00 2001
+@@ -1,6 +1,8 @@
+ ARCH=`uname -s`
+ if [ $ARCH = IRIX64 ]; then
+ 	ARCH=IRIX
++elif [ $ARCH = FreeBSD ]; then
++	ARCH=Linux
+ fi
+ SPDBV_TEMP=$HOME/SPDBV/temp
+ SPDBV_DOWNLOAD=$HOME/SPDBV/download
+@@ -38,7 +40,5 @@
+ #xrdb -override $SPDBV_BASE/app-defaults/Spdbv
+ 
+ #start the SPDBV, reroute stderr to nirvana
+-{
+-   $SPDBV_BASE/bin/$SPDBV_RELEASE.$ARCH $*
+-} 2> /dev/null
++$SPDBV_BASE/bin/$SPDBV_RELEASE.$ARCH $*
+ #done.