# env. for the printer

setenv PRINTER 0

# env. for Nenetrez

setenv NCBI /usr/local

# for pager

setenv LESS -Miea

setenv PAGER less

# for the editor

setenv EDITOR pico

# for tcsh

set ignoreeof

set autolist

# expand the X path

setenv XAPPLRESDIR /usr/local/lib/X11/app-defaults

# Netscape realted stuff

alias tin /usr/local/bin/tin -r news.bham.ac.uk
alias netscape /usr/local/bin/netscape
setenv MOZILLA_HOME /usr/local/netscape

if $?LD_LIBRARY_PATH then
        setenv LD_LIBRARY_PATH "$LD_LIBRARY_PATH":/usr/local/CosmoPlayer:/usr/local/rvplayer5.0b3:/usr/lib:/usr/local/lib:/usr/local/lib/netscape/plugins
else
        setenv LD_LIBRARY_PATH /usr/local/CosmoPlayer:/usr/local/rvplayer5.0b3:/usr/lib:/usr/local/lib:/usr/local/lib/netscape/plugins
endif



set path=($path /usr/local/rvplayer5.0b3)
set path=($path /SW/raster3d)


# setup for academic CHARMm, by Toni Pemberton & Steve Young
#

if ( -e ~/.charmm_on ) then

	setenv CHM_ROOT /SW/charmm24b2
	setenv CTOPPAR $CHM_ROOT/toppar
	setenv CHM_DOC $CHM_ROOT/doc
	setenv CHM_EXE $CHM_ROOT/exec/sgi/charmm
	setenv CHM_DATA $CHM_ROOT/msi
	set path=($path $CHM_ROOT/exec/sgi)

endif

#
# setup for modeller3
#
### begin modeller3 #######################################################
#
# Environment definitions for the main MODELLER version:
#
# Root directory for the Protein DataBank (not essential, can be omitted):

if ( -e ~/.mod3_on ) then
	setenv PDB /clients/pdb

#	Root directory for pre-installation MODELLER source 
#	(not essential, can be omitted):
	setenv MODROOT /SW/mod3

#	MODELLER key:
	setenv KEY MODELIRANJE

#	Root directory for installed MODELLER:
	setenv MODINSTALL /SW/modeller3

#	Set MODELLER environment variables and update the command path:
	if (-e $MODINSTALL/bin/setmodeller) source $MODINSTALL/bin/setmodeller
#
### end modeller3 #######################################################

endif

### Modeller 4, by Tony Pemberton

if ( -e ~/.mod4_on ) then
	setenv KEY MODELIRANJE
	setenv MODINSTALL /SW/modeller4
	if (-e $MODINSTALL/bin/setmodeller) source $MODINSTALL/bin/setmodeller
endif


###  XPLOR stuff, by John Smith
##if ( -e ~/.xplor_on ) then
##	if ( -e /SW/xplor3.1/sgi/pugh.ulogin.com ) source /SW/xplor3.1/sgi/pugh.ulogin.com
##	setenv XEXE $XPLOR/object_library/hrtxplor.exe
##endif

### GRASP stuff, by John Smith


if ( -e ~/.grasp_on ) then

	setenv GRASP /SW/grasp/grasp_data/data
	set path = ( $path /SW/grasp )

endif

### GCG stuff, by M. Cserzo

if ( -e ~/.gcg_on ) then
#	setenv OSNAME irix
	if ( -e /usr/gcg/gcgstartup ) source /usr/gcg/gcgstartup

# start up GCG after switching the shell, M. Cs.
	if ( $?SWITCH_THE_SHELL == 1 ) then
		gcg
		unsetenv SWITCH_THE_SHELL
	endif
endif



if ( -e ~/.xplor+_on ) then
	if ( -e /SW/xplor3851 ) source /SW/xplor3851/machine/supported/sgi/ulogin.com
endif

###QUANTA versions KJS

if ( -e ~/.quanta97_on ) then
        if ( -e /SW/msi/quanta97 ) source /SW/msi/quanta97/.setquanta
        if ( -e /SW/biosym ) source /SW/biosym/cshrc
endif

if ( -e ~/.quanta_on ) then
        if ( -e /SW/msi/quanta97 ) source /SW/msi/quanta97/.setquanta
        if ( -e /SW/biosym ) source /SW/biosym/cshrc
endif

### TURBO-FRODO staff, KJS

if ( -e ~/.turbo_on ) then
	setenv TURBO_DIR /SW/turbo_5.5/prog
	alias turbo $TURBO_DIR/prog/turbo
	alias turbo_6 $TURBO_DIR/prog/turbo_6
endif

alias readseq /SW/readseq/bin/readseq
alias molscript /SW/molscript/molscript
alias molauto /SW/molscript/exe/molauto.exe
alias rasmol /SW/RasMol2/rasmol
alias vmd /SW/vmd-1.2b2/bin/vmd
alias what_check /SW/whatcheck-4.99f/DO_WHATIF.COM
setenv PROSA_BASE /SW/prosa/data
alias prosa /SW/prosa/bin/prosaII
alias xmgr /SW/xmgr/xmgr/bin/xmgr
setenv GR_HOME /SW/xmgr/xmgr

### Procheck & Aqua staff, by miklos

if ( -e ~/.procheck_on ) source /SW/procheck/procheck3.4.4/setup.scr

# Maple V R4 stuff, by Miklos

if ( -e ~/.maple_on ) set path=($path /usr/local/maple/bin)

### Phases stuff

if ( -e ~/.phases_on ) set path=( $path /usr/local/phases )

### Povray 3 Environment setup, by gcoates 18/11/97

if ( -e ~/.povray_on ) set path= ( $path /SW/povray3/ )


### Parallel Virtual Machine setup by gcoates 18/11/97
### Needed by parallel charmm users.

if ( -e ~/.pvm_on) then
	set path= ( $path /SW/pvm3/lib)
	setenv PVM_ROOT /SW/pvm3
	setenv PVM_DPATH $PVM_ROOT/lib/pvmd
	setenv PVM_ARCH SGIMP64
	endif

### xanim setup by gcoates 18/11/97

alias xanim /usr/local/bin/xanim +f +Ak +B


### Harvard Charmm v 25b1 setup by gcoates 18/11/97

if ( -e ~/.charmm25_on ) then
	alias charmm25 /SW/charmm25b1/exec/sgi/charmm25
        alias charmm25_pvm /SW/charmm25b1/exec/sgi/charmm25_pvm
endif

### threader setup by osmart 4/12/97
if ( -e ~/.threader_on ) then
	setenv THREAD_DIR /SW/threader
	alias threader /SW/threader/threader
endif


#### Prepi setup by gcoates 16/12/97
if ( -e ~/.prepi_on ) then
	setenv PREPIDIR /SW/prepi
	alias prepi /SW/prepi/PREPI
endif

#### Shelx stuff

if ( -e ~/.shelx_on ) set path=($path /usr/local/shelx/bin)

#### solve setup osmart 21/1/98
if ( -e ~/.solve_on ) then
        setenv SOLVEDIR /SW/solve
        alias solve /SW/solve/solve
endif

# set-up for amps, Tony Pemberton
if ( -e ~/.amps_on ) then
	alias dayb /SW/amps/bin/dayb
	alias makeampscom /SW/amps/bin/makeampscom
	alias multalign /SW/amps/bin/multalign
	alias order /SW/amps/bin/order
	alias patt /SW/amps/bin/patt
	alias select /SW/amps/bin/select
	alias sorter /SW/amps/bin/sorter
endif


# AMBER v5.0 setup: nicked from the amber login scripts by Guy Coates  6/4/98


if ( -e ~/.amber_on ) then
	setenv OML_AMBER /SW/amber5.0/AMBER
	alias xleap $OML_AMBER/Leap/xleap
	alias tleap $OML_AMBER/Leap/tleap
	set path=($path $OML_AMBER/Leap $OML_AMBER/exe)
endif

# ImageMagick setup 6/7/98 osmart - problem with binaries so use oxford version
if ( -e ~/.ImageMagick_on ) then
	set path= ( $path /SW/ImageMagick/bin_from_oxford )
	echo "ImageMagick documentation in /SW/ImageMagick/ImageMagick-4.0.7/docs/"
endif

if ( -e ~/.sybyl_on ) then
	set path=($path /SW/trigo)
endif