setenv XTAL_DIR /net/fileserver/xtal
setenv SSH_PATH '/usr/bin/ssh'
setenv RSH_PATH '/usr/bin/rsh'
setenv LANG C
setenv LC_ALL C
setenv LD_LIBRARY_PATH '/usr/X11R6/lib:/usr/local/lib'
setenv SYMINFO '/net/fileserver/common/Software/xtal/ccp4_6.4.0.1/destination/ccp4-6.4.0/share/coot/syminfo.lib'
source /net/fileserver/users/PSFuser/.alias
# Change PSFuser into your own username
#------------------------------------------------------------------------------# Java definitions
#------------------------------------------------------------------------------setenv JAVA_HOME /usr/java/jdk1.5.0_02/bin
#
#------------------------------------------------------------------------------# Phenix environments and aliases
#------------------------------------------------------------------------------#source /net/fileserver/xtal/phenix-1.8.1-1168/phenix_env
#source /net/fileserver/xtal/phenix-1.8.2-1309/phenix_env
source /net/fileserver/xtal/phenix-1.8.4-1496/phenix_env
alias xtriage
'mmtbx.xtriage'
alias elbow
'elbow.builder'
alias metric_symmetry 'iotbx.explore_metric_symmetry'
alias hkl_convert
'iotbx.reflection_file_converter'
#
#------------------------------------------------------------------------------# CCP4 definitions
#------------------------------------------------------------------------------#source /net/fileserver/xtal/ccp4-6.3.0.1/ccp4-6.3.0/bin/ccp4.setup-csh
#alias ccp4mg /net/fileserver/xtal/ccp4-6.3.0.1/ccp4mg-2.7.0/bin/ccp4mg
#alias coot /net/fileserver/xtal/ccp4-6.3.0.1/coot-0.6.2/bin/coot
source /net/fileserver/common/Software/xtal/ccp4_6.4.0.1/destination/ccp4-6.4.0/setup-scripts/ccp4.setup-csh
alias ccp4mg /net/fileserver/common/Software/xtal/ccp4_6.4.0.1/destination/ccp4mg/bin/ccp4mg
#
#------------------------------------------------------------------------------# iMOSFLM
#------------------------------------------------------------------------------setenv MOSFLM_WISH /usr/local/bin/wish8.4
setenv MOSFLM_EXEC /net/fileserver/xtal/ccp4-6.3.0.1/ccp4-6.3.0/bin/ipmosflm
setenv GFORTRAN_UNBUFFERED_ALL 1
#alias imosflm /net/fileserver/xtal/ccp4-6.3.0.1/ccp4-6.3.0/bin/imosflm
#alias old_mosflm /net/fileserver/xtal/ccp4-6.0.2/bin/ipmosflm_7.0.2
#
#-------------------------------------------------------------------------------
# Solve & ReSolve environments and aliases
#------------------------------------------------------------------------------setenv CCP4_OPEN UNKNOWN
setenv SYMOP /net/fileserver/xtal/solve/lib/symop.lib # Don't need this as we have CCP4
#setenv SYMINFO /net/fileserver/xtal/solve/lib/syminfo.lib
setenv SOLVEDIR /net/fileserver/xtal/solve/lib
#
alias solve
/net/fileserver/xtal/solve/bin/solve
alias resolve /net/fileserver/xtal/solve/bin/resolve
alias resolve_pattern /net/fileserver/xtal/solve/bin/resolve_pattern
#alias resolve_setup 'limit stacksize unlimited' # For larger sizes of resolve
limit stacksize unlimited
# For larger sizes of resolve
#
#------------------------------------------------------------------------------# XDS interface environment
#------------------------------------------------------------------------------#
setenv XDSHOME
/net/fileserver/xtal/XDS
setenv XDSMANUALS /net/fileserver/xtal/XDS/XDS_html_doc
setenv XDSI
/net/fileserver/users/kurspe/soft/xdsi/xdsi2005_alpha
#
alias xdsi '/net/fileserver/users/kurspe/soft/xdsi/xdsi2005_alpha/xdsistart'
alias ang2xds '/net/fileserver/users/kurspe/ang2xds2'
alias xds_view '/net/fileserver/xtal/XDS_view/xds-viewer-0.6'
#
#------------------------------------------------------------------------------# Gerards & Alwyns environments and aliases
#------------------------------------------------------------------------------#setenv GKPATH '.:/usr/people/derek:/usr/public/graphics/omac:/net/salo/disk7/flatfile_db/external/pdb/online/native'
setenv GKLIB
'/net/fileserver/xtal/gerard/lib'
setenv ODAT
'/net/fileserver/xtal/graphics/ono/data/'
setenv OSYM
'/net/fileserver/xtal/graphics/ono/data/symm'
#
#------------------------------------------------------------------------------# PDB programs
#------------------------------------------------------------------------------alias sfconv /net/fileserver/xtal/sf_convert/sf-convert-v1.000-prod-bin-linux/bin/sf_convert
#
#------------------------------------------------------------------------------# ICM environments and aliases
#------------------------------------------------------------------------------#
setenv ICMHOME
/net/fileserver/xtal/icm
setenv ICMBROWSERPROHOME
/net/fileserver/xtal/icm-browser-pro
setenv MOLSOFTD_LICENSE_FILE
/net/fileserver/xtal/molsoft/license.dat
alias icmg '/net/fileserver/xtal/icm/icm -g'
alias icmb '/net/fileserver/xtal/icm-browser-pro/icmbrowserpro -g'
#
#------------------------------------------------------------------------------# Elves environments and aliases
#------------------------------------------------------------------------------alias elves
'/net/fileserver/xtal/Elves_1.2.5/Elves'
#
#------------------------------------------------------------------------------# Ligplot and hbplus
#------------------------------------------------------------------------------source /net/fileserver/xtal/ligplot/ligplot.setup
#
#------------------------------------------------------------------------------# CNS environments and aliasesquit
#------------------------------------------------------------------------------source /net/fileserver/xtal/cns_solve_1.3/cns_solve_env
#
#------------------------------------------------------------------------------# Whatcheck aliases
#------------------------------------------------------------------------------alias whatcheck "/net/fileserver/xtal/whatcheck/whatcheck"
#
#------------------------------------------------------------------------------# XtalView environments and aliases
#------------------------------------------------------------------------------#alias xtalview_setup "source /net/fileserver/xtal/XtalView/XtalView.env"
source /net/fileserver/xtal/XtalView/XtalView.env
#
#------------------------------------------------------------------------------# AutoDep & Validation environments and aliases
#------------------------------------------------------------------------------#setenv RCSBROOT /wwwadit/adit/rcsbapps
alias adit_startup "setenv RCSBROOT /wwwadit/adit/rcsbapps ; cd /wwwadit ; ./StartAdit.csh"
setenv RCSBROOT /usr/public/xtal/validation-v8.061-prod-bin-linux
alias validation 'validation-v8'
#
#------------------------------------------------------------------------------# T_coffee definitions
#------------------------------------------------------------------------------#
setenv CLUSTALW_4_TCOFFEE /net/fileserver/xtal/clustalx/clustalw
setenv SAP_4_TCOFFEE
/net/fileserver/xtal/t_coffee/sap/bin/sap
#
#alias t_coffee '/net/fileserver/xtal/t_coffee/bin/t_coffee'
#
#-----------------------------------------------------------------------# SCHRÖDINGER
#-----------------------------------------------------------------------setenv SCHRODINGER /home/data/xray/schrodinger1
#-----------------------------------------------------------------------#
#-----------------------------------------------------------------------# VASCo
#-----------------------------------------------------------------------alias vasco 'python /net/fileserver/users/mochma/vasco_moche/VASCo.py'
#-----------------------------------------------------------------------#
set mypathlist = ( $PATH /usr/sbin /usr/lib /usr/include /usr/etc /usr/local/bin /usr/local/lib /usr/local/include \
/net/fileserver/xtal/gerard/bin $XTAL_DIR/Elves_1.2.5 \
/usr/java/jdk1.5.0_02/bin $XTAL_DIR/shelx13 $XTAL_DIR/XDS /net/fileserver/xtal/t_coffee/bin $RCSBROOT/bin \
/net/fileserver/xtal/Adobe/Adobe/Reader8/bin/ \
$SCHRODINGER /usr/local/Adobe/Acrobat7.0/bin /opt/ActiveTcl-8.4/bin /net/fileserver/xtal/msms \
/net/fileserver/xtal/delphi/bin /net/fileserver/xtal/xdsapp \
/net/fileserver/xtal/xdsstat /net/fileserver/xtal/XDS_view \
/net/fileserver/xtal/molprobity/molprobity3.19.110929/bin/linux /net/fileserver/xtal/thinlink/tl/bin/ \
/net/fileserver/xtal/iRODS/clients/icommands/bin /net/fileserver/xtal/xdsgui ./ )
foreach dir ( ${mypathlist} )
if ( ${?PATH} ) then
if ( :${PATH}: !~ *:${dir}:* ) then
setenv PATH ${PATH}:${dir}
endif
else
setenv PATH ${dir}
endif
end
limit coredumpsize 0