1) It would
be helpful if your ".cshrc" file (in your home directory)
contains
the following alias:
alias xdisp345 'xdisp mar345 345mm 100 marpck'
2) Make a directory for your crystal data. Get your xray data from the Mar detector using "sftp".
3) Use "cd"
to move to the data where your xray data is.
To run denzo, type, for example: xdisp345 my_xray_data_001.mar3450
4) Peak seach (pick about 100 to 200 peaks)
5)
Find a "denzo.dat" file. Put it in the same directory as your
xray data.
Edit the denzo.dat file for your crystal.
6) Open
a new terminal window; cd to the same directory as data;
then type: denzo
then type: @denzo.dat
Unix trick to send output to a log file: denzo | tee denzo.log
7)
To run scalepack: Find a "scalepack.com" or "scale.com" file. Put
it in the same directory as your xray data.
Edit the scalepack.com file for your crystal.
Run scalepack by typing: scalepack < scalepack.com
> scalepack.log
****************************************************************
Getting your xray data (output from scalepack) into a format appropriate for CNS or CCP4:
1) For CCP4 format:
You can either
use the CCP4i graphical interface, or a unix script that invokes
the CCP4 programs
"scalepack2mtz" and "CAD".
An example of a unix script called "scalepack2mtz.sh" that should work is:
#!/bin/sh
set -e
scalepack2mtz
hklin my_data.sca \
hklout $CCP4_SCR/junk1.mtz <<eof
symm 18 #
this is your space group
end
eof
# convert
Is to Fs.
truncate hklin
$CCP4_SCR/junk1.mtz \
hklout $CCP4_SCR/junk2.mtz <<eof
title My xray
data
truncate yes
nresidue 149
labout
F=FOBS SIGF=SIGF
eof
# get correct
sort order and asymmetric unit
cad hklin1
$CCP4_SCR/junk2.mtz hklout my_data.mtz <<eof
labin file
1 ALL
sort H K L
end
eof
#
You can edit
the above unix script for your crystal, and then execute it by
typing its
filename (such as "scalepack2mtz.sh").
2) To get your data into CNS format:
You can use
the CCP4i graphical interface, or use a unix script the invokes
the CCP4 program
"mtz2various".
An example of a unix script called "mtz2cns.sh" that should work is:
#!/bin/csh
-f
mtz2various
\
hklin my_data.mtz
\
hklout my_data.cns
\
<<eof
OUTPUT CNS
LABIN FP=FOBS
SIGFP=SIGF
END
eof
#