Hello Joe,
You're either going to have to supply your script with something like a
.sca file and extract unit cell and space group from it, or you'll have
to supply those values on the command line.
First option in csh, apropos Jan's script:
#!/bin/csh -f
#
# run as "./phils_script1.csh dummy.sca"
#
set cell = `head -3 $1 | tail -1 | cut -b 2-60`
set sg = `head -3 $1 | tail -1 | cut -b 61-80`
unique hklout unique.mtz << eof
labout F=F SIGF=SIGF
symmetry $sg
resolution 1.6
cell $cell
eof
---- end script 1
The other option is to explicitly itemize everything
#!/bin/csh -f
#
# "./phils_script2.csh 79.1 79.1 37.9 90. 90. 90. P43212"
#
unique hklout unique.mtz << eof
labout F=F SIGF=SIGF
symmetry $7
resolution 1.6
cell $1 $2 $3 $4 $5 $6
eof
---- end script 2
In general I'd recommend putting some argument error checking in these
scripts, but that would make this post too long.
If still in print I recommend the "C shell Field Guide" by Anderson and
Anderson if you want to get further into Csh scripting. Python's also
not a bad option. At all costs avoid Perl.
Phil Jeffrey
Princeton
On 5/8/13 11:37 PM, Joe Chen wrote:
Hi All,
I am trying to write a shell script to streamline a few steps, one of
which is Unique, see below. As you can see, this program requires
symmetry and cell parameters. In CCP4 GUI Scalepack2mtz, these info are
automatically extracted from .sca file (first two lines). But I don't
know if there is a way to do this in script, so I don't need to type
these values for each dataset. Thank you in advance for your help.
#!/bin/sh
# unique.exam
#
# runnnable test script for the program "unique" - this will use this
# program to generate a reflection list containing null values.
#
set -e
unique hklout ${CCP4_SCR}/unique_out.mtz << eof
labout F=F SIGF=SIGF
symmetry p43212
resolution 1.6
cell 78.1 78.1 55.2 90.0 90.0 90.0
eof
--
Best regards,
Joe
