Re: [ccp4bb] question about CCP4 scripts
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Hash: SHA1
Dear Joe,
most ccp4 programs make use of space group and cell information if
present in the input file. The script you list below does not have an
input file (apparently it creates a dummy mtz-file with only a list of
Miller indices), so there is nothing to extract. E.g. a simple test
# scalepack2mtz hklin test.sca hklout test.sca eof
eof
confirms that scalepack2mtz extracts the information from the header
automatically and creates a valid mtz-file (I tend to give programs a
try the way I would like them to work, and if that does not work, I
start reading the manual or check on the web or post to a bb).
Regards,
Tim
On 05/09/2013 05:37 AM, 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
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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Re: [ccp4bb] question about CCP4 scripts
Typo:
To avoid crash/overwrite, should be
scalepack2mtz hklin test.sca hklout test.mtz eof eof
^^^
jbb
Jeffrey Bonanno, Ph.D.
New York Structural Genomics Research Consortium
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene
Sent: Thursday, May 09, 2013 4:26 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] question about CCP4 scripts
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Dear Joe,
most ccp4 programs make use of space group and cell information if present in
the input file. The script you list below does not have an input file
(apparently it creates a dummy mtz-file with only a list of Miller indices), so
there is nothing to extract. E.g. a simple test
# scalepack2mtz hklin test.sca hklout test.sca eof eof
confirms that scalepack2mtz extracts the information from the header
automatically and creates a valid mtz-file (I tend to give programs a try the
way I would like them to work, and if that does not work, I start reading the
manual or check on the web or post to a bb).
Regards,
Tim
On 05/09/2013 05:37 AM, 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
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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iD8DBQFRi12sUxlJ7aRr7hoRAurSAKDnNjVeJN0GvhDLzKmaYUX0mVUWggCePvTF
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Re: [ccp4bb] question about CCP4 scripts
Looks like my signature messed up the script too... scalepack2mtz hklin test.sca hklout test.mtz eof eof ^^^
Re: [ccp4bb] question about CCP4 scripts
At this point you do have the scalepack2mtz output file (BTW,
imosflm/aimless is wholeheartedly recommended by this convert), and you
can easily extract all the info from there. There is mtzdmp, of course,
but it's easier to parse the actual mtz file (hey, the records are
actually text). Like so:
egrep -oa SYMINF.{74} foo.mtz | awk '{print symm $5}'
Gives you the space group *number*, most ccp4 programs I know accept
that in addition to string symbol. But if you really need the latter,
echo symm $(egrep -oa SYMINF.{74} foo.mtz | cut -d' -f 2 | sed
s///g)
will do.
As for unit cell parameters, this should work
egrep -oa CELL.{76} foo.mtz | sed -n 1p
Keep in mind that this extracts the global cell and will be
problematic if you have multi-dataset file (which I presume you don't).
If you need Nth dataset grab DCELL record, e.g. for the dataset #1
egrep -oa DCELL.{75} foo.mtz | sed -n 2p
Cheers and
https://xkcd.com/208/
Ed
On Wed, 2013-05-08 at 23:37 -0400, 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
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
-- / Lao Tse /
[ccp4bb] question about CCP4 scripts
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 ${CCP4_SCR}/unique_out.mtz eof
labout F=F SIGF=SIGF
symmetry p43212
resolution 1.6
cell 78.1 78.1 55.2 90.0 90.0 90.0
eof
--
Best regards,
Joe
Re: [ccp4bb] question about CCP4 scripts
Hi Joe,
this line of code for csh/tcsh is awfully rickety-raggedy, it does the trick
though.
Jan
setenv spacegroup P3121
setenv noresidues 350
setenv lambda 1.5418
set unitcell = `head -3 ../hkl/output.sca | tail -1 | cut -b 4-60`
scalepack2mtz \
hklin ../hkl/output.sca \
hklout ./${dataset}_import.mtz \
eof ${dataset}_scalepack2mtz.log
symmetry $spacegroup
cell $unitcell
wave $lambda
end
eof
--
Jan Abendroth
Emerald BioStructures
Seattle / Bainbridge Island WA, USA
home: Jan.Abendroth_at_gmail.com
work: JAbendroth_at_embios.com
http://www.emeraldbiostructures.com
On May 8, 2013, at 8:37 PM, Joe Chen gch...@gmail.com 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
