Re: [ccp4bb] PERL system call to CCP4

Protein crystallography Programs for crystallography X-ray detectors
Basic tutorials:
Protein Peptide

CCP4bb navigation

CCP4bb <-- 2008 <-- January 2008 <-- 14 January 2008

Previous message:
Subject: Re: PERL system call to CCP4
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2008-01-14

Next message:
Subject: Re: MrBUMP FASTA
From: "Keegan, RM (Ronan)" r {- dot -} m {- dot -} keegan {- at -} DL {- dot -} AC {- dot -} UK
Date: 2008-01-14

Subject: Re: PERL system call to CCP4
From: Gerard DVD Kleywegt gerard {- at -} XRAY {- dot -} BMC {- dot -} UU {- dot -} SE
Date: 2008-01-14

hi,

> I am writing a PERL script to execute a number of CCP4 commands (ncsmask,
> pdbset, and dm) in succession. I have tried using system call or PIPE
> command, neither of which work. The ccp4 scripts generated work
> independently on the command line.

we do this in the eds map generation script. first create a little shell
script that runs the ccp4 programs:

------
# generate refmac script file
open (OUTFILE,">refmac.com")

die "$! can't open file refmac.com ";
select (OUTFILE);

if ($tls_flag ne "") {
print "$tlsextract XYZIN $pdbfile TLSOUT $tlsin > tlsext.log ";
}
------

etc.

and then execute it with the system command (of course, you have to make the
file executable first, or maybe "source" it instead of executing it - could
this have been your problem?):

------
close (OUTFILE);
system ("chmod 744 refmac.com");
system ("./refmac.com");
------

works fine on a plain-vanilla linux box

--dvd

p.s.: a propos an earlier thread, a solution is to use answers.com instead of
wikip... e.g.: http://www.answers.com/molecular%20geometry and
http://www.answers.com/topic/dihedral-angle?cat=technology and
http://www.answers.com/topic/alkane-stereochemistry - this should work in the
land of the great firewall; not sure about other orwellian countries (let me
know off-line if it doesn't)

******************************************************************
Gerard J. Kleywegt
[Fellow of the Resdep of the Swedish Ministry of Truth]
Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN

http://xray.bmc.uu.se/gerard/ mailto:gerard@xray.bmc.uu.se
******************************************************************
The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
******************************************************************

CCP4bb navigation

CCP4bb <-- 2008 <-- January 2008 <-- 14 January 2008

Previous message:
Subject: Re: PERL system call to CCP4
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2008-01-14

Next message:
Subject: Re: MrBUMP FASTA
From: "Keegan, RM (Ronan)" r {- dot -} m {- dot -} keegan {- at -} DL {- dot -} AC {- dot -} UK
Date: 2008-01-14