[ccp4bb] Off Topic: help locating CNS data
I have been presented with the problem of locating protein data for a structure which was refined here ten years ago with the CNS program. Unfortunately I have never used this program so do not know what type of files I am looking for (or how many files). Any suggestions please Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com
Re: [ccp4bb] Off Topic: help locating CNS data
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Rex, CNS uses input files, which are listed e.g. at http://cns.csb.yale.edu/v1.2/ When I used CNS I always had to use 'generate.inp' so i would start search for this. However, they can be freely renamed, I am afraid. Good luck, Tim On 09/21/2012 12:10 PM, Rex Palmer wrote: I have been presented with the problem of locating protein data for a structure which was refined here ten years ago with the CNS program. Unfortunately I have never used this program so do not know what type of files I am looking for (or how many files). Any suggestions please Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQXEDhUxlJ7aRr7hoRAs5rAKD5w3VlVFECMzVgPU56G/biy6AsfwCgxM41 1vG/TghWgjLKNb9qp3NDHtU= =LegZ -END PGP SIGNATURE-
Re: [ccp4bb] Off Topic: help locating CNS data
As was mentioned, the diffraction data files can be named according to the user's wish. But I'd try to locate files with extensions .hkl, .xpl, .cv (and .cns? although I have never seen that extension used myself) Fred. On 21/09/12 12:10, Rex Palmer wrote: I have been presented with the problem of locating protein data for a structure which was refined here ten years ago with the CNS program. Unfortunately I have never used this program so do not know what type of files I am looking for (or how many files). Any suggestions please Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494
Re: [ccp4bb] Off Topic: help locating CNS data
Add another extension to your search: *.mtf If your structure was refined with CNS, chances are you'll find its Molecular Topology File somewhere. Best of luck, Jon 2012/9/21 vellieux frederic.velli...@ibs.fr As was mentioned, the diffraction data files can be named according to the user's wish. But I'd try to locate files with extensions .hkl, .xpl, .cv (and .cns? although I have never seen that extension used myself) Fred. On 21/09/12 12:10, Rex Palmer wrote: I have been presented with the problem of locating protein data for a structure which was refined here ten years ago with the CNS program. Unfortunately I have never used this program so do not know what type of files I am looking for (or how many files). Any suggestions please Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494 -- Jon Agirre, PhD Unit of Biophysics (CSIC-UPV/EHU) http://www.ehu.es/jon.agirre http://sourceforge.net/projects/projectrecon/ +34656756888
Re: [ccp4bb] Off Topic: help locating CNS data
If you are looking for reflection files, the tricky part is that in CNS
format they did not include the unit cell parameters. Just to locate
them, it may be helpful to know that they contain a header that looks
like this
NREFlection= 49238
ANOMalous=FALSe { equiv. to HERMitian=TRUE}
DECLare NAME=FOBS DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=TEST DOMAin=RECIprocal TYPE=INTE END
so if you are in *nix environment something like this
egrep -rl '^[ ]DECLare NAME.*DOMAin=RECIprocal' .
I am sure perl masters will laugh at my awkward attempts at using
regular expressions.
Cheers,
Ed.
On 09/21/2012 06:10 AM, Rex Palmer wrote:
I have been presented with the problem of locating protein data for a
structure which was refined here ten years ago with the CNS program.
Unfortunately I have never used this program so do not know what type
of files I am looking for (or how many files).
Any suggestions please
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
