Re: [ccp4bb] Any calculation function in CCP4 to analyze coordinate file?
There are tools to do this - eg REFMAC will tell you no of residues and atoms. PDBSET baverage/ rwcontents etc all offer bits of info, but i guess it would be useful to have a more organised report.. Eleanor On Feb 27 2012, Jan Dohnalek wrote: We have been doing a bit of this using a simple program under Linux - pdbskim. A linux binary available on request. Very simple output though, focused on infromation on occ, Bs alternatives, etc to help make decisions during structure refinement. Jan On Sat, Feb 25, 2012 at 11:59 PM, WENHE ZHONG wrote: Dear members, Just have a silly question past my mind: is there any program in CCP4 can be used to analyze coordinate file (.pdb format) to have a very general/overall discription about the structure? --such as the total number of protein residues/water/ligand, the total atoms of protein/water/ligand, the average b-factor of protein/water/ligand, the number of residues which have alternative side chians, and so on. Thank you. King regards, Wenhe -- Professor Eleanor Dodson YSNL, Dept of Chemistry University of York Heslington YO10 5YW tel: 00 44 1904 328259 Fax: 00 44 1904 328266
Re: [ccp4bb] Any calculation function in CCP4 to analyze coordinate file?
We have been doing a bit of this using a simple program under Linux - pdbskim. A linux binary available on request. Very simple output though, focused on infromation on occ, Bs alternatives, etc to help make decisions during structure refinement. Jan On Sat, Feb 25, 2012 at 11:59 PM, WENHE ZHONG wrote: > Dear members, > > Just have a silly question past my mind: is there any program in CCP4 can > be used to analyze coordinate file (.pdb format) to have a very > general/overall discription about the structure? --such as the total number > of protein residues/water/ligand, the total atoms of protein/water/ligand, > the average b-factor of protein/water/ligand, the number of residues which > have alternative side chians, and so on. > > Thank you. > > King regards, > Wenhe > -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 340 Fax: +420 296 809 410
Re: [ccp4bb] Any calculation function in CCP4 to analyze coordinate file?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Wenhe, what you name 'general' may in fact be quite specific and hence running a single program without any options provided is rather unlikely to give the answers you seek. moleman2 and other USF utilities (not a ccp4 program) come closest to what you are looking for, I guess. Cheers, Tim On 02/25/2012 11:59 PM, WENHE ZHONG wrote: > Dear members, > > Just have a silly question past my mind: is there any program in CCP4 can > be used to analyze coordinate file (.pdb format) to have a very > general/overall discription about the structure? --such as the total number > of protein residues/water/ligand, the total atoms of protein/water/ligand, > the average b-factor of protein/water/ligand, the number of residues which > have alternative side chians, and so on. > > Thank you. > > King regards, > Wenhe > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPSjqNUxlJ7aRr7hoRArlyAKD5GfPxWr8At/y/8kQ7byhfbWTZogCgoXmL +dnIgQhmPFR1w3uR4GBVtS8= =OVKy -END PGP SIGNATURE-
[ccp4bb] Any calculation function in CCP4 to analyze coordinate file?
Dear members, Just have a silly question past my mind: is there any program in CCP4 can be used to analyze coordinate file (.pdb format) to have a very general/overall discription about the structure? --such as the total number of protein residues/water/ligand, the total atoms of protein/water/ligand, the average b-factor of protein/water/ligand, the number of residues which have alternative side chians, and so on. Thank you. King regards, Wenhe
