Any calculation function in CCP4 to analyze coordinate file?

From: WENHE ZHONG
Date: 25 February 2012 22:59

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

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From: Tim Gruene

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

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From: Jan Dohnalek

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

--
Jan Dohnalek, Ph.D

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From: Eleanor Dodson


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