Re: [ccp4bb] sequential renumbering of a messed up pdb file

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: sequential renumbering of a messed up pdb file
From: "Ralf W {- dot -} Grosse-Kunstleve" rwgk {- at -} YAHOO {- dot -} COM
Date: 2008-08-01

Yet another alternative: you can do this with iotbx.pdb. Loop over the hierarchy in the
standard manner (http://cctbx.sourceforge.net/sbgrid2008/tutorial.html, v1_loop_over_atoms.py)
and insert chain.id = new_chain_id, rg.resseq = new_resseq into the loops. The only trick is
to add the bookkeeping for new_chain_id and new_resseq.
Ralf

----- Original Message ----
From: William Scott
To: CCP4BB@JISCMAIL.AC.UK
Sent: Thursday, July 31, 2008 4:09:11 PM
Subject: [ccp4bb] sequential renumbering of a messed up pdb file

Hi folks:

I am hoping there is a simple answer I have overlooked to the
following question. I have a pdb file in it that has multiple
residues that have the same number and chain ID, and I want to force
them to be renumbered sequentially. Is there a simple way to do so
(eg, pdbset) or am I doomed to fixing it manually?

Thanks.

Bill Scott

William G. Scott

Contact info:
http://chemistry.ucsc.edu/~wgscott/

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Beamline Stability Issues
From: Lucas Sanfelici lsanfelici {- at -} LNLS {- dot -} BR
Date: 2008-08-01

Next message:
Subject: Map conversion
From: Sampath Natarajan sams76 {- at -} GMAIL {- dot -} COM
Date: 2008-08-01