Re: [ccp4bb] Renumber residues working PDB file - Applying a sequences numbering to PDB file

[Mark J. van Raaij]

I guess you could also get pdbset to do it in one go, using various lines 
(being careful to use the right order and not “overwrite” residues with the 
same name).
Ideally you’d want to run only the renumber part of a auto-build program like 
buccaneer or arp-warp, without the rebuilding or refinement, might be a nice 
little addition to ccp4.

Mark J van Raaij
Dpto de Estructura de Macromoleculas, lab 20B
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. +34 91 585 4616 (internal 432092)
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/


> On 5 Feb 2023, at 08:03, Eleanor Dodson 
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Usually you can bully coot into doing it but by bit. Say you need to renumber 
> A 1-8. I often have to change the chain id to Z say then renumber Z. And so 
> on . Then go back once you have finished and reset chain id fir Z1-8 to A. 
> Tedious but possible! 
> 
> Or just run a few cycles of buccaneer with your structure - buccaneer should 
> do the job fir you...
> Eleanor
> 
> On Sat, 4 Feb 2023 at 22:11, Matt McLeod  > wrote:
> Hi all,
> 
> I have been refining a structure and somehow along the way the residue 
> numbers have completely shifted.  For instance, the first section of residues 
> are shifted by say 8 numbers, then there is a gap from where the resnumbers 
> go from 121, 151, 152, 153...and so on.  Its quite the mess.
> 
> Is there a way to take a sequence file with residue numbers correct and apply 
> these to the PDB file?  I have tried Renumber Residues in coot but this isnt 
> working, it just shifts some of them and does opposite shifts elsewhere since 
> its so discontinuous. Align and mutate just shifts them incorrectly from the 
> inputted sequence without applying the sequence file number to the PDB.
> 
> Any suggestions would be appreciated before I go and do this all manually...
> Matt
> 
> 
> 
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Re: [ccp4bb] Renumber residues working PDB file - Applying a sequences numbering to PDB file

[Eleanor Dodson]

Usually you can bully coot into doing it but by bit. Say you need to
renumber A 1-8. I often have to change the chain id to Z say then renumber
Z. And so on . Then go back once you have finished and reset chain id fir
Z1-8 to A. Tedious but possible!

Or just run a few cycles of buccaneer with your structure - buccaneer
should do the job fir you...
Eleanor

On Sat, 4 Feb 2023 at 22:11, Matt McLeod  wrote:

> Hi all,
>
> I have been refining a structure and somehow along the way the residue
> numbers have completely shifted.  For instance, the first section of
> residues are shifted by say 8 numbers, then there is a gap from where the
> resnumbers go from 121, 151, 152, 153...and so on.  Its quite the mess.
>
> Is there a way to take a sequence file with residue numbers correct and
> apply these to the PDB file?  I have tried Renumber Residues in coot but
> this isnt working, it just shifts some of them and does opposite shifts
> elsewhere since its so discontinuous. Align and mutate just shifts them
> incorrectly from the inputted sequence without applying the sequence file
> number to the PDB.
>
> Any suggestions would be appreciated before I go and do this all
> manually...
> Matt
>
> 
>
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[ccp4bb] Renumber residues working PDB file - Applying a sequences numbering to PDB file

[Matt McLeod]

Hi all,

I have been refining a structure and somehow along the way the residue numbers 
have completely shifted.  For instance, the first section of residues are 
shifted by say 8 numbers, then there is a gap from where the resnumbers go from 
121, 151, 152, 153...and so on.  Its quite the mess.

Is there a way to take a sequence file with residue numbers correct and apply 
these to the PDB file?  I have tried Renumber Residues in coot but this isnt 
working, it just shifts some of them and does opposite shifts elsewhere since 
its so discontinuous. Align and mutate just shifts them incorrectly from the 
inputted sequence without applying the sequence file number to the PDB.

Any suggestions would be appreciated before I go and do this all manually...
Matt



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