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: chromophore in GFP
From: sheng CUI sheng {- at -} LMB {- dot -} UNI-MUENCHEN {- dot -} DE
Date: 2008-08-01

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Subject: Re: sequential renumbering of a messed up pdb file
From: "William G {- dot -} Scott" wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2008-08-01

Dear Martin et al:

This, along with some scripting in coot and my favorite shell (zsh),
did the trick.

Many thanks to all who replied, and apologizes for what in retrospect
must have been a very poorly-worded question.

Maybe this functionality can be incorporated in the next release of
perlmole.

Bill Scott

On Jul 31, 2008, at 9:05 PM, Martin.Laurberg wrote:

> Bill,
> Almost there then (I wrote the line without checking)..
>
> I moved the 'P' one position to the left and now it works, provided
> first
> atom record of every atom record is the phosphor (/ P /) atom :
>
>
> perl -ne 'BEGIN{$i=0}if (/^ATOM/)
> {if (substr($_,12,4) =~ / P /){$i++};
> substr($_,22,4,sprintf("%4.0f",$i))}{print}' file.pdb
>
>
>
>
>
> On Thu, 31 Jul 2008, William G. Scott wrote:
>
>> turned them all to zeros
>>
>>
>> William G. Scott
>>
>> Contact info:
>> http://chemistry.ucsc.edu/~wgscott/
>>
>>
>> On Jul 31, 2008, at 5:03 PM, Martin.Laurberg wrote:
>>
>>> Bill, if each residue starts at the same atom name, something
>>> close to
>>> this might work:
>>>
>>> perl -ne 'BEGIN{$i=0}if (/^ATOM/){if (substr($_,12,4) =~ / P /){$i+
>>> +};
>>> substr($_,22,4,sprintf("%4.0f",$i))}{print}' file.pdb
>>>
>>>
>>> /Martin
>>>
>>>
>>> --
>>> Martin Laurberg, PhD
>>> Noller Laboratory
>>> 225 Sinsheimer Laboratories
>>> University of California at Santa Cruz
>>> CA-95064 Santa Cruz
>>> USA
>>>
>>> Tel +1 (831) 459 35 84
>>> Fax +1 (831) 459 37 37
>>>
>>>
>>> On Thu, 31 Jul 2008, William Scott wrote:
>>>
>>>> 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: chromophore in GFP
From: sheng CUI sheng {- at -} LMB {- dot -} UNI-MUENCHEN {- dot -} DE
Date: 2008-08-01

Next message:
Subject: Pymol movie ration along any axis
From: Jerry McCully for-crystallizaiton {- at -} HOTMAIL {- dot -} COM
Date: 2008-08-02