Re: [ccp4bb] antibody refinement in REFMAC with Kabat numbering

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

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Subject: Re: antibody refinement in REFMAC with Kabat numbering
From: John Pak john {- dot -} pak {- at -} UTORONTO {- dot -} CA
Date: 2007-04-05

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From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2007-04-06

Subject: Re: antibody refinement in REFMAC with Kabat numbering
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-04-05

It looks like a bug. Insertion code should have been used in NCS
restraint definitions. It seems it does not. I will try to fix
it asap.

Insertions are usually no problem. Problems arise when you have
deletions (i.e. residue numbering is
not sequential). Then you need to use LINK record with TRANS name for
the link.

Garib

On 5 Apr 2007, at 18:43, John Pak wrote:

> Thank you for the replies everyone.
> I ended up removing NCS in refmac, and that seems to have corrected
> the problem. Now the inserted residues (100A, 100B, etc) seem to
> have refined properly, so I guess it was an NCS issue trying to put
> all the similarily labelled residues to the same spot.
>
> Anyways, I want to have NCS refinement, so I'll try putting the
> LINK info in the header and try NCS again.
>
>
>>
>> -----Original Message-----
>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf
>> Of John
>> Pak
>> Sent: Thursday, April 05, 2007 7:40 AM
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: [ccp4bb] antibody refinement in REFMAC with Kabat numbering
>>
>> Hi all.
>>
>> I'm currently refining an Fab structure. All was going reasonably
>> well
>> until I renumbered the PDB according to the Kabat numbering
>> convention.
>> After which, REFMAC does not refine the inserted residues properly
>> (ie.
>> residues 82A, 82B, 100A, 100B, 100C, etc.). It refines these
>> residues into
>> a steric jumble. I think REFMAC can't recognize that the residues
>> are
>> connected or something.
>>
>> So my question is, how do you refine this type of PDB in REFMAC?
>> Or do you
>> just wait until the refinement is done, then change all the
>> residue numbers
>> and connect entries in the header afterwards?
>>
>>
>>
>

CCP4bb navigation

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

Previous message:
Subject: Re: antibody refinement in REFMAC with Kabat numbering
From: John Pak john {- dot -} pak {- at -} UTORONTO {- dot -} CA
Date: 2007-04-05

Next message:
Subject: predicting protease cleavage sites in proteins?
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2007-04-06