Re: [ccp4bb] verifying a molecular replacement solution (test case where the true structure is known)

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

Previous message:
Subject: Re: Molecular Replacement
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-01-19

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Subject: cannot find the other molecule in the asymmetric unit
From: Xun Lu xluncsu {- at -} GMAIL {- dot -} COM
Date: 2010-01-19

Subject: Re: verifying a molecular replacement solution (test case where the true structure is known)
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-01-19

Ask Kevn Cowtan for his newest csymmatch ( or is it in ccp4.6.3?)

csymmatch -pdbin-ref sol1.pdb -pdbin sol2.pdb

It checks origins as well as moving sol2 to the closest symmetry copy of
sol1.pdb

A brilliant program - should be part of many many pipelines..

Eleanor

Martyn Winn wrote:
> reforigin
> http://www.ccp4.ac.uk/dist/html/reforigin.html
> Does exactly what you want, but requires that the 2 PDB files have the
> same atoms - the CAONLY option can help with missing atoms, but it still
> won't work unless you have mutated your search model to the target
> sequence.
>
> solution_check
> A utility from the Balbes package, included as a stand-alone binary in
> the latest ccp4.
>
> Alternative origins are documented in:
> http://www.ccp4.ac.uk/dist/html/alternate_origins.html
>
> HTH
> Martyn
>
> On Mon, 2010-01-18 at 11:47 +0900, Francois Berenger wrote:
>> Hello,
>>
>> 1) In the case I know the true structure (I am verifying I use Phaser
>> correctly), is there a program to do so?
>>
>> Some other questions, if I am to write this program by myself:
>>
>> 2) is there a list somewhere of the translation ambiguities for
>> each spacegroup?
>> For example, in P1 it would say me any translation on any axis
>> is fine.
>>
>> 3) is there a list of permissible origins for each space group?
>> For example, in P212121 it would say me there are 8 possible choices
>> and list them for me.
>>
>> I already know of symop.lib, but I don't think it has some of the
>> information I am looking for.
>> I also know the csymmatch example program of the clipper library, it
>> does part of what I intend to do.
>>
>> Thanks a lot,
>> Francois.

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

Previous message:
Subject: Re: Molecular Replacement
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-01-19

Next message:
Subject: cannot find the other molecule in the asymmetric unit
From: Xun Lu xluncsu {- at -} GMAIL {- dot -} COM
Date: 2010-01-19