Re: [ccp4bb] molecular replacement

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

Previous message:
Subject: molecular replacement
From: intekhab alam faisaldbg {- at -} GMAIL {- dot -} COM
Date: 2010-05-21

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Subject: Re: Question: Refmac5 stats reported in pdb REMARK 3
From: Christine Zardecki zardecki {- at -} RCSB {- dot -} RUTGERS {- dot -} EDU
Date: 2010-05-21

Subject: Re: molecular replacement
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2010-05-21

Dear intekhab,

a few suggestions:
- are you sure of the space group or might there be alternatives?
- is you protein globular or modular, i.e., is it worth running MR with stable
subdomains one after the other?
- try a poly-alanine model (e.g. chainsaw can do this for you, pdbset probably,
too)
- did you get overloads? If so, collect a low resolution pass to get correct
intensities even at the poor resolution end.
- what is your low resolution limit? Did you use the default or could you extend
it?
- did your crystal(s) suffer from radiation damage? It might be worth collection
only a complete data set with not too high multiplicity.

Good luck, Tim

On Fri, May 21, 2010 at 08:01:10PM +0900, intekhab alam wrote:
> Hi all
> I am trying to do molecular replacement with low resolution (4Ã…) using
> Molrep and Phaser.
>
> Overall R-factor is 11.3%, completeness 95.4%, I/sigma 2, and Chi^2 0.95.
>
> Identities between my protein and templates were more than 80%.
>
> I couldnâ€™t get correct solution.
>
> Rotation function, translation score, and contrast were low, and they had no
> significance, though I changed the range of resolution.
>
> Molrep suggested solution coordinates clashed with symmetry molecules.
>
> I tried MR after remove clashed regions, but another clashes happened.
>
> In the case of phaser, there were many clashes, too.
>
> Please, give me any suggestion.
> Should I concern about any options when I run MR programs?
>
> Hope you guys will be interested to answer!!!!!!
> Thanks in advance
>
>
> --
> INTEKHAB ALAM
> LABORATORY OF STRUCTURAL BIOINFORMATICS
> KOREA UNIVERSITY, SEOUL

--
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

CCP4bb navigation

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

Previous message:
Subject: molecular replacement
From: intekhab alam faisaldbg {- at -} GMAIL {- dot -} COM
Date: 2010-05-21

Next message:
Subject: Re: Question: Refmac5 stats reported in pdb REMARK 3
From: Christine Zardecki zardecki {- at -} RCSB {- dot -} RUTGERS {- dot -} EDU
Date: 2010-05-21