Re: [ccp4bb] question about getting rid of model bias in refinement

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

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From: James Holton JMHolton {- at -} LBL {- dot -} GOV
Date: 2008-07-27

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Subject: Re: question about getting rid of model bias in refinement
From: "Das, Debanu" debanu {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2008-07-27

Hi Bill,
In PHENIX you can use the following commands for making different omit maps:

A simple composite omit map can be made by:
phenix.autobuild data=data.mtz model=coords.pdb composite_omit_type=simple_omit

An iterative build omit map:
phenix.autobuild data=w1.sca model=coords.pdb omit_box_pdb=target.pdb
composite_omit_type=iterative_build_omit

SA omit map:
phenix.autobuild data=w1.sca model=coords.pdb omit_box_pdb=coords.pdb
omit_res_start_list=3 omit_res_end_list=4 omit_chain_list=A
composite_omit_type=sa_omit

phenix.autobuild data=data.mtz model=coords.pdb omit_box_pdb=target.pdb composite_omit_type=sa_omit

For more details:
http://www.phenix-online.org/documentation/autobuild.htm#anch159

Regards,
Debanu.

-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of William G. Scott
Sent: Saturday, July 26, 2008 11:12 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] question about getting rid of model bias in refinement

Hi Sun:

It might be worth doing a simulated annealing omit refinement in phenix or CNS, with the residues in question omitted. CNS also allows you to make a composite-omit map. I haven't seen that in phenix yet but presumably it is doable.

Bill

William G. Scott

Contact info:
http://chemistry.ucsc.edu/~wgscott/

On Jul 25, 2008, at 10:53 PM, Sun Tang wrote:

> Hello Everyone,
>
> I have a question about getting rid of model bias in refinement with
> refmac. I solved the structure with molecular replacement. After final
> refinement of the structure, I found out some key amino acids in the
> structure and wanted to make sure their conformations are correct. I
> omitted these amino acids (by setting occupancy to zero) and refined
> the structure. I manually fit the amino acids into the density and
> refined the structure again. I found these amino acids return to the
> precious conformations even though the conformations I fit were
> different. Should I omit these amino acids from the beginning of the
> refinement? What is the best way to get rid of the model bias? Your
> suggestions are greatly appreciated!
>
> Best,
>
> Sun
>
>
>

CCP4bb navigation

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

Previous message:
Subject: Re: Beamline Stability Issues
From: James Holton JMHolton {- at -} LBL {- dot -} GOV
Date: 2008-07-27

Next message:
Subject: Re: MR problem --molrep
From: Carl_Soja allbette {- at -} GMAIL {- dot -} COM
Date: 2008-07-27