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:[log in to unmask]] On Behalf Of William G. Scott
Sent: Saturday, July 26, 2008 11:12 AM
To: [log in to unmask]
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
>
>
>
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