Basically my reasoning for doing this is a low data-to-parameter ratio, which makes B-factor refinement unfeasible. So far I have had nice results with breaking the complex into rigid subdomains. So i was basically just thinking of a way I could refine the structure best, without using too many parameters.
I see now how this can be done in Phenix. I will give it a try.
Thanks for all of your suggestions!
I see now how this can be done in Phenix. I will give it a try.
Thanks for all of your suggestions!
Jason Porta
Graduate Student
Eppley Structural Biology Facility
Dept. Biochemistry & Molecular Biology
University of Nebraska Medical Center
Omaha, NE 68198
(402) 559-5533
To: CCP4BB@JISCMAIL.AC.UK
From: Pavel Afonine <pafon...@lbl.gov>
Sent by: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK>
Date: 12/01/2009 03:31PM
Subject: Re: [ccp4bb] Refining residues as rigid bodies
Hi Jason,
yes, technically you can refine each residue as a rigid body in
phenix.refine (as Fred explained), but:
- why wouldn't you consider a more sensible (in my opinion) strategy
running a combined refinement job that contains rigid body refinement of
bigger rigid domains, SA in Cartesian or torsion angle space, as well as
ADP refinement (group or isotropic individual)? You can do it all in one
phenix.refine run.
- often the side chains are far away from the density so it is beyond
the convergence radius of gradient driven minimization or SA to put them
into density. To address this case phenix.refine has "a still
experimental" option that fixes side chains automatically by performing
real-space grid search and local real-space refinement performed for
each side chain, going residue-by-residue. Details are explained here
(slide #11):
http://cci.lbl.gov/~afonine/rsr/afonine_05OCT2009_.pdf
Let me know if you have questions.
Pavel.
On 12/1/09 1:18 PM, Partha Chakrabarti wrote:
> Hi Jason,
>
> Instead of doing rigid body refinement of each residue, you may
> consider rigid.inp of CNS or an equivalent strategy in Phenix which
> will do SA, rigid body and B factor refinement, followed by either
> composite omit (CNS) or 'prime & switch' of phenix (rather resolve) to
> "fix" the side chains.
>
> Cheers, Partha
>
>
>
> On Wed, Dec 2, 2009 at 2:00 AM, Jason Porta <jpo...@unmc.edu> wrote:
>
>> Hi everybody,
>>
>> I am currently refining a 3 ang structure and would like to do rigid body
>> refinement treating each residue as a separate rigid body. I have looked
>> through several refinement packages, but do not see a way to do this without
>> having to type each residue in manually (there are 512 residues total).
>> Preferably, I would carry out the refinement in Refmac5, but any advice
>> pertaining to any program would be greatly appreciated.
>>
>> Thanks in advance for any help.
>>
>> Jason Porta
>> Graduate Student
>> Eppley Structural Biology Facility
>> Dept. Biochemistry & Molecular Biology
>> University of Nebraska Medical Center
>> Omaha, NE 68198
>> (402) 559-5533
>>
>>
