Re: [ccp4bb] Refmac5 restrained refinement could not keep the changes made in Turbo

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

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Subject: Re: MolRep with Phaser using a partial existing solution
From: Tim Grune tim {- dot -} grune {- at -} SYNCHROTRON {- dot -} VIC {- dot -} GOV {- dot -} AU
Date: 2007-05-17

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Subject: Re: MolRep with Phaser using a partial existing solution
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-05-18

Subject: Re: Refmac5 restrained refinement could not keep the changes made in Turbo
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-05-18

Have you adjusted the wighting scheme from 2A - you want to relax the
geometric restraints at 1.2A - best to use WEIGHT AUTO..

Eleanor

XJ XJ wrote:
> Dear all,
> I am having a problem with refining my structure using
> refmac5. Basically, I am trying to make some small
> changes to several places on the backbone. But the
> thing is that, after restrained refinement, the
> changes I made would be all gone and the chain stayed
> exactly where they were before I made those changes.
> I'm using Turbo for building the model. The
> resolution I'm working on now is 1.2 A.
> The refmac was working fine when I was working at a
> lower resolution (2 A) and I was able to rebuild a
> whole helix and refine successfully with refmac.
> Right now, I am still able to change rotamers of
> single residues and refmac will keep these type of
> changes for me. It is only when changes are made on
> the backbones that refmac will refine the structure
> back to what it was before the changes were made.
> Other than refining to highest resolution 1.2 A, I'm
> pretty much using all the default parameters from the
> restrained refinement, except that, under Geometric
> parameters, I changed all the overall wt restraints
> from 1.0 to 2.0. Weighing term has been varied from
> 0.3 to 0.5 and no difference was made.
> I guess it's probably some small mistakes I made while
> running the refmac, but I can't figure out what it is.
> Can anyone help me out real quick? Thanks!
> Regards,
> Xiaofei
>
>
>
> ____________________________________________________________________________________Boardwalk for $500? In 2007? Ha! Play Monopoly Here and Now (it's updated for today's economy) at Yahoo! Games.
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>

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

Next message:
Subject: Re: MolRep with Phaser using a partial existing solution
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-05-18