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

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CCP4bb <-- 2007 <-- May 2007 <-- 17 May 2007

Previous message:
Subject: LINK record in PDB file for REFMAC5?
From: Jie Liu jie {- at -} TRIMER {- dot -} MED {- dot -} CORNELL {- dot -} EDU
Date: 2007-05-17

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Subject: MolRep with Phaser using a partial existing solution
From: Jay Thompson jay {- dot -} xtalman {- at -} GMAIL {- dot -} COM
Date: 2007-05-17

Subject: Refmac5 restrained refinement could not keep the changes made in Turbo
From: XJ XJ nesky_jia {- at -} YAHOO {- dot -} COM {- dot -} CN
Date: 2007-05-17

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

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CCP4bb navigation

CCP4bb <-- 2007 <-- May 2007 <-- 17 May 2007

Previous message:
Subject: LINK record in PDB file for REFMAC5?
From: Jie Liu jie {- at -} TRIMER {- dot -} MED {- dot -} CORNELL {- dot -} EDU
Date: 2007-05-17

Next message:
Subject: MolRep with Phaser using a partial existing solution
From: Jay Thompson jay {- dot -} xtalman {- at -} GMAIL {- dot -} COM
Date: 2007-05-17