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Re: [ccp4bb]: problem with Refmac5



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"David J. Schuller" wrote:
> 
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> 
> Hi,
> 
> I am having some trouble with Refmac5.  I am using CCP4 4.2.1, REFMAC
> 5.1.24.  I am seeing the problem both on a Linux box and on an Alpha/Tru64
> system.
> 
> I have a very early, rough version of my model from the first round of
> building.  I put it into REFMAC. Rigid body fitting went OK.  When I
> tried refinement with restraints, with the script below on the Linux box
> it blew up my Histidines and scattered them over a large volume.  I tried
> the same script on the Alpha, and a great number of residues were blown
> up.  Next, still on the Alpha, I added "WEIGHT MATRIX 0.2" to tighten the
> restraints. Most of the protein looked OK, but the Histidines were still
> blown apart.  I.e. on the Alpha with weight 0.2 it looked about like on
> the Linux with the default weight (0.5).
> 
> I checked the problems page and didn't see anything like this mentioned.
> My script is below. Are there any obvious errors? Should I drop the weight
> even lower for early refinement?
> 
> Thanks.
> 


 one excellent way to blow up a model with NCS restraints is if the
initial one has large differences between the different copies.
 HIS 15A one way round and HIS15B the other makes an ideal munching
scenario?


 Could that have happened?

 But it is also worrying that results on the Alpha and Linux are not the
same..

 Eleanor