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Re: [ccp4bb]: problem with Refmac5



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Thanks for the tips.  My resolution is 1.8.  I did another round of 
modeling today, then ran some geometry idealization before restrained 
refinement.  This time I used a Matrix weight of 0.2 with no problem.  I 
seem to be past the trouble, which I will attribute to the bad geometry 
of my initial model (exactly why I wanted to refine it! :)

My R is down to 0.33 already, and I still have the NCS restraints tight.


Cheers,

On Sat, 16 Nov 2002, Aleks Roszak wrote:

> You did not mention what resolution of data you are refining against. I am
> using the same version of Refmac5, 5.1.24, on SGI machine (I don't think your
> problem has anything with the system you are running it on ...) and I see very
> strong dependence (not linear) of the 'Weight Matrix' factor on the resolution
> of my data to keep the geometry decent. For example, for refinements of very
> similar structures (the same space group, cell and the no. of molecules in the
> AU) at resolutions 1.95A, 2.5A. 2.75A, I use weight matrix of 0.3, 0.1 and
> 0.07, respectively, while for some strong data 'artificially' cut at 2.1A
> (diffracting to 1.9A) I have used 0.35. For another structure, at 2.0A, I have
> used 0.24.
> 
> I think to be able to use weight matrix of 0.5, or higher, you need still
> higher resolution data, and I did not run such refinements using Refmac version
> 5.1.24.
> When using Refmac 4 in the past at 1.5A resolution I have used weight matrix
> even as high as 3.0 but I think you can't compare these values between versions
> 4 and 5. Also, the geometry, and especially planarity of rings like histidines,
> was not that good in version 4 as it is in version 5, and to compensate I had
> to play with some geometry restraints, which was not very convenient.


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                        David J. Schuller
                        modern man in a post-modern world
                        MacCHESS, Cornell University
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