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Re: [ccp4bb]: problem with Refmac5
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Hi David,
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.
I hope this wiil be of help,
Cheers,
Aleks
On Nov 15th, David J. Schuller wrote:
> Subject: [ccp4bb]: problem with Refmac5
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> *** CCP4 home page http://www.ccp4.ac.uk ***
>
> 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.
>
> =======================================================================
> "Reductionism is one of those words that makes me want
> to reach for my revolver." - Richard Dawkins
> =======================================================================
> David J. Schuller
> modern man in a post-modern world
> MacCHESS, Cornell University
> djs63@cornell.edu
> ----------------------------------
> #!/bin/csh -f
> #
> refmac5 \
> HKLIN ../../ccp4/lys_free.mtz \
> HKLOUT refm02.mtz \
> XYZIN refm01.pdb \
> XYZOUT refm02.pdb \
> >refmac2.out \
> <<EOF
> #
> LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag
> LABO FC=FC PHIC=PHIC FWT=2FOFCWT PHWT=PH2FOFCWT -
> DELFWT=FOFCWT PHDELWT=PHFOFCWT
> MAKE HYDR ALL
> MAKE CHECK 0
> REFI TYPE REST
> REFI RESI MLKF
> REFI BREF ISOT
> NCSR NCHAINS 8 CHAINS A B C D E F G H NSPANS 1 1 310 1
> #
> SCAL TYPE BULK
> NCYC 15
> MONI FEW
> end
> EOF
> #
>
>-- End of excerpt from David J. Schuller
--
**************************************************************************
* Aleksander W. Roszak, Ph.D. E-mail: aleks@chem.gla.ac.uk *
* Protein Crystallography Fax: +44-(0)141-330 4888 *
* Department of Chemistry Tel: +44-(0)141-330 4476 *
* University of Glasgow +44-(0)141-330 6180 *
* Glasgow G12 8QQ +44-(0)141-330 6449 *
* Scotland, U.K. Web: http://www.chem.gla.ac.uk/~aleks *
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