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Re: [ccp4bb]: molecular replacement woes!
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Hello,
While several colleagues have pointed out the possibility of wrong space
group assignment, I would like to say something else.
> (monitor no. is .262) but on minimization refinement i get unreasonable r
> and free_r values. my final r is 0.5163 and the final free_r is 0.5231.
This is not particularly bad, if it is just after minimization. The
important thing is does the Rfree drop? I suppose you have checked the MR
solution has no spatial clashes with symmetry neighbours? At this point
you can calculate 2Fo-Fc map and see if you have reasonably good and
connected density surrounding your model, especially in regions that you
expect high structural homology, e.g. beta-sheets. Also I would do a
simulated annealing to see if Rfree drops. One more thing, when you do the
first few rounds of refinements, do not use all your high resolution data
straight away. You should start with a high resolution limit that is more
or less consistent with the one you used to do MR and increase this
gradually as refinement goes on. And you also need to check the overall
B-factor after minimization or SA. If your MR solution is wrong, chances
are you can get unreasonably low B-factors and they got all reset to zeros.
Wai
===================================================================
Yu Wai CHEN, Ph.D. .................. email:ywc@mrc-lmb.cam.ac.uk
Centre for Protein Engineering, tel:+44-(0)1223-402148
MRC Centre, Hills Rd, Cambridge CB2 2QH, UK fax:+44-(0)1223-402140
WWW homepage: http://www.mrc-cpe.cam.ac.uk/~ywc