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Dear Lynn Ten Eyck,
I fully agree with you and post this reply only because of the students
that are new to crystallography. Even interpretation of the electron
density of the chemically well known protein polypeptide chain has a
wide grey area: surface side chains, flexible loops and termini,
alternate conformations, etc. (you all know that, of course!).
Interpretation of waters, ions, or any other compounds from the
crystallization buffer is even more fuzzy. But I agree with you, that
one should try the best to get both a physically and chemically
reasonable model. I must admit, however, that even with a well-refined
protein with, say, 2 A with R/Free-R ~ 15/19% and good stereochemistry,
I still have the feeling that there are errors that I didn't
detect/correct, and this is certainly true. As in the saying " . . .
protein refinement is never finished but aborted . . ." (was it you,
Phil, who said that?)
Best regards,
Dirk.
Lynn Ten Eyck wrote:
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Please do *NOT* just add what are essentially content-free dummy atoms
just to lower the R. This just adds extra parameters to soak up
potentially valuable information about the quality of the structure.
The real refinement problem is to find a physically plausible model
that, properly adjusted, fits the data to within the experimental error
of the data. Uninterpreted blobs are not a molecular model. If you DO
put a molecular component on that density, you are in effect saying "I
really believe, just as strongly as I believe the conformation of the
main chain, that this density is (say) an acetate ion." Do you? If so,
put it in, but you have actual chemical evidence for the composition of
the protein chain.
Best regards,
Lynn Ten Eyck
--
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Dirk Kostrewa
Paul Scherrer Institut
Life Sciences, OFLC/110
CH-5232 Villigen PSI, Switzerland
Phone: +41-56-310-4722
Fax: +41-56-310-5288
E-mail: [EMAIL PROTECTED]
http://sb.web.psi.ch
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