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I hate to toot my own horn, but it *could* be water. See:
Collins et al, PNAS, 102:16668
Non specificly bound water can appear to be smeared out, and water does
not need to be specifically bound in order to appear in hydrophobic cores.
Marcus Collins
*****************************************************************************
Marcus D. Collins
Gruner Biophysics Group, Cornell University Dept. of Physics, LASSP
(h) 607.347.4720 (w) 607.255.8678 (c) 607.351.8650
"You have opened a new door, and I share this with you,
for I have been where you are now."
*****************************************************************************
On Thu, 8 Dec 2005, Andrew Wong wrote:
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
>
>
> Hi
>
> Understood and agree. Perhaps my wordings in the original post can be a
> bit better.
>
> Perhaps I should ask what have others *found* to be inside the hydrophobic
> core/region :) Anyway, in one of the structures I'm working on, there'r 2
> (identical) hydrophobic cores, generated by 2mol/ASU (not NCS-averaged,
> yet). Each core has 2 blobs of stray density, all appear to have the same
> shape. They can't be H2O, neither shape nor size fit, but yet seems abit
> too small for MES (in the condition). Just curious what they are, that's
> all. It's a 1.6A data set.
>
> Anastassis Perrakis: "...'better modelling' not 'better R'.."
> Ok yes, better modelling :) Thanks
>
> Andrew
> --------------------
> PhD Student
> Dept of Biochemistry
> Queen's University
> Kingston ON Canada
>
> On Thu, 8 Dec 2005, Dirk Kostrewa wrote:
>
> > *** For details on how to be removed from this list visit the ***
> > *** CCP4 home page http://www.ccp4.ac.uk ***
> >
> >
> > 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:
> >
> > >*** For details on how to be removed from this list visit the ***
> > >*** CCP4 home page http://www.ccp4.ac.uk ***
> > >
> > >
> > >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
> > >
> > >
> > >
> > >
> >
> >
> > --
> >
> > ****************************************
> > 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
> > ****************************************
> >
> >
>
>
>
