I may be a pessimist, but I'd focus my efforts on getting
experimental phases. It can be hard to tell a correct
molecular replacement solution from garbage with that kind of
data, and it can be a real time sink because its hard to know
when to quit.
If you can get an SeMet data set, even it it doesn't provide
enough phasing power to crack the problem, you can use the
positions of Se peaks in anomalous diff maps to check possible
molecular replacement solutions.
Good luck!
Phoebe Rice
---- Original message ----
>Date: Fri, 21 May 2010 20:23:23 +0530
>From: Vineet Gaur <vineetgaur1...@gmail.com>
>Subject: Re: [ccp4bb] molecular replacement
>To: CCP4BB@JISCMAIL.AC.UK
>
> Also check if you have correctly estimated no. of
> molecules in asymmetric unit.
>
> On Fri, May 21, 2010 at 4:58 PM, Tim Gruene
> <t...@shelx.uni-ac.gwdg.de> wrote:
>
> Dear intekhab,
>
> a few suggestions:
> - are you sure of the space group or might there
> be alternatives?
> - is you protein globular or modular, i.e., is it
> worth running MR with stable
> subdomains one after the other?
> - try a poly-alanine model (e.g. chainsaw can do
> this for you, pdbset probably,
> too)
> - did you get overloads? If so, collect a low
> resolution pass to get correct
> intensities even at the poor resolution end.
> - what is your low resolution limit? Did you use
> the default or could you extend
> it?
> - did your crystal(s) suffer from radiation
> damage? It might be worth collection
> only a complete data set with not too high
> multiplicity.
>
> Good luck, Tim
> On Fri, May 21, 2010 at 08:01:10PM +0900, intekhab
> alam wrote:
> > Hi all
> > I am trying to do molecular replacement with low
> resolution (4Å) using
> > Molrep and Phaser.
> >
> > Overall R-factor is 11.3%, completeness 95.4%,
> I/sigma 2, and Chi^2 0.95.
> >
> > Identities between my protein and templates were
> more than 80%.
> >
> > I couldn’t get correct solution.
> >
> > Rotation function, translation score, and
> contrast were low, and they had no
> > significance, though I changed the range of
> resolution.
> >
> > Molrep suggested solution coordinates clashed
> with symmetry molecules.
> >
> > I tried MR after remove clashed regions, but
> another clashes happened.
> >
> > In the case of phaser, there were many clashes,
> too.
> >
> > Please, give me any suggestion.
> > Should I concern about any options when I run MR
> programs?
> >
> > Hope you guys will be interested to answer!!!!!!
> > Thanks in advance
> >
> >
> > --
> > INTEKHAB ALAM
> > LABORATORY OF STRUCTURAL BIOINFORMATICS
> > KOREA UNIVERSITY, SEOUL
>
> --
> --
> Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
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Phoebe A. Rice
Assoc. Prof., Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
RNA is really nifty
DNA is over fifty
We have put them
both in one book
Please do take a
really good look
http://www.rsc.org/shop/books/2008/9780854042722.asp
