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If poor geometry is the problem, it might be worth running your model through the molprobity server. This validation software will point out potential problems, i.e. Ramachandran outliers or poor rotomers. The website for the server is: http://molprobity.biochem.duke.edu/ -bob On 7/5/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** an 11% gap seems worrisome to me. When things are that overfit, I think it can be harder to find the problems just by looking at how the model-as-built fits the 2FoFc. There are lots of "bad" ways to get a side chain into density. You should check the geometry carefully, and if a residue has poor a fit in the Ramachandran plot, or if it has sub-optimal side chain dihedrals, first lego the backbone, then lego the side chain, and you'll probably find a better way to stuff the same thing into the density. It seems to me that the more automatic PI's think map-fitting should be, the more eclipsed leucines land in the databank ... -Phoebe At 09:55 AM 7/5/2006, you wrote: >*** For details on how to be removed from this list visit the *** >*** CCP4 home page http://www.ccp4.ac.uk *** > > >Did you refine the model after the molecular replacement? If so, do not do >so. Look at the maps directly and try to correct for any errors you see, >especially considering the difference maps (at 3 sigma). > >If you run refinement without looking at the maps it would smoothen the >differences between the MR Model and your data and that is not desired at >this stage. > >Tim > >-- >Tim Gruene >Institut fuer anorganische Chemie >Tammannstr. 4 >D-37077 Goettingen > >GPG Key ID = A46BEE1A > > >On Wed, 5 Jul 2006, [utf-8] Li Sheng wrote: > > > *** For details on how to be removed from this list visit the *** > > *** CCP4 home page http://www.ccp4.ac.uk *** > > > > > > Dear Tim Gruene, > > > > This structure is a mutant of a protein previously solved. The space > groups for the wild type protein is P2(1)2(1)2(1) for one crystal and > C222(1) for the other. The conditions of crystallization for the two > proteins are different. Of course, this structure is solved by molecular > replacement. We have not added water molecules now. > > We have tried both Rafmac and CNS, and the restraints was set to 0.05. > But we'll try again. Anyway, thank you all. > > > > > > ================= 2006-7-5 15:51, your message: Re: > [ccp4bb]:================= > > > > -----BEGIN PGP SIGNED MESSAGE----- > > Hash: SHA1 > > > > How did you create to this model? Was the gap between R and Rfree this > > high from the very beginning? If not, try to find out where the gap became > > so high. > > > > - - did you introduce too many water molecules? You can overfit your data > > this way by pretending noise were waters > > - - do you have to tighten the weights of stereochemical restraints? If you > > use refmac5, try setting it to 'AUTO' or something below 0.1. A good > > indicator off the weight being too high is the list of rmsd's at the end > > out the refmac5 logfile. > > > > Look at your difference map (fofc) at +/- 3 sigma, not 2 sigma. You want > > that map to show as little density as possible (either 3 or 2 sigma, but 3 > > is more realistic, I dare say). > > > > Tim > > > > - -- > > Tim Gruene > > Institut fuer anorganische Chemie > > Tammannstr. 4 > > D-37077 Goettingen > > > > GPG Key ID = A46BEE1A > > > > > > On Wed, 5 Jul 2006, [gb2312] Li Sheng wrote: > > > > > *** For details on how to be removed from this list visit the *** > > > *** CCP4 home page http://www.ccp4.ac.uk *** > > > > > > > > > Hi, dear all, > > > > > > Please do me a favour. I ever collected a data set of 2.7A. The space > > > group is C2. The model fit the 2fofc map and the omit map very well. The > > > R factor > > > is 0.26 now but R free is 0.37 and can not be minished. What kind of > > > error can cause such a gap between R factor and R free? > > > Thanks in advance. > > > > > > > > > Sincerely yours, > > > Li > > > 2006.06.07 > > > > > -----BEGIN PGP SIGNATURE----- > > Version: GnuPG v1.4.1 (GNU/Linux) > > > > iD8DBQFEq8PcUxlJ7aRr7hoRAmpBAJ49RvoOuaXYNtD0S/ErcqCctbsHUgCg9+rG > > 8xzBUsvicmQqcAYD62OU+K4= > > =Pb/D > > -----END PGP SIGNATURE----- > > > > > > . > > > > > > > ============================================================================================ > > > > > > Sincerely yours, > > Li Sheng > > 2006-07-05 > > __________________________________________ > > Email:[EMAIL PROTECTED] > > Institute of Biochemistry and Cell Biology > > Institutes for Biological Sciences > > Chinese Academy of Sciences > > 320 Yue-Yang Road, Shanghai 200031, China > > Tel: +86-21-5492-1217 > > __________________________________________ > > --------------------------------------------------------------------------------------------------------------------------- Phoebe A. Rice Assoc. Prof., Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 fax 773 702 0439 http://bmb.bsd.uchicago.edu/index.html http://www.nasa.gov/mission_pages/cassini/multimedia/pia06064.html
