Thank you so much for your replies. CCP4 refinement file is showing warnings that the Glc units are at distance (1.4-2.1A) greater than the acceptable one by the program (1.33A) from each other even though I got the model from a published pdb file. so the pdb file generated only shows me dotted lines instead of bonds, but when I do a real space refinement, the Glc come closer together and show full bonds then. Am I on the right track here?
Thanks again, Remie On May 21, 2014, at 7:28 AM, Jon Agirre <[email protected]> wrote: Hi, be very careful with the link records that Refmac generates for the sugars. If the wrong anomer is indicated (i.e. beta linkage for MAN, which should be alpha), the refinement process will distort them (e.g. generate something else instead of a 4C1 conformation) and that has an impact on the R-factors and especially on the geometry. Depending on how many sugars you have in your structure and how well refined they are, you could see differences in the R-factors ranging from 0% to 2%. Jon -- Dr Jon Agirre York Structural Biology Laboratory / Department of Chemistry University of York, Heslington, YO10 5DD, York, England http://www.york.ac.uk/chemistry/research/ysbl/people/research/jagirre/ +44 (0) 1904 32 8253 On May 21, 2014, at 6:13 AM, Tim Gruene <[email protected]> wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear Remie, > > the R-factor is a complicated thing that depends on things like > weighting factors and solvent model - several things that are not part > of your model and that need to be adjusted by the refinement program > during refinement. > > That's why I think what you observe is pretty normal - I wouldn't worry. > > Best, > Tim > > On 05/20/2014 06:55 PM, Remie Fawaz-Touma wrote: >> Hi all, >> >> I am trying to refine a structure in CCP4 and the final R factor is >> about 1% lower than the initial but for the first “task/cycle” >> within the same refinement job in CCP4, R factor starts off higher >> than the input data R factor. >> >> I have a structure with multiple sugars attached, I did the first >> refinement after building the sugars with a lib file that worked >> well and the R factor did go down significantly but every time I >> try to refine again to lower it more, the above happens. >> >> Any suggestions? >> >> Thank you. >> >> Remie >> > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Icedove - http://www.enigmail.net/ > > iD8DBQFTfHwtUxlJ7aRr7hoRAo9lAKCqbUz1ceG6JY9BeX0SHPiz8wsneQCg0RGA > WKG9cTujB6wbzMSzgxZNtd4= > =O3jF > -----END PGP SIGNATURE-----
