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Re: [ccp4bb] How to refine large moleculars? |
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CCP4bb navigationCCP4bb <-- 2008 <-- January 2008 <-- 09 January 2008Subject: Re: How to refine large moleculars? From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK Date: 2008-01-09 I use all the COOT validation tools - Ramachandran, diff map peaks etc to try to pinpoint errors. Also anomalous difference maps hoping to verify S positions and check the sequence fitting. You could let Arp/Warp rebuild it from the existing model and check it gives the same interpretation.. Can you get higher resolution data? It might be worth pushing the data integration a bit further since I think Arp/Warp works better the higher the resolution. Eleanor Juergen Bosch wrote: > How does the Molprobity report look like ? > > How many Rama outlieres, bad Cbeta, rotamers ? > What's your percentile ? > Look at the multicriterion chart to fix your problems :-) > > http://molprobity.biochem.duke.edu/ > > Juergen > > Yongchao Li wrote: > >> Dear all, >> Thanks for all replies. >> After water addition, R work is 0.27 and R free 0.33. >> TLS and NCS results no significant approve. >> Space group seem right, other space group like P21212 is worse. >> From truncate result, it is not twinning. >> >> More detail is below: >> space group P212121 a=150.099 b=148.581 c=153.429 >> resolution: 2.0 A >> completeness: 92.3 % (58%), near complete to 2.15 A.(last shell 90.7%) >> Rsym: 0.076 (34.0) >> I/sigma = 20 (2.5) >> >> >> >> */Chavas Leo >> >> Dear Li, >> >>> I don't know how to reduce them. >> >> >> I second Tim in the fact that you should give more details on what >> you tried to do as well as your statistics (resolution, data >> quality etc.). For instance, did you had water molecules? Did you >> try TLS refinement? Do you have a wrong symmetry? >> >> HTH. >> >> Kind regards. >> >> Leo >> ------------------------------------------------------------ >> Chavas Leonard, Ph.D. >> Research Associate >> ------------------------------------------------------------ >> Faculty of Life Sciences >> The University of Manchester >> The Michael Smith Building >> Oxford Road >> Manchester Lancashire >> M13 9PT >> ------------------------------------------------------------ >> Tel: +44(0)161-275-1586 >> e-mail: Leonard.Chavas@manchester.ac.uk >> >> >> >> >> ------------------------------------------------------------------------ >> Be a better friend, newshound, and know-it-all with Yahoo! Mobile. >> Try it now. >> > > > > > CCP4bb navigationCCP4bb <-- 2008 <-- January 2008 <-- 09 January 2008 |
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