Re: [ccp4bb] Rfree is 20%,why still green and red density?

2013-06-27 Thread James Holton
Auftrag von *?? *Gesendet:* Mittwoch, 26. Juni 2013 06:05 *An:* CCP4BB@JISCMAIL.AC.UK *Betreff:* [ccp4bb] Rfree is 20%,why still green and red density? Hi everyone, I now meet some problems when trying to solve structure.Space group is P6422, and Mathews function shows

[ccp4bb] AW: [ccp4bb] Rfree is 20%,why still green and red density?

2013-06-26 Thread Herman . Schreuder
An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Rfree is 20%,why still green and red density? Hi everyone, I now meet some problems when trying to solve structure.Space group is P6422, and Mathews function shows there are 4 molecules in one asymmetry unit. However, Phenix-autobuild shows only 2

Re: [ccp4bb] AW: [ccp4bb] Rfree is 20%,why still green and red density?

2013-06-26 Thread Bernhard Rupp
The Matthews function is based on an average protein crystal with 50% solvent. Not sure what that a 'Matthews function' exactly would be - and that an assumption of 50 solvent content is made anywhere in the Vm calculation is new to me. The only defensible prior that goes into the

Re: [ccp4bb] Rfree is 20%,why still green and red density?

2013-06-26 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jiang Yan, how many reflections to you have in the free-set. At P6422 with a resolution of 2.8 you may have only a few hundred and thus not get a reliable Rfree value. Its low value may be due to overfitting. What does the cyrstal packing look

Re: [ccp4bb] Rfree is 20%,why still green and red density?

2013-06-26 Thread Bernhard Rupp
you may have only a few hundred and thus not get a reliable Rfree value. The estimate for the error in R free as a function of the number of reflections is as follows: Brunger initially estimated^35 that the uncertainty in R-free is proportional to (Nref )^-1/2, which is reasonable to assume

Re: [ccp4bb] Rfree is 20%,why still green and red density?

2013-06-26 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Sure, but in P6422 with 2.8A I'd say that 5% of reflections are more likely near 40-50 than 'a few hundreds' if the cell too small. And most people simply flag 5% of their reflections without checking how many these really are. Splitting these up into

Re: [ccp4bb] Rfree is 20%,why still green and red density?

2013-06-26 Thread Robbie Joosten
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard Rupp Sent: Wednesday, June 26, 2013 13:31 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Rfree is 20%,why still green and red density? you may have only a few hundred and thus not get a reliable Rfree value. The estimate for the error in R

[ccp4bb] Rfree is 20%,why still green and red density?

2013-06-25 Thread 姜艳
Hi everyone, I now meet some problems when trying to solve structure.Space group is P6422, and Mathews function shows there are 4 molecules in one asymmetry unit. However, Phenix-autobuild shows only 2 molecules in on one asymmetry unit, after refinement, Rfree=20%,(resolution is 2.8A).