Re: [ccp4bb] R-free flag problem

Dear all, Thank you very much for your suggestions. I try Pavel's easy method. Hopefully, the result from phenix.model_vs_data would be enough for PDB.   Best wishes,   Vinson     发件人： Pavel Afonine pafon...@lbl.gov 收件人： PHENIX user mailing list pheni...@phenix-online.org 抄 送：

Re: [ccp4bb] R-free flag problem

Dear Vinson, I would still be interested about what was the cause of the missing R-free flags and how you resolved it (I hope I did not miss an email). Kind regards, Tim On Fri, Oct 22, 2010 at 02:33:03PM +0800, Vinson LIANG wrote: Dear all, Thank you very much for your

[ccp4bb] coot-0.5.2-osx-universal.dmg.gz

I am looking for coot-0.5.2-osx-universal.dmg.gz Anybody out there that can help? - J. -

Re: [ccp4bb] Regarding space group P1, P21

Dear CCP4BB members, Thank you very much for your overwhelming help and discussion about data analysis. Kind regards, Mohinder -- Mohinder Pal

Re: [ccp4bb] R-free flag problem

I must note that it is also interesting to know why the sfcheck produced the R-factor that is twice as high. Of course, the R/Rfree are not supposed to match precisely (as I recall, sfcheck uses Babinet bulk solvent correction which is presumably inferior to the mask-based approach), but 28.6

[ccp4bb] Diamond MX BAG Training

To all Diamond MX BAG Principal Investigators Group Leaders, Diamond Light Source will be holding a training day for MX BAG Users on Wednesday 8th December 2010. Numbers are limited to twenty and places will be allocated on request with a limit of one applicant per BAG. The aim of the day is

[ccp4bb] Babinet solvent correction [WAS: R-free flag problem]

Ethan pointed out to me that Babinet-principle based solvent correction is not always inferior to mask-based approach. My belief was based on some old observations which were in fact made prior to mask implementation in refmac and thus not exactly side-by-side comparisons. I hereby recant my

[ccp4bb] AKTA FPLC system available [off-topic]

Hi List, We have a complete AKTA FPLC available. Has latest Unicorn software and fraction collector. Please email me off-list or if you are interested. Thanks, Erin ress...@gmail.com 510-344-6633

Re: [ccp4bb] Babinet solvent correction [WAS: R-free flag problem]

Hi Ed, may be not always (in a sense that mask-based one sometimes may leave a negative footprint in areas where there is no solvent), but I still want to remind this paper where there is some discussion about exponential vs mask-based bulk solvent model:

Re: [ccp4bb] Babinet solvent correction [WAS: R-free flag problem]

On Fri, Oct 22, 2010 at 11:01 AM, Ed Pozharski epozh...@umaryland.eduwrote: Ethan pointed out to me that Babinet-principle based solvent correction is not always inferior to mask-based approach. On Friday, October 22, 2010 11:17:53 am Pavel Afonine wrote: Hi Ed, may be not always (in a

[ccp4bb] RE : [ccp4bb] Babinet solvent correction [WAS: R-free flag problem]

Dear Ethan, Just answering your last remarks, very many years ago I've done tests (unpublished) where I tried to estimate the magnitudes Fbulk and PHASES Pbulk for the reflections due to bulk solvent. It came out that : - for high-resolution reflections the magnitudes are small (everybody

Re: [ccp4bb] Babinet solvent correction [WAS: R-free flag problem]

Hi Ethan, Do you know of any published or unpublished results that compare the R factors achieved by Babinet treatment with those obtained from the state-of-the-art mask models? I afraid I don't know about published ones, and I see Sacha replied for unpublished one. I could spend a few

Re: [ccp4bb] R-free flag problem

Dear Ed, It turns out that the format of the structure file I sent to the PDB guys is not right. I found out this when running phenix.model_vs_data. After I resent the structrue file, sfcheck gives something OK, which is, High_Res Low_Res Compl  Num_Ref  R_obs   R_work  R_free  Corr(Fo-Fc)