[ccp4bb] The 10% Gap between R-factor and R-free

Good Morning to ALL, I encountered large gaps between R-factor and R-free, eg. 10% and 11%, during refining several structures with either Refmac or Phenix.refine. The data were reduced and scaled at resolution with I/SIGMA higher than 2.3. The model fits and density pretty well

Re: [ccp4bb] The 10% Gap between R-factor and R-free

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Wenhua, a large gap between R1 and Rfree is often inficative for overfitting. Take a look at the following: - - how many water molecules are there in total? Do they all chamically make sense, do some of them have large B-values? Water molecules

Re: [ccp4bb] The 10% Gap between R-factor and R-free

Hi Wenhua You didn't say what resolution your structure is: that's critical to deciding how significant is the R-factor difference (or more strictly the ratio). There are other factors such as solvent content: generally anything which affects the obs/param ratio (such as NCS restraints) will

Re: [ccp4bb] Refinement of data with pseudo translation symmetry

Well - your R values will probably appear higher than normal - there will be zones where all reflections are weak.. but the maximum likelihood targets are meant to deal with this reasonably well. It seems to work and the maps usually look OK! Eleanor On 25 November 2013 22:31, Niu Tou

Re: [ccp4bb] Stereo monitor

Dear all, Thanks to all for the information, especially to Jeroen for the detailed comments and thanks to Kay for the Wiki link, that was really helpful! So one possible option among others seems to be: - NVIDIA Quadro K600 - Asus VG278HR Just to get it right: Although the K600 is listed under

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Re: [ccp4bb] The 10% Gap between R-factor and R-free

Hi Wenhua, concerning phenix.refine: just run it again with weights optimization and it should fix the problem (assuming everything else done right: such as you are using correct refinement strategy). If using weights optimization does not help then let me know off list or on Phenix mailing list

Re: [ccp4bb] Stereo monitor

YES!, this new card will work (once properly set-up under linux). I triple checked the new k600 card actually has a dual-link DVI and it has. So, no problem linking it to the VG278HR. It is listed "windows only" because it lacks the 3-pin

Re: [ccp4bb] Stereo monitor

Thanks! On Tue, Nov 26, 2013 at 5:03 PM, mesters mest...@biochem.uni-luebeck.dewrote: YES!, this new card will work (once properly set-up under linux). I triple checked the new k600 card actually has a dual-link DVI and it has. So, no problem linking it to the VG278HR. It is listed

[ccp4bb] SSRL ; Can not access

Hi folks, I can not access to SSRL from yesterday. smbnxs1.slac.stanford.edu. or smbnxs2.slac.stanford.edu I wonder something is wrong in the server. Please let me know what happened to the SSRL if you know that. Thanks to all. Daniel

Re: [ccp4bb] SSRL ; Can not access

I just checked, and am logging on fine. Oli On Tue, Nov 26, 2013 at 9:40 AM, Daniel philoje...@gmail.com wrote: Hi folks, I can not access to SSRL from yesterday. smbnxs1.slac.stanford.edu. or smbnxs2.slac.stanford.edu I wonder something is wrong in the server. Please let me know what

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[ccp4bb] trying to trace main chain of loop region in two alternative ways

Hello everyone, The electron density of my structure displays two alternative traces for the main chain in a loop region. Is there a way I can refine the structure with both the alternative main chains in place with 50% occupancy each? Thanks, Shy -- Shyamosree Bhattacharya 4th year Graduate

Re: [ccp4bb] trying to trace main chain of loop region in two alternative ways

I am using Refmac5 to refine my protein structure. Shy