Re: [ccp4bb] peroxy-glutamate?

As you suggest, it depends on the contour level. Looking through a list of 17 dicarboxylates that I found problematic, there were 4 (actually two and their ncs-mates) that showed disconnected density for the carboxylate at 1.4 sigma as in the figure I sent. Going up to 2 sigma, four more

[ccp4bb] Postdoc position available - Imperial College London - Prof Dale Wigley

—— Martin Wilkinson mwilk...@ic.ac.uk Imperial College Lab 245 2nd Floor, SAF building Imperial College Road London SW7 2AZ —— HM2017001 Research Associate Advert QC SW - extended2.pdf Description: HM2017001 Research Associate Advert QC SW

Re: [ccp4bb] Poor density fit.

Thanks Bert, I did understand not to delete such atoms or set occupancy to zero from forum and literature. However, colleagues in the vicinity informed to take approaches i mentioned earlier. Therefore, I thought to take opinion from forum if something has changed recently. Thanking, On Thu,

[ccp4bb] AW: [ccp4bb] Poor density fit.

Dear Vipul, the first thing I would check is why one chain has good and the other chain has poor side chain density. Are the B-factors of one chain much higher than of the other? Does one chain have more/better crystal contacts to stabilize its position in the crystal? Is the structure

Re: [ccp4bb] Poor density fit.

This has been discussed before, I guess more than once I think most people (I'm sure i'll be corrected if wrong) would favor not removing any atoms or setting occupancies to zero and let the invisible atoms be accounted for by high B-factors (either set manually or just letting refinement

[ccp4bb] Poor density fit.

HI all. I am solving protein structure with 2.16A resolution. There are two chain in an asymmetric unit. I see that in one of the chain, many residues' density for side chains is incomplete and therefore results in poor density fit. *I want to know your opinions for the approach I have taken.

Re: [ccp4bb] very high B-factor

Sorry, the R-factor gap of no6 is 5.23%, not 6.23%, I have made a mistake. I have check the b-factor of the residue with "B-factor variance" value of 417 in coot-->menu-->distance-->residue info., the b-factor value of each atom of the residue is very similar with that of in pdb file, though

Re: [ccp4bb] very high B-factor

Hi, I'm working on a crystal structure with resolution of 2.2A. At the final > step, I use different strategies to refine the structure, they are: > no4: strategy=individual_sites+individual_adp+tls / set_b_iso=20 > results: Rwork/free=0.2052/0.2658 b-factor=11.4/136.8/48(min/max/average) > >

Re: [ccp4bb] very high B-factor

Hi Vipul and Qiaoling, Setting occupancies to 0 will give somewhat misleading results. It is good to test whether density will disappear or not, but not for the final model. Users of the model might misinterpret it. Especially if you start leaving out 'random' poorly fitting atoms. High

Re: [ccp4bb] peroxy-glutamate?

I have seen anomalous "flecks" bespangling an protein's internal cavity which had a couple of cysteines in it, and I assumed that these were liberated sulphurs (they were not Fourier-truncation-like.) I would agree with Andrew that diffusion should not be large, but alighting on the nearest

Re: [ccp4bb] very high B-factor

1) the difference is 5.23 % and it is good and acceptable. 2) if higher value belongs to residue, then you need to change the rotamer Using coot , follow menu-->distance-->residue info. You will get to know to whom 417 B factor value belongs. Meanwhile, just check if modeled residue or part of

Re: [ccp4bb] peroxy-glutamate?

Le Jeudi 4 Mai 2017 12:25 CEST, Andrew Leslie a écrit: Dear Andrew, We looked in details to this problem of diffusion at ca. 100 K with bromine in "Ennifar et al., Acta D58(2002)1262" and we concluded "It was attempted to derive a value for the diffusion coefficient

Re: [ccp4bb] peroxy-glutamate?

Dear Ed, I find your electron density quite interesting, because generally (I think, I would be happy to be corrected on this) when de-carboxylation of Asp/Glu occurs due to radiation damage, there is no evidence of what happens to the resulting CO2 group. One interpretation of

Re: [ccp4bb] very high B-factor

Hi Vipul, Thanks for your quick reply. 1. Actually, i mainly comparing the gap between Rwork and Rfree which should be <5%, and then the overall b-factor, RMSD of bond and angle. For me, no5 is the best one, but the "B factor variance Graphs" make me uncomfortable. The R-factor gap of no6

Re: [ccp4bb] very high B-factor

Hi, 1> Well, it seems you are just comparing Max value across all protocols. You should compare average values as it also takes into account no. of atoms with given values of B factor. As per refinement results, it seems though no. 6 has highest B factor value, number of atomic outliers are