[ccp4bb]

Respected Sir, I am sorry I wrote it wrongly, its resolution- independent X-ray weight rather. I use ccp4i so the input for the weight is what i mentioned previously- "Refinement parameters- weighing term (when auto weighing is turned off)" in refmac. Thanking you With Regads M. Kavyashree -I

[ccp4bb]

Respected Sir, Yes, the weight mentioned in the paper was weight matrix, but the one i used was the option under "Refinement parameters- weighing term (when auto weighing is turned off)". But If I really wasnt to change the weight matrix where should I change (in the code?)? No, I dint mean a big

Re: [ccp4bb] Optimisation of weights

Respected Sir, For one of the structures that I did optimisation had values - (resolution of the data - 2.35Ang) Before optimization- (Bfactor weight=1.0, X-ray Weight - auto) R factor 0.2362 R free0.2924 -LLfree 7521.8 rmsBOND 0.0160 zBOND 0.660 After optimisation- (B-factor weight

[ccp4bb]

bulletin board Date: 10/14/2011 12:34PM Subject: Re: [ccp4bb] Optimisation of weights Hi Kavya The resolutions of the structures mentioned in the paper were only examples, the Rfree/-LLfree minimisation method (which are actually due to Axel Brunger & Gerard Bric

[ccp4bb] Optimisation of weights

Dear users, Can the optimization of the X-ray weighing factor and B-factor (overall wt) as mentioned in the paper Acta Cryst. (2007). D63, 1274–1281 by Dr.Ian Tickel, be used for the refinement of the data sets beyond the resolution range mentioned in the paper: 1.33 - 2.55 Ang? Also the structur

[ccp4bb] Processing problem

Dear users, I was trying to process a C2221 data in two different versions of imosflm (7.0.4 and 7.0.7) using same set of frames, later on scaled using scala in ccp4 6.1.2. But for m surprise the statistics were quite different in two cases: In case of 7.0.4: Ove

Re: [ccp4bb] High B-factor for metal

Dear Sir, I have labeled it rightly. When I was trying to refine using the method I mentioned it was giving some less than 1 while some more than 1 as occupancy. I am trying to match with the peaks now. Thanking you With regards M. Kavyashree > Dear Kavyashree, > > Did you properly label the

Re: [ccp4bb] High B-factor for metal

Dear Sir, The resolution is 2.35Ang. I was trying to refine Cadmium occupancy using the option of "SAD data directly" in refmac (as it cadmium gives anomalous signal at 1.54179 wavelength) and then use the obtained occupancy of those atoms to refine in usual way. It used to to refine occupanci

[ccp4bb] High B-factor for metal

Dear users, I have refined a structure in R3 with cadmium bound to it, which was present in the crystallization condition. There are 2 chains in the asu. The structure is twinned. R and Rfree is around 22% and 28%. One of the cadmium has extremely high B-factor of 127, I tried replacing it with

Re: [ccp4bb] Twinning

> this can screw up your statistics on twinning and this can be due to > the NCS rotation > axis (or will be based on what you say) parallel to a crystallographic > symmetry axis. > just check that. it should still refine though but this will have > opposite effect to twinning, > so it can be probl

Re: [ccp4bb] Twinning

a dimer in asu which are related by a 2 fold, so there was no indication of any pseudo translation and protein is bound to 10-12 cadmiums. Could this off origin peak be due to the presence of the heavy atoms? how can i rule out the presence of this pseudotranslation as indicated in sfcheck? Thanking

Re: [ccp4bb] Twinning

mpared twinned structure with those two structures it does not vary much. > Hope this helps > cheers > Padayatti PS > With Regards Kavya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

[ccp4bb] Twinning

possibility? Thanking you With Regards Kavya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.