[ccp4bb] Job posting: Postdoctoral position in X-ray crystallography and protein biochemistry

A postdoctoral position Bardwell Lab at the University of Michigan and the Howard Hughes Medical Institute is available for an expert in X-ray crystallography and protein biochemistry. The Bardwell laboratory focuses on discovering and characterizing new chaperone proteins, including structural

[ccp4bb] autoSHARP: Am I on the right track?

Dear all Following on the previous thread on Fe-SAD, there is a solution(?) from autoSHARP with an OK-ish map and model. A quick refinement with phenix.refine gave me an R/Rfree of 28/31 % (2 A, although for the phasing run I told autoSHARP to use only up to 2.5 A). However, the model was

Re: [ccp4bb] autoSHARP: Am I on the right track?

Hi Mohamed, Did you check the model after autoSHARP? If yes, then how does it look like? ‎I guess your solution given by autoSHARP was not correct one and it couldn't build the proper model. That is the reason why you see a lot of dummy atoms. I would say the dummy atoms are not useful at all.

Re: [ccp4bb] High B factor

It seems to be common for people to make the incorrect assumption that the average of the atomic B factors in the PDB file should equal the Wilson B. The Wilson B is actually a weighted average of the individual B factors where the weighting is rather mysterious, but the small B factors have

[ccp4bb] crunch2 failed

Dear Members, crunch2 job failed with an error message. #CCP4I TERMINATION STATUS 0 "crank::crank binary and crank XML version do not match while executing "error $message" Can someone give any solution? Thanks, Raj

[ccp4bb] workshop on cryo-EM and single-particle analysis in Melbourne, Australia

Dear All: The ARC Centre of Excellence for Advanced Molecular Imaging and EMBL Australia announce a workshop on cryo-EM and single-particle analysis to be held at Monash University, Melbourne, Australia, 1-3 February 2017, preceding the LorneProteins meeting . The

Re: [ccp4bb] High B factor

Sorry for not making the problem clear! The overall B factor for the 3.0 A structure is around 98.00 A*2. Most of the deposited structures in the PDB site around this resolution has an av B around 70 A*2 All other statistics looks fine. I got a warning message while trying to upload the

Re: [ccp4bb] High B factor

Hi Sunanda They don't need to be "better" ... they need to be in agreement with you experimental B factor ... Wilson plot? Best Carlos On 10/13/16 04:59, sunanda williams wrote: Hi all, I have a structure at 3.0 A and R/Rfree of 24/28. The mean B value is around 98. The B value is

Re: [ccp4bb] Coot on MacOsX undo button

On 12/10/2016 19:03, Jan van Agthoven wrote: Looks like the undo button on Coot doesn't work. I installed Coot-0.8.6 on MacOsx El Capitan. Anyone knows what could be the problem? Perhaps you have started coot from a directory to which you do not have write access? What does it say in the

Re: [ccp4bb] Software to know the common folds in a protein

Thank you all for suggestions. “Do not be embarrassed by your failures, learn from them and start again.” Thanks & Regards, VIKRAM DALAL Research Scholar Macromolecular Crystallographic Unit Department of Biotechnology Indian Institute of Technology Roorkee (INDIA) On Thu, Oct 13, 2016

Re: [ccp4bb] Software to know the common folds in a protein

“Do not be embarrassed by your failures, learn from them and start again.” Nice quote, except when it refers to the brain surgeon working on you Cheers, BR On Thu, Oct 13, 2016 at 3:38 PM, Vikram Dalal wrote: > Thank you all for suggestions. > > > > > “Do not

[ccp4bb] Software to know the common folds in a protein

Hi everyone, We are solving a protein structure and we want to know the folds which are present in it. Suggest me the best software or server which can be used to find the common folds in my protein. Thanks & Regards,

Re: [ccp4bb] Software to know the common folds in a protein

Hi, You could try the DALI server or pdbefold. Both give you pretty much the same information. Christian Am 13.10.2016 um 13:03 schrieb Vikram Dalal: Hi everyone, We are solving a protein structure and we want to know the folds which are present in it. Suggest me the best software or

Re: [ccp4bb] Metrics for hkl2map (Fe SAD)

Dear Mohamed, more important than the absolute values of CCall/CCweak is the distribution of these statistics among the solution-trials of one SHELXD computation job (i.e. based on a particular data set). In the HKL2MAP scatter-plot, there should be at least one, or a set of, solutions that

[ccp4bb] Job posting: Postdoctoral positions in structural biology of herpesviruses

Postdoctoral positions are available in the laboratory of Katya Heldwein at Tufts University School of Medicine (Boston, MA). Her lab investigates the mechanisms by which herpesviruses manipulate host membranes and intracellular traffic to enter and escape from the host cells using a

Re: [ccp4bb] High B factor

I fully agree with Dale in not understanding what the problem is. Perhaps I have a better chance if you clearly explain what exactly you mean by "is there any way to better the B factors". Pavel On Thu, Oct 13, 2016 at 12:57 PM, Dale Tronrud wrote: >I'm sorry but I