Re: [ccp4bb] interesting map problem

Hi Eleanor, I wonder if in fact this is the problem. I of course didn't think properly about it. The cell is the same, sort of, and I think you have put your finger on my error. It is the same data more or less, I was reprocessing a dataset, to slightly higher resolution using the same images as f

Re: [ccp4bb] interesting map problem

Christine - can you attach the relevant log files! Eleanor On Fri, 17 Dec 2021 at 22:59, Ethan A Merritt wrote: > On Friday, 17 December 2021 14:04:17 PST Christine Gee wrote: > > Hi, > > > > I recently came across this strange issue. I was using aimless in CCP4 to > > scale my data and apply an

Re: [ccp4bb] interesting map problem

On Friday, 17 December 2021 14:04:17 PST Christine Gee wrote: > Hi, > > I recently came across this strange issue. I was using aimless in CCP4 to > scale my data and apply an Rfree from a reference .mtz > > Neither the reference or the file I was working with had higher resolution > than 1.5 > Ho

Re: [ccp4bb] interesting map problem

Well - that should not happen! Are the cell dimensions the same for the new data and the reference set? E On Fri, 17 Dec 2021 at 22:04, Christine Gee wrote: > Hi, > > I recently came across this strange issue. I was using aimless in CCP4 to > scale my data and apply an Rfree from a reference .mt

[ccp4bb] interesting map problem

Hi, I recently came across this strange issue. I was using aimless in CCP4 to scale my data and apply an Rfree from a reference .mtz Neither the reference or the file I was working with had higher resolution than 1.5 However aimless wrote out h, k, l and Rfree to 0.4. I did not click the button t

[ccp4bb] EMBO Practical Course on High throughput protein production and crystallization, Marseille, July 2022

Dear colleagues, I am glad to announce the "EMBO Practical Course on High throughput protein production and crystallization", hosted at the laboratory AFMB in Marseille, France, from 4 to 13 July 2022. On behalf of the organizers I would like to ask you to please let your colleagues and stude

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Re: [ccp4bb] the complex structure of protein and DNA

Hi, I agree with Mark, the R factors suggest that your model is more or less complete. It does not seem like that DNA is bound to your protein. Without knowing more about your project, it’s hard to make specific suggestions, but here goes: * Have you actually checked that there is DNA in

[ccp4bb] Available postdoctoral position in crystallography

Hi all, The Structural Genomics Consortium at the Goethe University Frankfurt offers immediately a position of a Postdoctoral Scientist (m/f/d) limited initially until 31st December 2023. Please see attached for job description. We are looking for a motivated and experienced structural bioc

Re: [ccp4bb] the complex structure of protein and DNA

Hi, With this resolution and R-factors, I would guess you are not missing that much – certainly not large bits of DNA. Do you have Phosphate or Sulphate in the crystallisation buffer? If so, you may just be seeing Phosphate/Sulphate where the DNA would bind. Cheers, Mark Dr S.M. Roe, X-Ray F

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[ccp4bb] cryo-ET postdoc position in mitochondrial genome maintenance - Center for Protein Research at the University of Copenhagen

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Re: [ccp4bb] the complex structure of protein and DNA

Dear Petr, Thank you very much for your reply! The complex structure was refined finally to 2.44 Å resolution with an Rwork of 23.7% and an Rfree of 27.4%. We didn't try automatic DNA building tools, I don't know much about this. Thank you very much for your advice, I'm going to study it.