[ccp4bb] Coot and Phenix inappropriately handle heavy atom alternative conformations

2017-01-12 Thread Buth Sergii
Dear Community, I work on a crystal structure of a trimeric protein with a total mass of 191 kDa. Data resolution is 2.4A. Protein crystallizes in the presence of 800 mM ZnSO4, and, as a result, contains above 40 zinc ions attached to the protein molecule. Certain ions are diffused and/or partia

[ccp4bb] Completely Off-Topic: Intracellular Glutamate Concentration

2017-01-12 Thread Keller, Jacob
This is one source paper I found recently, and there are lots of others. doi:10.1038/nchembio.186 JPK From: Napoleao Fonseca Valadares [mailto:n...@ifsc.usp.br] Sent: Thursday, January 12, 2017 12:18 PM To: Keller, Jacob Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Completely Off-Topic De

Re: [ccp4bb] CCP4BB Digest - 10 Jan 2017 to 11 Jan 2017 (#2017-12)

2017-01-12 Thread Whitley, Matthew J
Hi Claire, Isn’t the simplest answer just that the EDS server is calculating the completeness for a different amount of data (high res limit of 1.92 Å), whereas in your Depositor data it was only calculated to a high res limit of 2.1 Å? This would probably be the result of you measuring reflec

Re: [ccp4bb] Completely Off-Topic

2017-01-12 Thread Napoleao Fonseca Valadares
Dear Jacob, You did not miss the 101 class, it is just too much to remember. E. coli metabolome when growing on glucose (Lehninger, 2013): http://www.fullonline.org/science/ecoli_metabolome.png The book does not provide explanation for this, but I remember reading somewhere else that glutama

Re: [ccp4bb] Issues with Coot & XQuartz

2017-01-12 Thread hari jayaram
Hi All I tried coot and pymol with OSX Sierra 10.12.2 and Xquartz 2.7.11 aall the way through 2.7.8 after seeing this post. Pymol ( self compiled 1.8.2 ) 80% of the time on two different machines stops responding to the mouse. Coot behaves the same way where smooth rotation my mouse is severely a

Re: [ccp4bb] Completely Off-Topic

2017-01-12 Thread Harry Powell
Can I just make the point that the subject "Completely off-topic" is completely useless if you're searching through the archives for anything? Since it's attracted quite a bit of correspondence, this obviously isn't off-topic at all! Harry -- Dr Harry Powell Chairman of International Union of

Re: [ccp4bb] Completely Off-Topic

2017-01-12 Thread David Schuller
I wonder if anyone has tried glutamate as a cryprotectant for proteins. If the [] is that high, it may make a stable environment for proteins. I have no idea what effect it might have on ice formation. https://amb-express.springeropen.com/articles/10.1186/2191-0855-3-36 /Bacillus subtilis/ n

[ccp4bb] CCP4 study weekend 2017 talks

2017-01-12 Thread Charles Ballard
Dear All for those of you who could not watch the live stream, Stuart and Laura have got the sessions up on https://sas.stfc.ac.uk/vportal/index.jsp Under "CCP4 Study Weekend 2017" Best wishes Charles

[ccp4bb] two postdoctoral positions in Oxford

2017-01-12 Thread Lidia Vasilieva
Two Postdoctoral positions – Towards deciphering mechanisms of transcriptional and post-transcriptional gene regulation in eukaryotic cells Two postdoctoral positions are available early 2017 in the laboratory of Lidia Vasiljeva funded by Senior Research Fellowship from the Wellcome Trust at t

Re: [ccp4bb] Off-topic question about SEC

2017-01-12 Thread Nicolas RICHET
Dear Reza, Regarding the molecular weights (60 to 360 kDa), the low salt concentration seems to drive the assembly of an hexamer. Salt concentration could have a drastic effect on protein oligomerization. If your A280 profile of the 360 kDa peak looks good (symmetric and in the resolution limits),

Re: [ccp4bb] Completely Off-Topic

2017-01-12 Thread Jon R Sayers
Following on I read somewhere a while back that potassium conc in E. coli is estimated in the 30-300 mM range (http://book.bionumbers.org/what-are-the-concentrations-of-different-ions-in-cells/ ) . In other mor

Re: [ccp4bb] Off-topic question about SEC

2017-01-12 Thread Nicolas FOOS
Dear Reza, in the past I had work with protein able to oligomerize reversibly but when oligomerization happened, even if I was able to separate and obtain monomeric protein, protein was not in a good condition. Have you try to characterize the two different states by DLS ? To discriminate

Re: [ccp4bb] Completely Off-Topic

2017-01-12 Thread Reza Khayat
I don't think this is taught in Biochem101. You didn't miss it. The cytoplasm is quite viscous, like jello. Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 From: CCP4 bulletin board [CCP4BB@JISCM

Re: [ccp4bb] Completely Off-Topic

2017-01-12 Thread Tim Gruene
Dear JPK, I was not aware of the absolute numbers, but maybe they are little suprising: when your tinned food contains 'yeast extract' it is equivalent to monosodium glutamate, which is commonly used as flavour enhancing agent. I am not a chemist to worry about it, but yeast seems to have a ful

[ccp4bb] AW: [ccp4bb] PDB validation of structure factors

2017-01-12 Thread Herman . Schreuder
Dear Claire, I am not a Phenix expert, but to me the discrepancy lies in the resolution ranges reported. The completeness of Depositor goes to 2.1 Å, while the completeness of EDS goes to 1.92 Å. Could it be that the cutoff of 2.1 Å was used for refinement, while the data were processed to 1.92