Re: [ccp4bb] Big density blobs near Arg and His residues or Thr residues

I would try chloride and potassium in those sites and see whether that refines well. Cheers, Robbie On 17 Apr 2019 07:49, WENHE ZHONG wrote: Dear all, We found a huge density blob close to residues Arg and His (see attached) and another big density blob near three Thr residues (see attached)

Re: [ccp4bb] High Rfree in last Shell

Ah, even though it seems a long time ago, approximately one out of every two referee comments that I receive complain about our modern methods for processing, scaling and reporting our data collection/processing/refinement statistics. I’m afraid it’s an ongoing effort at education. Diana *

Re: [ccp4bb] High Rfree in last Shell

Jan, tell your reviewer to join us all in the 21st century. Diederichs and Karplus, Science, about 2 decades ago.  (Technically, 2012 , but it really is a long long time ago now.) On 16/04/2019 18

Re: [ccp4bb] High Rfree in last Shell

Dear all, The last resolution shell is 3.1-3.2 Å. I corrected high resolution Rmerge and Rmeas which seemed truncated, and added cc1/2. Rsym is Rpim which was a typo. Resolution range (Å) 49.2-3.1 49.3-3.1 Rfactor (%)

Re: [ccp4bb] naive question how to add GTP as a residue to a nucleic acid chain and refine!

At least last fall, the state of the art for getting your T7-transcribed RNA to start with a triphosphate in phenix was to add this file (edited for your chains, of course) through the gui (if you use the gui). Thanks to Deepak Koirala and Nigel Moriarty for help in working this out. * Phoeb

Re: [ccp4bb] High Rfree in last Shell

Sorry, I meant to write Why are the values for R(free) in parentheses LOWER than R(factor) in parentheses? Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND

Re: [ccp4bb] High Rfree in last Shell

Why are the the values for R(free) in parentheses higher than R(factor) in parentheses? I would not expect that to happen, if the same resolution limits for the last shell are used for both values. And I echo the previous commentator, please provide the resolution limits for the values in parent

Re: [ccp4bb] High Rfree in last Shell

Dear all, on top of other peoples remarks and out of interest: (1) What is the supposed difference between Rmerge and Rsym in your table and what software/tool computed those? Are you sure Rsym is not supposed to be Rpim? There is a slight historical difference between the Rmerge

Re: [ccp4bb] High Rfree in last Shell

> I’ve been told that the Rfree factor in the last shell are too high. > that's rubbish. You can not judge the absolute value without looking at the data and the model. If you have a certain amount of disorder, smearing, freezing effects, ice rings, and/or diffuse scatter, your Rfree will be hi

Re: [ccp4bb] High Rfree in last Shell

Dear Jan, You statistics look quite solid. R-factors are not good criteria to judge the resolution cut-off. The weighting schemes in refinement programs have much improved since the late 1990s. A good starting point to learn more is Rupp's "Against Method: Table 1 -Cui Bono?", https://doi.org/

[ccp4bb] High Rfree in last Shell

Hi everyone, I’m trying to publish two structures at 3.1Å resolution with the following refinement statistics: Resolution range (Å) 49.2-3.1 49.3-3.1 Rfactor (%)24.0 (32.4)

Re: [ccp4bb] A ccp4I2 question

yes one can Cheers Christian On Tue, Apr 16, 2019 at 1:19 PM Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > Can one export of project started under linux to a windows system? > > Eleanor > > -- > > To unsubscribe from the CCP4BB list, click t

[ccp4bb] A ccp4I2 question

Can one export of project started under linux to a windows system? Eleanor To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

[ccp4bb] ISBCC2019

Last week for the low-rate registration at the 7th International School on Biological Crystallization (ISBC2019). May 26th to 31st, in Granada, Spain. 2019 For more information, please visit http://www.isbcgranada.org/. Best regards, The ISBC 2019 Organizing Committee INVITED SPEAKERS

[ccp4bb] Research Associate position in Biochemistry, Cambridge, UK

Molecular mechanisms of meiotic recombination A postdoctoral position is available in the group of Prof. Luca Pellegrini in the Department of Biochemistry of the University of Cambridge, to work on meiotic recombination, the cellular process responsible for generation of sexual diversity and fe