[ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

Dear All, For me this whole discussion is an example of a large number of people barking at the wrong tree. The real issue is not whether data processing programs print amongst many quality indicators an Rmerge as well, but the fact that the PDB and many journals still insist on using the Rmerg

[ccp4bb] latest XDS only using a single thread

Dear all, I have recently installed the latest version of XDS (Linux 64 bit) and found that xds_par is only using a single thread despite having MAXIMUM_NUMBER_OF_PROCESSORS= 16 In the latest version (licensed till Sep 2017) XDS is using the full number of threads with the same XDS.INP / data

Re: [ccp4bb] latest XDS only using a single thread

Hi Florian, difficult to say without knowing more details. a) you should be using the XDS version that identifies itself with BUILT=20170615 b) are you using xds or xds_par? Only xds_par is parallelized, xds is single-threaded c) I assume your machine has >1 core, and a DELPHI-sized batch of fr

[ccp4bb] Joint PhD studentship Oxford/Diamond - entry 2017

Dear all, The Oxford Interdisciplinary Bioscience (http://www.biodtp.ox.ac.uk) is funding a joint PhD studentship between Diamond and the Division of Structural Biology (STRUBI, Oxford). The aim of the project is to unravel the mechanism of viral fusion of pestiviruses using crystallographic an

Re: [ccp4bb] latest XDS only using a single thread

Hi Kay, thanks for your quick response! a) I am using BUILT=20170615 on Ubuntu 14.04. b) xds_par c) My machine has 2 cores (4 threads possible). The dataset contains 3600 frames. On a different machine (Opensuse) running an older built (20170215), xds_par uses all available cores (12) when usi

[ccp4bb] Two PhD positions at the Interfaculty Institute of Biochemistry - Prof. Thilo Stehle

Dear CCP4BB-Users, On behalf of Prof. Thilo Stehle I would like to post a job offer for two PhD positions (see below) at the Interfaculty Institute of Biochemistry. Best Regards, Georg *Two PhD positions at the Interfaculty Institute of Biochemistry** * We offer two PhD positions in t

Re: [ccp4bb] latest XDS only using a single thread

Hi Florian, please send me your XDS.INP and .LP files by email. thanks, Kay On 2017-07-10 13:24, Florian Sauer wrote: > Hi Kay, > > thanks for your quick response! > > a) I am using BUILT=20170615 on Ubuntu 14.04. > b) xds_par > c) My machine has 2 cores (4 threads possible). The dataset cont

[ccp4bb] [SOLVED] Re: [ccp4bb] latest XDS only using a single thread

Dear all, after looking through my input file, Kay found that the problem was the option SECONDS=600 which limits XDS to run in a single thread. Deleting the line allowed running on all available cores. Florian please send me your XDS.INP and .LP files by email. thanks, Kay On 2017-07-

Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

Dear Herman The new PDB deposition system (OneDep) allows you to enter values for Rmerge, Rsym, Rpim, Rrim and / or CC half. If, during deposition, you do not provide a value for any of these metrics then we will ask you for a value for one of them. Also, PDB format is a legacy format for th

[ccp4bb] crystallization optimization

hello everyone! I get a condition (10% w/v PEG 6000, 100mm HEPES PH7.0) in which my protein grow small needle like crystals, how can i optimize it to get bigger crystals? the attach is the crystals figure. thanks in advance sincerely Liuqing Chen

Re: [ccp4bb] Ramachandran oultliers increase upon restrained refinement

4% outliers at < 3A seems a little high to me. A trick that often works for me is to truncate the side chains surrounding the offending peptide to Ala or Gly, optimize the backbone, and then put the side chains back on. Often that makes it clear that a different rotamer would work better. +++

Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

What is the difference between Rmerge and Rsym - I thought they were the same? Rrim == Rmeas I think Phil > On 10 Jul 2017, at 15:18, John Berrisford wrote: > > Dear Herman > > The new PDB deposition system (OneDep) allows you to enter values for Rmerge, > Rsym, Rpim, Rrim and / or CC half.

[ccp4bb] SHELXE: peptide occupancy refined to negative value

Dear all, since SHELX is now part of CCP4, this question is not entirely off-topic. I'm trying to solve structures by S-SAD. Substructure looks weak but ok if the right resolution cutoff is picked in SHELXD. SHELXE is happy to do its thing for a while but then gives up with a "Peptide occupancy

Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

On 10/07/17 16:42, Phil Evans wrote: What is the difference between Rmerge and Rsym - I thought they were the same? Rrim == Rmeas I think The descriptions and formulae for most of these R values as used by the PDB can be found in the pdbx exchange dictionary, in the REFLNS_SHELL category. (

Re: [ccp4bb] [ccp4bb] Rmergicide Through Programming

> > (2) Rsym has just: > >> R sym value in percent. > > see > . > To be honest, if that is the official definition it does make me wonder what > it is doing in the dictionary at all. > > Reg

Re: [ccp4bb] crystallization optimization

Microseed them into two or three random screens. Search for MMS and rMMS online. Good luck Patrick On 10 July 2017 at 15:47, Liuqing Chen <519198...@163.com> wrote: > hello everyone! > I get a condition (10% w/v PEG 6000, 100mm HEPES PH7.0) in which my > protein grow small needle like crys

[ccp4bb] How to determine Quaternary symmetry

Hi , I have a protein which has A4 stoichiometry. I am trying to find symmetry component which should be D2 but one axis looks like translated which does not make it perfect D2. I am wondering if there is any tool which I can use to determine Quaternary symmetry. thanks -- Vand

Re: [ccp4bb] How to determine Quaternary symmetry

Hard to comment without more detail. What is your cell and point group symmetry? Do you know space group? What is likely asymmetric unit content? Is there a non-crystallographic translation and if so what is it? All this information given in GUI2 data processing report. Eleanor On 10 July 2017

Re: [ccp4bb] How to determine Quaternary symmetry

You can try http://www.eppic-web.org. It will give you a full enumeration of all symmetric assemblies present in the crystal. If the assembly you are looking at is not symmetric (within a certain approximation) it will not be listed in the results. Hope it helps Jose On Mon, Jul 10, 2017 at 12:

Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

Hello, I think this needs a little bit of crystarchaeology. Rmerge and Rsym used to be different. This was at a time when data sets were typically collected from several crystals. Pre-cryo cooling, with data recorded on photographic film (Arndt-Wonacott cameras). Rmerge = agreement R-factor fr