Re: [ccp4bb] R: [ccp4bb] Heavy atom vs light atoms density

2020-06-10 Thread Jrh Gmail
Dear Vito I looked at the examples of I3C in 3e3d, 3e3s and 3e3t and certainly the latter two show clear 2Fo-Fc for several I3Cs at a range of occupancies. So my mention of the different difference maps’ effectiveness does not apply. Hermann and Eleanor suggestions hopefully will explain your

Re: [ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

2019-11-04 Thread Jrh Gmail
Dear Michael The Rmerge in the strong intensity bin of 0.079 is untypically high it seems to me. Were the diffraction images underexposed? Best wishes John Emeritus Professor of Chemistry John R Helliwell DSc_Physics > On 3 Nov 2019, at 23:19, Michael Jarva wrote: > >  > Hi CCP4BB, > >

Re: [ccp4bb] tNCS incompatible with cell dimensions

2019-06-01 Thread Jrh Gmail
Dear Kevin You could try reindexing into P1, then run Phaser and with its solution as input to Zanuda determine the space group. Best wishes, John Emeritus Professor of Chemistry John R Helliwell DSc_Physics > On 31 May 2019, at 21:09, Kevin Jude wrote: > > Hello community, I wonder if

[ccp4bb] UK Open Research Data Task Force Final Report

2019-03-17 Thread Jrh Gmail
Dear Colleagues The UK Open Research Data Task Force Final Report is here:- https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/775006/Realising-the-potential-ORDTF-July-2018.pdf This will be of general interest. As well as contributing to this report

Re: [ccp4bb] FW: [ccp4bb] old data - headers

2019-01-31 Thread Jrh Gmail
Hello Harry I used SRS 7.2 and 9.6 at a wide variety of monochromatic wavelengths for resonant scattering (AD) studies. But I can imagine high intensity application PX measurements were made at those specific wavelengths which you mention. Greetings from Novosibirsk, John Emeritus Professor of

[ccp4bb] An overview of our crystallographic science

2018-03-01 Thread Jrh Gmail
Dear Colleagues, I prepared this overview of our crystallographic science in Biosciences Reports at the invitation of the Biochemical Society, which I imagine you would be interested in:- http://www.bioscirep.org/content/37/4/BSR20170204 It is open access. All best wishes, John Emeritus

[ccp4bb] protein quantification with carbohydrates

2015-03-10 Thread Gmail
Dear all, I have a (heavily and heterogeneously) glycosylated protein that has very low OD280 absorption. I wondered whether the glycans will have any effect on the accuracy of BCA or Bradford assay. Amino acid analysis doesn’t seem to be any better because carbohydrates will interfere with

[ccp4bb] (Off-topic) Analogs of CDP-choline for crystallization

2015-01-26 Thread Gmail
Dear CCP4 members, I’m working on a phosphocholination pathway in which the enzyme utilizes the substrate Cytidine-diphosphate-choline (CDP-choline) as phosphocholione-donor. I’m enquiring about the possible analogs of CDP-choloine for cocrystallization with the enzyme as well as for the

Re: [ccp4bb] Confusion about space group nomenclature

2014-05-02 Thread Jrh Gmail
Dear George My student class would not find that IUCr dictionary definition helpful. What they do find helpful is to state that they cannot contain an inversion or a mirror. To honour Sohnke is one thing but is it really necessary as a label? You're from Huddersfield I am from Wakefield ie

Re: [ccp4bb] Confusion about space group nomenclature

2014-05-02 Thread Jrh Gmail
think belongs to them? Maybe students would not be as refractory to the idea as might first be thought. With best wishes, Gerard. -- On Fri, May 02, 2014 at 05:42:34PM +0100, Jrh Gmail wrote: Dear George My student class would not find that IUCr dictionary definition

Re: [ccp4bb] metals disapear

2014-04-30 Thread Jrh Gmail
Dear Dean An example, albeit not a metal, can be found here:- http://journals.iucr.org/s/issues/2007/01/00/xh5011/xh5011.pdf Such specific damage has a long history:- http://www.sciencedirect.com/science/article/pii/0022024888903223 An X-ray sensitive metals centre is the Mn5Ca OEC of PS II and

[ccp4bb] IUCr Diffraction Data Deposition Working Group

2014-04-05 Thread Jrh Gmail
Dear Colleagues, We wish to let you know that the Triennial report for 2011 to 2014 on diffraction data deposition matters, prepared by the IUCr Diffraction Data Deposition Working Group (DDD WG) is now available at:- http://forums.iucr.org/viewtopic.php?f=21t=343 Best wishes, John, Brian and

Re: [ccp4bb] twinning problem ?

2014-03-12 Thread Jrh Gmail
Dear Jacob For a review of this topic see http://www.tandfonline.com/doi/full/10.1080/08893110310001643551#.UyCVLikgGc0 I also refer you to the more recent OUP IUCr book Chayen, Helliwell and Snell ie which includes these topics:-

[ccp4bb] N-linked glycans mediate inter-molecular protein-protein interactions

2014-02-05 Thread Gmail
Dear colleagues, I am looking for structures of protein complexes in which N-linked glycans mediate inter-molecular protein-protein interactions. Can anyone point me in the right direction? Thanks! Tianyu Gmail via foxmail

[ccp4bb] Postdoctoral position in UC Irvine

2013-10-29 Thread Gmail
UNIVERSITY OF CALIFORNIA, IRVINE DEPARTMENT OF PHYSIOLOGY BIOPHYSICS POSTDOCTORAL SCHOLAR One postdoctoral position is available immediately in Dr. Rongsheng Jin’s laboratory at the Department of Physiology and Biophysics, UC Irvine, and will remain open until filled. The new postdoctoral

Re: [ccp4bb] need suggestions

2013-04-16 Thread Flip GMAIL
Hi Afshan, Have look at http://www.douglas.co.uk/Scaling_Up.htm, Patrick has some general tips on scaling up. Elsewhere on his site you'll find tips for conversion to microbatch, you may want to try that out as well. I assume the screen crystals were not big enough to mount? Flip Op

Re: [ccp4bb] Bfactor is zero?

2010-12-20 Thread Ezra's gmail
On 12/20/2010 10:34 AM, Zhibing Lu wrote: Hi All, Recently I solved a structure in which some water molecules have Bfactors at 0 and overall wilson Bfactor is 0.654 based on PHENIX refinement. Is it possible? Bill Lu Hi Bill, What resolution are you working with here? An overall Wilson B

Re: [ccp4bb] .cv to .mtz conversion

2010-10-02 Thread Ezra's gmail
On 9/28/2010 10:41 AM, Jeremiah Farelli wrote: We recently had this problem in our lab. No matter what we tried, we could not get convert2mtz (or any other program) to work properly. We were probably doing something wrong with the fortran? Depending on how far along you are, you can try

Re: [ccp4bb] how to optimize crystallization of a membrane proteinf

2010-09-01 Thread Ezra's gmail
I cannot say what you have - running a gel, MS, etc of a washed crystal could confirm what you have. What you did not indicate is if your lack of diffraction was of frozen or unfrozen crystals. I have seen too many cases where it is the cryo condition killing diffraction. So if you have not tried

Re: [ccp4bb] how to optimize crystallization of a membrane proteinf

2010-09-01 Thread Ezra's gmail
I cannot say what you have - running a gel, MS, etc of a washed crystal could confirm what you have. What you did not indicate is if your lack of diffraction was of frozen or unfrozen crystals. I have seen too many cases where it is the cryo condition killing diffraction. So if you have not tried

Re: [ccp4bb] Query regarding GST fusion protein purification

2010-08-29 Thread Ezra's gmail
It sounds like list your GST construct is not binding to the column (or very well) when the peptidase is attached. GST needs to form a dimer to binding to the column - I suspect that your construct interferes with dimer formation - when the peptidase is present, but when not there due to