Re: [ccp4bb] ctruncate bug?

Hi James, Concerning XDSCONV, I cannot reproduce your plot. A Linux (64bit) program "test_xdsconv" which allows to input I, sigI, , and mode, where I: measured intensity sigI: sigma(I) : average I in resolution shell mode: -1/0/1 for truncated normal/acentric/centric prior is at ftp://turn5.biol

[ccp4bb] Bruker webinar series

Dear Colleagues As part of Bruker's continuing webinar series on macromolecular crystallography techniques, Dr. Andrea Thorn from the Medical Research Council's Laboratory of Molecular Biology in Cambridge will present a one-hour interactive webinar entitled "In-House Sulfur SAD Phasing

Re: [ccp4bb] ctruncate bug?

On Wed, 19 Jun 2013 14:19:19 +0100, Kay Diederichs wrote: >I wonder if problem b) is why Evans and Murshudov observe little contribution >of reflections in shells with CC1/2 below 0.27 in one of their test cases, >which had very anisotropic data. sorry, forgot the reference. The paper is "Ho

Re: [ccp4bb] ctruncate bug?

To add to the discussion a plot of the acentric K&W from -10 to 10 (normalised wrt sqrt(sigma) ). ftp://ftp.ccp4.ac.uk/ccb/aZF2.pdf, black dots are F/sqrt(sigma) while blue is corresponding plot for sigma The value drops from 0.42 to 0.28 going from h = -4 to h = -10. Note: for this we are hea

[ccp4bb] Jerry Karle

Jerry Karle died a couple of weeks ago, and one of us here learned about it by noticing his obituary in the NY Times: http://www.nytimes.com/2013/06/15/health/jerome-karle-94-dies-nobelist-for-crystallography.html?_r=0 He's well known to those of us who started in this field when the solving o

Re: [ccp4bb] ctruncate bug?

Dear Kay and Jeff, frankly, I do not see much justification for any rejection based on h-cutoff. French&Wilson only talk about I/sigI cutoff, which also warrants further scrutiny. It probably could be argued that reflections with I/sigI<-4 are still more likely to be weak than strong so F~0 se

Re: [ccp4bb] str solving problem

Dear Robert I have cross checked by running the gel and silver stain that confirms it is only the protein i am targeting. no exact hit was obtained for this cell parameter and SG, as it previously checked during "balbes" run... thanks and regards pramod On Wed, Jun 19, 2013 at 2:28 PM, Rober

Re: [ccp4bb] ctruncate bug?

Hi Ed, While I don't think French and Wilson argue explicitly for the h>-4.0 requirement in their main manuscript, if you look at the source code included in the supplementary material for this paper, they include this in their implementation, which is what I worked from. Charles, do you happen t

Re: [ccp4bb] amro selem

http://www.alliancecorporation.com/gtjxdgki/dqtyk/psx/ycqd/uuens/fdcl/opzb.htm Best regards, amro selem

[ccp4bb] 10,000 NMR structure milestone reached!

The Worldwide Protein Data Bank (wwPDB; http://wwpdb.org) is excited to announce that the number of structures available in the PDB archive determined using Nuclear Magnetic Resonance (NMR) spectroscopy has passed the 10,000 mark! Since the first biomacromolecular NMR structure was archived in

Re: [ccp4bb] 10,000 NMR structure milestone reached!

Yeah, but they're mostly wrong though. *runs away and hides* On Jun 19, 2013 5:02 PM, "Gary Battle" wrote: > The Worldwide Protein Data Bank (wwPDB; http://wwpdb.org) is excited to > announce that the number of structures available in the PDB archive > determined using Nuclear Magnetic Resonance

Re: [ccp4bb] ctruncate bug?

On Wed, 19 Jun 2013 11:01:22 -0400, Ed Pozharski wrote: >Dear Kay and Jeff, > >frankly, I do not see much justification for any rejection based on >h-cutoff. I agree > >French&Wilson only talk about I/sigI cutoff, which also warrants further >scrutiny. It probably could be argued that reflecti

Re: [ccp4bb] 10,000 NMR structure milestone reached!

Is that allowing for the fact that each deposition contains approximately 30 models? If it doesn't take account of that, that could be 300,000 "structures"; if it does, it could be 300... On 19 Jun 2013, at 17:07, David Briggs wrote: > Yeah, but they're mostly wrong though. > > *runs away an

Re: [ccp4bb] 10,000 NMR structure milestone reached!

Is that 300,000 "structures"- or 300,000 "guesses"? I didn't get very far - I'll start running again On Jun 19, 2013 5:17 PM, "Peter Artymiuk" wrote: > Is that allowing for the fact that each deposition contains approximately > 30 models? If it doesn't take account of that, that could be 300

[ccp4bb] postdoctoral position available in the Pyle lab at Yale

Dear all on behalf of Prof. Pyle, I would like to inform you that a postdoctoral position is available in our lab at Yale. Please, see announcement below. Kind regards Marco Marcia The Pyle laboratory at Yale (www.pylelab.org) is looking for an exceptional and highly motivated postdoctoral ca

Re: [ccp4bb] str solving problem

On Jun 17, 2013, at 12:36 PM, Pramod Kumar wrote: >> I have a crystal data diffracted around 2.9 A*, >> during the data reduction HKL2000 not convincingly showed the space group >> (indexed in lower symmetry p1), while the mosflm given C-centered >> Orthorhombic, and again with little play ar

[ccp4bb] postdoctoral position available in the Pyle lab at Yale

Dear all on behalf of Prof. Pyle, I would like to inform you that a postdoctoral position is available in our lab at Yale. Please, see the announcement below. Kind regards Marco Marcia The Pyle laboratory at Yale (www.pylelab.org) is looking for an exceptional and highly motivated postdoctoral c

Re: [ccp4bb] str solving problem

Yes, I would agree with Francis that diffraction shows contribution from several lattices, which could lead to misindexing. However, it should be feasible to get a model that refines from this sort of data. Pramod - could you please post your data processing statistics from your scaling program? B

[ccp4bb] reversed stereo issue in coot and pymol

I am sure if others have the similiar experience as me, sometimes when I launch pymol and coot, I got the reversed stereo view which is pretty annoying. I am using the ASUS VG278H LCD monitor... Thanks in advance for your advice.

[ccp4bb] Definition of diffractometer

Somewhere I got the idea that a diffractometer is an instrument that measures one reflection at a time. Is that the case, and if so what is the term for instruments like rotation camera, weisenberg, area detector? (What is an area detector?). Logically I guess a diffractometer could be anything

Re: [ccp4bb] Definition of diffractometer

On Wednesday, June 19, 2013 11:11:01 am Edward A. Berry wrote: > Somewhere I got the idea that a diffractometer is an instrument that measures > one > reflection at a time. Is that the case, and if so what is the term for > instruments > like rotation camera, weisenberg, area detector? (What is a

Re: [ccp4bb] Definition of diffractometer

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Ed, to me, an '-ometer' is a device that measures whatever you put in front of the 'o', so in case of a diffractometer that's a device that measures diffraction. Best, Tim On 06/19/2013 08:11 PM, Edward A. Berry wrote: > Somewhere I got the ide

Re: [ccp4bb] Definition of diffractometer

Wait, so a geometer measures ges, an odometer measures ods, and a kilometer measures kils? --dvd On Thu, 20 Jun 2013, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Ed, to me, an '-ometer' is a device that measures whatever you put in front of the 'o', so in case of a

[ccp4bb] Need Feedback on our new secondary structure assignment program, SST

Hello group, I am posting here for the first time. We developed a new secondary structure assignment program (SST) based on the Bayesian method of minimum message length inference: http://bioinformatics.oxfordjournals.org/content/28/12/i97.abstract?keytype=ref&ijkey=AWyPEpQZaKi7Hne Minimum mes

Re: [ccp4bb] Definition of diffractometer

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Yes, but you need to know the 'geo' has to do with earth, so geometers measure the earth to make maps, odo, I believe has to do with smell, and kilometer is hyphenated kilo-meter, no kil-ometer, so the origin of that word is nothing to do with 'ometer

Re: [ccp4bb] Definition of diffractometer

an Odometer measures hodós: wikipedia: The word derives from the Greek words hodós ("path" or "gateway") and métron ("measure"). In countries where Imperial units or US customary units are used, it is sometimes called a mileometer or milometer, or, colloquially, a tripometer. Tim Gruene wrote: