[ccp4bb] Ph.D. positions in Barcelona

Dear all, I just learned that the attached PDF was not passed to the BB. Here is the add. Best, Xavier *4 PhD student positions available at the Structural Biology Department of IBMB-CSIC*. *Unit of Excellence “María de Maeztu**”* The “María de Maeztu” Structural Biology Unit of IBMB-CSIC

[ccp4bb] Diamond MX Beamline Training 15-16th July

Dear all, The Diamond Light Source Macromolecular Crystallography group would like to invite both our academic and industrial users to MX beamline training sessions on the 15th -16th July 2015. The aim is to provide MX users with sufficient training to be able to operate any of the Diamond MX

[ccp4bb] PhD fellowship at the Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen

PhD fellowship in crystallography of G protein-coupled receptors The Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen is pleased to announce that a PhD fellowship will be available from Oct 1st 2105 or soon thereafter in discussion

Re: [ccp4bb] How many is too many free reflections?

Dear Dusan, Following up on Gerard's comment, we also read your nice paper with great interest. Your method appears most useful for cases with a limited number of reflections (e.g., small unit cell and/or low resolution) resulting in 5% test sets with less than 1000 reflections in total. It

[ccp4bb] PhD position in Goettingen, Germany. Computational Biophysics

PhD position in Computational Biophysics Topic: Molecular dynamics simulations of X-ray scattering experiments A PhD position is available in the group of Dr. Jochen Hub at the Georg-August-University Göttingen, Germany. The application deadline is July 5, 2015. For more details, please visit

[ccp4bb] Thanks to informal query respondents

Hi Fellows, thanks again to all who took the time to respond (often very extensively) to my queries regarding funding experience and resource distribution. The summary is available now ahead of print: http://www.ncbi.nlm.nih.gov/pubmed/26051321 Let's hope it has some positive

Re: [ccp4bb] zalman 3d monitors

I think the Zalman's are not available anymore. When our last one died we bought the Asus VG23AH (also passive 3D). Works similar to the Zalman for Coot and Pymol, Best, Daniel On Wed, Jun 10, 2015 at 5:00 AM, Peng GONG 055a9db99734-dmarc-requ...@jiscmail.ac.uk wrote: Hi Tom, I think any

[ccp4bb] MoRDa - new MR pipeline

Dear all, MoRDa is a pipeline for molecular replacement protein structure solution with X-ray data. MoRDa is based upon its own domain database. The software package contains a database and a set of programs for structure solution. The package is available for Mac or Linux. You can find more

Re: [ccp4bb] Alternative ways to get electron density map other than EDS server

It works again now. Sorry for the inconvenience. --Gerard On Tue, 9 Jun 2015, Xiao Lei wrote: Hi All, I am trying to get electron density map of some pdb structures, I know there is a database called Electron density server (EDS http://eds.bmc.uu.se/eds). But somehow these days I can not

Re: [ccp4bb] .sfrm format problem

hi If you pre-process the images with the Bruker utility frm2frm* you should be able to transform them into a format that Mosflm can process. * it used to be called frm2frm, but may now be called something else - someone from Bruker should be able to help you! Harry -- Dr Harry Powell, MRC

[ccp4bb] .sfrm format problem

Dear All, We havecollected the data from a Bruker x-ray machine, it was in .sfrm format which isnot readable by mosflm and hkl2000. Can you people help me how to workout this problemby mosflm or any other suitable software . Thanks in advance

Re: [ccp4bb] .sfrm format problem

Hi Harry, We have tried the frm2frm sofware but it didn't work out for as. On Wednesday, 10 June 2015 12:54 PM, Harry Powell ha...@mrc-lmb.cam.ac.uk wrote: hi If you pre-process the images with the Bruker utility frm2frm* you should be able to transform them into a format that

Re: [ccp4bb] .sfrm format problem

Tarun, in my group we used to have a Proteum6000 CCD from Bruker. With the right detector descriptions from the HKL folks we able to use HKL2000, talk to the hkl folks, you may also need another license covering that detector though. Alternatively Bruker provides the Proteum suite (I think that

Re: [ccp4bb] Thanks to informal query respondents

Your Figure 1 suggest a secret message - or at least I view it that way. The early steps “basic research” seems to be funded by Euros, while the in silico part is funded in Dollars. Or was that unintentional ? Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School

[ccp4bb] Postdoctoral position in Amgen

I would like to draw your attention to a postdoctoral position in Amgen San Francisco. Please apply through the following link. http://careers.amgen.com/en/jobs/descriptions/postdoctoral-fellow-molecular-engineering-south-san-francisco-job-5461195 Xiaoshan Min Molecular Structure Amgen San

Re: [ccp4bb] .sfrm format problem

Hi Tarun, Carsten is right the Proteum2 software is really good. I can send you some introduction pdfs and for SADABS (scaling) I am currently writing an SOP, the manual is also well written. Besides this the program to unwarp and convert images, is in the instrument tab. Best regards,

Re: [ccp4bb] .sfrm format problem

I don't think the .sfrm ending means that the data can or can not be read by non-Bruker software. The crucial difference is between warped and unwarped data, if I understand correctly. XDS (and I think MOSFLM) can only process unwarped data. As Harry says, there is an unwarping utility from

Re: [ccp4bb] .sfrm format problem

of course, Kay is right; I just assumed that the frames were warped, or not corrected for spatial distortion. Mosflm does require unwarped data from the Bruker CCD detectors. I haven't seen images from their CMOS detectors which may not require unwarping (but probably will...). Harry -- Dr

Re: [ccp4bb] twinned data refinement

On Wednesday, 10 June, 2015 17:35:25 Mengbin Chen wrote: Hello everyone, I am refining a 2.5 angstrom structure whose phase is solved by molecular replacement with a search probe determined by SAD with 3 angstrom resolution. While I am able to see densities of a bunch of water molecules and

[ccp4bb] twinned data refinement

Hello everyone, I am refining a 2.5 angstrom structure whose phase is solved by molecular replacement with a search probe determined by SAD with 3 angstrom resolution. While I am able to see densities of a bunch of water molecules and ligands in the MR solved structure, which means that the phase

Re: [ccp4bb] twinned data refinement

Thank you Jacob and Ethan! I haven't put water molecules into the density blob, which aren't many out there, but I fitted the ligands in already. Molbrobity statistics are not yet great, since there are 13.5% rotamer outliers. Will adjust the models manually, and try refmac and TLS refinement.

Re: [ccp4bb] .sfrm format problem

Dear Carsten, dear Tarun are you sure HKL can process the unwarped images? As far as I understand, the distortion is detector specific, i.e. each detector has its own undistortion description. As Kay pointed out, reading sfrm is not a problem, it is very well documented (and a neat format). Once