[ccp4bb] Position for an experienced PhD-level structural biologist with sales and commercial experience

Dear All, I'd like to call your attention to a position announcement for a PhD level structural biologist to join a new biotechnology company called HarkerBIO. I am posting this announcement for any members of the CCP4 board that may be looking for positions but please note that I am not

[ccp4bb] P3212--1's in Space Group Names?

Dear Crystallographers, I don't understand what the 1's are doing in space group names like P3212 or P3112--can someone fill me in? Not easy to google this one. JPK *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr,

Re: [ccp4bb] crystal anisotropy measurement?

Dear Cosmo, you may calculate effective resolution of your data set along different directions using the program EFRESOL (article in press in J.Appl.Cryst., the method is described by Urzhumtseva et al., 2013, Acta Cryst D69, 1921-1934). You can download the program from

[ccp4bb] P212121 with strong Patterson peak at 0.5, 0.5, 0.5

We have data at ~3.2 A for a crystal that looked clearly like primitive orthorhombic while indexing in HKL2000 (or Mosflm). Based on the systematic absences I called it P212121 during scaling. However, we are having some unexpected issues with finding a Mol. Rep. solution using a model that is

Re: [ccp4bb] P212121 with strong Patterson peak at 0.5, 0.5, 0.5

Hi JK, we recently worked on a crystal with similar symmetry and I would recommend you to read the two papers listed below. If you visually do see the weak reflections, the space group is primitive orthorhombic (and not body-centered orthorhombic). The strong Patterson peak at ~0.5, ~0.5, ~0.5

[ccp4bb] close contacts

Dear all, Is it possible to remove all the close contacts from the PDB structure in coot. Please suggest -- WITH REGARDS Rohit Kumar Singh Lab. no. 430, P.I. Dr. S. Gourinath, School of Life Sciences, Jawaharlal Nehru University New Delhi -110067

Re: [ccp4bb] P3212--1's in Space Group Names?

Hi Jacob If you look at SGs P312 and P321in ITC-A you'll see that they are quite different in terms of the arrangement of the a.u.s relative to the symmetry axes. So essentially the 1's are there to distinguish these. The extra 1 or 2 after the 3 of course signifies a screw axis. Note that for

Re: [ccp4bb] how to reduce protein solubility

Thank you, everyone! Francesca From: Enrico Stura [est...@cea.fr] Sent: Tuesday, February 17, 2015 3:00 AM To: CCP4BB@jiscmail.ac.uk; Mattiroli,Francesca Subject: Re: [ccp4bb] how to reduce protein solubility Francesca, The most common failure is to have

[ccp4bb] OT: PhD position available

Dear colleagues I have an MRC-funded PhD position currently available in my lab to study proteins involved in sporulation of the human pathogen Clostridium difficile (details below). I would appreciate if you can pass the information to potential students and/or advertise it in your

[ccp4bb] 20th Anniversary Structural Biology Symposium - Registration is OPEN

20th ANNIVERSARY SCSB Structural Biology Symposium You and your colleagues are cordially invited to join us for the20th Anniversary Structural Biology Symposium to be held at Levin Hall on the University of Texas Medical Branch Campus on beautiful Galveston Island

[ccp4bb] Computational Crystallography Newsletter - Volume 6, Number 1

I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of

Re: [ccp4bb] Refinement with phase/FOM and HL coefficients

Potentially there is more information in the 4 parameters HLA HLB HLC HLD which can describe a bi-modal distribution of phase probabilities( that would be generated by experimental phasing) than can be carried by the 2 parameter PHI FOM which will describe a uni-modal distribution. However if

[ccp4bb] crystal anisotropy measurement?

Hi all, I have a anisotropic crystal with cell dimensions of 78, 78 345. Is there a method for quantitatively measuring the the anisotropy of my diffraction data and a way to compare my data to that of similarly anisotropic crystals? -Cosmo

Re: [ccp4bb] Cis-peptide bond checking

Dear all, The version of Refmac that I currently use through ccp4i has If following features are found in coordinate file then make restraints to maintain them: activated by default for cis-peptides. I usually deactivate it during refinement, but this means that if one does nothing and moving

[ccp4bb] Zero or non-zero FOM DELFWT coefficients?

Hello All, I've noticed that the figure-of-merit (FOM) and weighted difference map coefficients (e.g. DELFWT) for the test set (FreeR_flag = 0) of reflexions in an MTZ file as produced by a certain well-known ML refinement program are all zero, while the same coefficients produced by another

Re: [ccp4bb] how to reduce protein solubility

Hi Francesca, Try some zinc (1mM + ) in your protein buffer? Zinc tends to make a lot of things less soluble in my hands. Dave On Tue, 17 Feb 2015 04:34 Mattiroli,Francesca francesca.mattir...@colostate.edu wrote: Hi all, I am struggling with a protein complex that is too soluble. I have

Re: [ccp4bb] how to reduce protein solubility

Hi Francesca, You could try using reductive methylation, this has always lead to a loss of solubility (and protein!) in my experience­. Jena bioscience and Hampton research sell kits. Best regards, Paul.. [EvotecLogoMail] Paul A. McEwan Ph.D. Principal Scientist, Structural Biology +44. (0)1235

Re: [ccp4bb] how to reduce protein solubility

Francesca, The most common failure is to have an excessive amount of salt (salting in/ salting out), glycerol or other solubilizing ingredient in your protein solution. I would suggest that you change the pH and reduce the salt in your protein solution, by microdialysis if you do not have

[ccp4bb] Refinement with phase/FOM and HL coefficients

Dear all In a few places (Refmac and Phenix, maybe there are also others), there is an option to use either phase/FOM or HL for refinement and DM. Is there any difference between these two? The dataset in question is a Fe SAD dataset. Thanks. Mohamed

Re: [ccp4bb] how to reduce protein solubility

Just a possibility for salvage of your already set-up drops: You can spike the reservoirs with some highly concentrated precipitant (no matter what as long as it sucks more water out of your drop). It does not solve your problem but maybe you can revive a few drops and get more information