[ccp4bb] Post-doctoral position at Heinrich Heine University, Duesseldorf
Post-doctoral position in structure-function studies on plant-selective herbicides Weed control by selective herbicides is an important instrument to secure global food supply. Recent structural and biochemical studies in our lab have identified new selective inhibitors of a protein essential for plant growth and development. In a collaborative research project funded by the Ministry of Innovation, Science and Research of the state NRW, we aim to establish a detailed structural and functional view of the mode of action of these substances. Other work packages of the interdisciplinary research project will address the effect of these substances on typical soil bacteria and study response dynamics of photosynthesis and whole plant growth to the localized or generalized application of these compounds. Our institute and the associated X-Ray Facility and Crystal Farm of the Heinrich Heine University has facilities for protein crystallography (e.g., Bruker-AXS Prospector X8, Incoatec Microfocus beam, Formulatrix Rockimager imaging system, crystallisation robots Beckman Biomek 3000, Matrix Hydra II, Formulatrix NT8). Our lab is also well equipped with instruments for biochemical and biophysical analysis (e.g., microscale thermophoresis, fluorescence spectroscopy, UV/VIS spectroscopy). We are looking for a highly motivated individual with a strong interest in biochemical and structural characterization of protein-ligand complexes to complement our team. The ideal candidate will have experience and a successful track record of in biochemistry and protein crystallography. The position is available immediately, with funding available for two years at a salary according to the German Public Service salary scale EG 13 TV-L. Please send a cover letter discussing your interests in the laboratory and the project as well as your CV and the names of 2 individuals as references to Professor Dr. Georg Groth, Institute of Biochemical Plant Physiology, Heinrich Heine University, Duesseldorf, 40204 Duesseldorf, Germany (georg.groth[at]hhu.de). Applications will be reviewed until the position is filled. For more information about the lab see http://www.BioChemPlant.hhu.de Best regards, Daniel -- Daniel Schlieper email: daniel.schlie...@tuxomania.net Biochemische Pflanzenphysiologie phone: +49 211 8115232 Heinrich-Heine-Universitaet fax : +49 211 8113569 40204 Duesseldorf, Germany http://www.biologie.uni-duesseldorf.de
Re: [ccp4bb] molrep question - how get our ducks in a row?
Hello Gloria, I usually let Coot display the nearest symmetry molecules (as CA) and save those that fit: Option Save Symmetry Coordinates... and pick the molecule to save. Best regards, Daniel -- Daniel Schlieper email: daniel.schlie...@tuxomania.net Biochemische Pflanzenphysiologie phone: +49 211 8115232 Heinrich-Heine-Universitaet fax : +49 211 8113569 40204 Duesseldorf, Germany http://www.biologie.uni-duesseldorf.de On Thu, 23 Feb 2012, Gloria Borgstahl wrote: Hello all, We are solving a superstructure of a protein complex with 2 parts. Built 6 of the first part and they are all sensibly stacked next to each other. Then we read this into molrep as the fixed model and solved for the second part. The solution was found but the 6 for the second model are in different ASU's and unit cells. What is the easiest way to get everyone together in one asu? We can think of hard ways to do it, but any advice? Thanks, Gloria
Re: [ccp4bb] DSSP server
Hi Jane, the Whatif server lists the secondary structure according to DSSP. http://swift.cmbi.ru.nl/servers/html/index.html - Protein analysis - Secondary Structure, symmetry and accessibility Best regards, Daniel -- Daniel Schlieper email: daniel.schlie...@tuxomania.net Biochemie der Pflanzen phone: +49 211 8115232 Heinrich-Heine-Universitaet fax : +49 211 8113569 40225 Duesseldorf, Germany http://www.biologie.uni-duesseldorf.de
Re: [ccp4bb] 27.5% R/29% Rfree for 1.75A structure (details updated)
Dear Jinjin Zhang, what happens if you treat your data as perfect twin? Maybe you do have a twin after all. Best regards, Daniel -- Daniel Schlieper email: [EMAIL PROTECTED] Molecular Motors Group phone: +44 1883 722306 (x 305) Marie Curie Research Institute fax : +44 1883 714375 The Chart, Oxted RH8 0TL, UK web : http://mc11.mcri.ac.uk On Tue, 29 Jul 2008, JINJIN ZHANG wrote: Dear All, Here are updated details for the high R problem of my 1.75A structure. 1. Protein 100 aa, peptide 6 aa, co-crystalized 2. Space group: P43212. Overall R-fac: 0.3. Redundancy: 5 for 98% of reflections. B-factor:55 3. CNS refinement 4. Phenix xtriage checked, no twinning is suspected. 5. Water molecules added Thanks a lot for all your comments and suggestions. Best, Jinjin Zhang
Re: [ccp4bb] Imidazole's ability to chelate metal ions
Hi Ed, do you have an rule of thump estimating what imidazol concentration would be bad? I suppose 50 mM is not high enough to be bad. I once kept a protein at 4 deg C in 50 mM Imidazole/HCl, 5 mM NaN3, 1 mM DTT, pH 7.0). The protein was fine for about half a year. Maybe I was very lucky. Best regards, Daniel -- Daniel Schlieper email: [EMAIL PROTECTED] Molecular Motors Group phone: +44 1883 722306 (x 305) Marie Curie Research Institute fax : +44 1883 714375 The Chart, Oxted RH8 0TL, UK web : http://mc11.mcri.ac.uk On Fri, 18 Jul 2008, Thomas Edwards wrote: I was wondering - why is imidazole bad for proteins? I've always heard that high concentrations are bad for proteins, but a bit of googling did not reveal the answer. Does it actually react with side chains, or cause unfolding/aggragation? Just wondering... Good tip with the His-SELECT media - thanks Artem! Ed __ T.Edwards Ph.D. Garstang 8.53d Astbury Centre for Structural Molecular Biology University of Leeds, Leeds, LS2 9JT Telephone: 0113 343 3031 http://www.bmb.leeds.ac.uk/staff/tae/ http://www.bmb.leeds.ac.uk/staff/tae/ http://www.bmb.leeds.ac.uk/staff/tae/Research The doubter is a true man of science; he doubts only himself and his interpretations, but he believes in science. ~Claude Bernard From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Jacob Keller Sent: 18 July 2008 01:04 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Imidazole's ability to chelate metal ions Dear Crystallographers, Does anybody happen to know whether imidazole is able to chelate metal ions in solution? It seems reasonable that since it can compete for binding to IMAC resins, it should have some affinity for at least Ni++ and Co++, but what about metal ions like Ca++ and Mg++? I assume that the affinity is weak, but at the concentrations at which we are wont to use it in our elutions (~100-500 mM), does it not seem likely that other metal ions are being competed away from our proteins as well? Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROTECTED] ***
[ccp4bb] 3D mouse?
Hi, has anybody tried 3dconnexion's space mouse with O, coot or ccp4mg? How does it compare to a normal mouse or to a 6 knob rotary encoder? http://www.3dconnexion.com/ Best regards, Daniel -- Daniel Schlieper email: [EMAIL PROTECTED] Molecular Motors Group phone: +44 1883 722306 (x 305) Marie Curie Research Institute fax : +44 1883 714375 The Chart, Oxted RH8 0TL, UK web : http://mc11.mcri.ac.uk
Re: [ccp4bb] How to show density map in pymol?
Dear Yang Li, to quote from Stefan Schmelz's post on this topic: Date: Mon, 29 Oct 2007 08:40:42 + From: Stefan Schmelz [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] pymol help Dear Yanming, To show pretty density of a model you have to import a ccp4 density map and display it around your ligand. The simplest solution is using ccp4 and tick the box Generate weighted difference maps files in CCP4 format when running Refmac5 (one or two cycles are enough). Specify names for FWT and DelFwt maps and rename the maps afterwards to *.ccp4. This renamed map (e.g. fwt.ccp4) can be opened in pymol. [...] -- Daniel Schlieper email: [EMAIL PROTECTED] Molecular Motors Group phone: +44 1883 722306 (x 305) Marie Curie Research Institute fax : +44 1883 714375 The Chart, Oxted RH8 0TL, UK web : http://mc11.mcri.ac.uk On Wed, 31 Oct 2007, yang li wrote: Hi All, If I want to show the density map in pymol--like coot open mtz file--, what format should I use? It seems pymol doesnot recognise the mtz format . Thanks!
Re: [ccp4bb] R-sleep
Does Refmac prints this value (observations (with restraints) over parameter) somewhere in the log file? Maybe it does, and I just cannot find it. However, I do find the numbers of observation, restraints and atoms, so it is easy to calculate manually. But wouldn't it be useful to have this value calculated at each refinement step? Best regards, Daniel On Mon, 1 Oct 2007, Ian Tickle wrote: [...] we are working with an observation/parameter count ratio of say 3 (naturally I'm counting the geometric restraints with the X-ray observations). [...] -- Daniel Schlieper email: [EMAIL PROTECTED] Molecular Motors Group phone: +44 1883 722306 (x 305) Marie Curie Research Institute fax : +44 1883 714375 The Chart, Oxted RH8 0TL, UK web : http://mc11.mcri.ac.uk
Re: [ccp4bb] Eden SUSE linux libfftw.so.2
Hi Juergen, it might be worthwhile to search for this library in SuSE's software installation program. It should be in the development section. The RPM file from another provider will probably work, too. If all else fails, you can install it from the sources (www.fftw.org). Best regards, Daniel -- Daniel Schlieper email: [EMAIL PROTECTED] Molecular Motors Group phone: +44 1883 722306 (x 305) Marie Curie Research Institute fax : +44 1883 714375 The Chart, Oxted RH8 0TL, UK web : http://mc11.mcri.ac.uk
