Re: [ccp4bb] step refine speed of wincoot
Hi, If you feel the refinement to be too slow, you may turn off the smooth centering (in preferences) or change the centering steps to a smaller number to save unnecessary graphical calculations. To go extreme, you may even remove the real time display commands in the scripts - also a way to test if the difference observed is due to different graphical efficiency. Reducing the size of the displayed map also help. The other thing you may need to consider is that coot/wincoot will save a backup file each time it updates the model, which means on each step of the refinement you have a new file generated. If your windows disk is terribly fragmented then sure you will spend a lot of time on writing these files. The other thing is, windows has a different file caching mechanism from linux, this can also cause a huge difference when a few hundred small temporary files are queued for writing. My impression is that both the ext2/3 file system and the way linux handles caching are more efficient for this kind of situations. You may try deleting the files in wincoot\coot-backup periodically and defragmenting that partition. Making a virtual disk in the RAM to put your backup directory there could be something to experiment on too. Zhijie -- From: Xiaopeng Hu huxp...@mail.sysu.edu.cn Sent: Sunday, March 20, 2011 9:22 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] step refine speed of wincoot Dear all, I found the step refine speed of wincoot is much slower than that of linux coot (with the same pc). Is it normal or I need to configure something with the wincoot? best, Xiaopeng Hu
[ccp4bb] Post-doc project in Grenoble (France)
Contract: Contract/Project Salary range: ? 35,000 and 45,000EUR annual gross Employer: Institut de Biologie Structurale de Grenoble Workplace: Grenoble - FRANCE Skill area: Biology, Medicine, Health - Physics *Application deadline: 4/15/2011* The Institut de Biologie Structurale (IBS), in Grenoble (France) is a research centre in a field that is essential for understanding fundamental biological mechanisms : STRUCTURAL BIOLOGY. IBS is also part of the Partnership for Structural Biology (PSB) whose primary objective is to study proteins of biomedical interest. The PSB constitutes a further step in the development of the region as an International centre of excellence for structural biology. The Partnership for Structural Biology include three pan-European institutes: the ESRF, the world's foremost synchrotron X-ray source, the ILL, a world centre for neutron scattering, the EMBL, the Grenoble Outstation of the European Molecular Biology Laboratory. * Mission: * A two-year post-doctoral position is asked in an application for a grant funded by « Vaincre la Mucoviscidose » and the CV of a candidate must be added to the project. The candidate will be integrated in the « Heavy Metal and Signaling » team at the Institut de Biologie Structurale (IBS) de Grenoble (http://www.ibs.fr/groups/metalloproteins-group/heavy-metal-and-signaling/), close to ESRF, and will participate to a project that aims at addressing the mechanisms by which the P. aeruginosa FUR protein interacts with the first- and second-generation peptide inhibitors already identified by our partners. The proposed study will complete the picture of a fundamental physiological process that is relevant to virulence (iron metabolism) and assess its potential as a new target (iron regulation) for alternative therapeutics. We now need to improve our knowledge on the FUR-antiFUR inhibitor interactions and to obtain a third generation of inhibitors. Deciphering the structure-function relationships of protein/inhibitor complexes will help to design new antibacterial molecules as well as to get insights into the FUR protein mechanism. The candidate will focus on experiments related to biophysics of protein-inhibitor interactions such as determination of the thermodynamic parameters (Biacore technology available in the IBS) and determination of structures by X-Ray diffraction. The HMS group will provide the biochemistry support of the project and our collaborators will bring their experience in conception of FUR inhibitors as well as interaction studies by two-hybrid and/or molecular docking. * Candidates profile: * Structural biology, crystallization, X-ray diffraction, structure determination, thermodynamics, SPR (Biacore). Candidates must have obtained their PhD since less than two years. *Contact: * Send CV and two letters of reference to: jacques.co...@ibs.fr attachment: jacques_coves.vcf
[ccp4bb] Postdoctoral fellow position in structural biology
Dear all, on behalf of Jia-huai Wang, I post this message. For inquiries please contact Jia-huai at jw...@dfci.harvard.edu. Postdoctoral fellow position in structural biology Peking University, College of Life Sciences seeks to recruit dedicated postdoctoral fellows to carry out structural and functional investigation of cell surface receptors in immune and nervous systems. The successful candidates will focus his/her research on elucidation of molecular mechanism with which these receptors play the part in neuronal development and the immune function in central nervous system (CNS). These include their functions in synapse formation and neuron-glia interaction that mediates key immunological protection for CNS. The project is the close collaborative efforts between Professor Jia-huai Wang's structural biology lab and Professor Yan Zhang's neuroscience lab. Position requires PhD. degree with a strong background in molecular biology and protein chemistry. Experiences in crystallography and/or neuroscience will be a plus, but not absolutely required. Highly motivated individuals are encouraged to apply. The position will be based at Peking University in Beijing, China, with opportunity of doing some research at Harvard Medical School in Boston. Peking University is one of the leading academic institutions in China. The College of Life Sciences is equipped with the state-of-art facilities in structural biology for X-ray crystallography, NMR, EM and single molecule studies. The well-known beautiful campus is located at Chinas most advanced academic center with more than 100 research institutes and a dozen highly respected universities. Historically Peking University also has a large international community and attracts students and postdoctoral fellows from all over the world. Interested candidates please email a cover letter, CV, 3 reference names, as well as email address and telephone number to Drs. Jia-huai Wang or Yan Zhang at jw...@red.dfci.harvard.edu and yanzh...@pku.edu.cn. For more information on Wangs group, please see the website: http://wang.dfci.harvard.edu The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[ccp4bb] Postdoctoral position at Princeton University
Postdoctoral position at Princeton University A position is available in the laboratory of Prof. Fred Hughson to apply biochemical and structural approaches to the study of bacterial cell-cell communication, also known as quorum sensing. We are especially interested in the receptors bacteria use to detect small-molecule signals emitted by other cells, and in identifying and characterizing antagonists that block communication. A strong background in biochemistry and/or x-ray crystallography is essential. Please e-mail cover letter, c.v., and names of three references to hugh...@princeton.edu.
[ccp4bb] R and Rfree in twinned crystals
Dear users, What is the allowed range of difference between R and Rfree for structures with twinning? I have a data in R3, after MR (dimer in asu) and Refinement using Refmac-5.5.0102, I ended up getting R ~ 0.231 and Rfree ~ 0.293, difference seemed to be little high. For twinning correction, twin refinement option in Refmac was used. Twinning fraction ~ 0.1. And during refinement (10 cycles) the R-factor was not converging. So is this behavior observed only in case of twinned structures? Kindly give some suggestions. Thanking you With Regards kavya
[ccp4bb] cTruncate failure after data scaling
Dear CCP4, I have encountered the following error message when scaling a recently collected data set. The program run with command: /home/applications/CCP4-6.1.13/ccp4-6.1.13/bin/ctruncate -hklin /tmp/tfr35668/Diamond270211_21_2_mtz.tmp -hklout /tmp/tfr35668/Diamond270211_21_4_mtz_S-SAD1_P43212.tmp -colin /*/*/\[IMEAN,SIGIMEAN\] -colano /*/*/\[I(+),SIGI(+),I(-),SIGI(-)\] -colout S-SAD1_P43212 has failed with error message CCP4MTZfile - internal error terminate called after throwing an instance of 'clipper::Message_fatal' The data have been integrated in imosflm with no apparent problems and Scala scales the data. The problem seems to be that ctruncate then falls over when trying to output the data (I specified the ctruncate run from within the scala window in the CCP4i gui). Searching for this error message doesn't bring up anything useful so could anyone suggest what might be going wrong? Thanks very much, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717
[ccp4bb]
SET CCP4BB REPRO
[ccp4bb] X-ray equipment available
We have the following X-ray diffraction equipment to give away: 1. Rigaku RU300 rotating anode X-ray generator with Haskris cooling system and Charles Supper focusing mirrors. Have not been used lately but are in good working condition. 2. Mar345 area detector. Not in working conditions. Probably good for parts. The equipment is located in Watertown Massachusetts. If interested you will have to arrange for the transport. For more information please contact me directly. With kind regards Zenon Grabarek Principal Scientist Boston Biomedical Research Institute Watertown MA 02472, USA tel 617-658-7805 email: graba...@bbri.org
[ccp4bb] what to do with disordered side chains
The results of the online survey on what to do with disordered side chains (from total of 240 responses): Delete the atoms 43% Let refinement take care of it by inflating B-factors41% Set occupancy to zero12% Other 4% Other suggestions were: - Place atoms in most likely spot based on rotomer and contacts and indicate high positional sigmas on ATMSIG records - To invent refinement that will spread this residues over many rotamers as this is what actually happened - Delet the atoms but retain the original amino acid name - choose the most common rotamer (B-factors don't inflate, they just rise slightly) - Depends. if the disordered region is unteresting, delete atoms. Otherwise, try to model it in one or more disordered model (and then state it clearly in the pdb file) - In case that no density is in the map, model several conformations of the missing segment and insert it into the PDB file with zero occupancies. It is equivalent what the NMR people do. - Model it in and compare the MD simulations with SAXS - I would assumne Dale Tronrod suggestion the best. Sigatm labels. - Let the refinement inflate B-factors, then set occupancy to zero in the last round. Thanks to all for participation, Ed. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
[ccp4bb] kinase purification
Hi All, I am trying to express a kinase but unfortunately there is aggregation happening as the protein is purified over a column. SInce I am new to the field of kinase expression and purification, I was wondering if someone could provide me with a couple of good references that can hit the ground running for me. I would also very much appreciate any helpful suggestions that anyone might have. thanks Neeraj
Re: [ccp4bb] kinase purification
You can use ATP agarose for purification and include the cofactor required right from expression till purification steps. On Tue, Mar 29, 2011 at 8:10 PM, Neeraj Kapoor nkap...@mail.rockefeller.edu wrote: Hi All, I am trying to express a kinase but unfortunately there is aggregation happening as the protein is purified over a column. SInce I am new to the field of kinase expression and purification, I was wondering if someone could provide me with a couple of good references that can hit the ground running for me. I would also very much appreciate any helpful suggestions that anyone might have. thanks Neeraj
Re: [ccp4bb] kinase purification
There is a paper from John Kuriyan on co-expressing a phosphatase with c-Src kinase domain to enable bacterial expression of homogenous protein ( PMID: 16260764). Also look at work from E. Goldsmith (PMID: 16829129) Lastly, I would suggest general approaches, such as: varying the ends of the DNA construct; checking different buffers (EDTA, reducing agents, glycerol, pH, ligands) with use DLS or analytical gel filtration to check for aggregation. Also try low temp induction, or different fusion proteins. Maybe this is a good thing. With our favorite protein we often get aggregation of half the protein. We assume this is the misfolded protein. We pellet this and have dozens of structures using the supernatant. So maybe your aggregation is a feature and not a bug. Kendall Nettles On Mar 29, 2011, at 8:10 PM, Neeraj Kapoor wrote: Hi All, I am trying to express a kinase but unfortunately there is aggregation happening as the protein is purified over a column. SInce I am new to the field of kinase expression and purification, I was wondering if someone could provide me with a couple of good references that can hit the ground running for me. I would also very much appreciate any helpful suggestions that anyone might have. thanks Neeraj
[ccp4bb] MR with MD trajectories
Dear all, I have a protein molecule with two flexible domains. For a 2.8 angstrom data, I could get MR solution for the larger domain but not for the smaller domain (around 80 aminoacids). The second domain appears as extra density showing its presence , but does not allow manual model building on it, since it appers to be smeared. I would like to run a phaser with some 3 structures that I have for this protein from a simulation. Would it be possible to do this in my computer? If so, how can I do this? Any suggestions on this will be appreciated. Thanks in advance. regards, Wandu
