[ccp4bb] CCP4MG Version 2.4.3
Dear All, Version 2.4.3 of the CCP4 Molecular Graphics Program (CCP4MG) has just been placed on the downloads page: Please note, the change of download location. http://www.ccp4.ac.uk/MG/download/ This release is largely a bug fix release over 2.4.2, it features: * Fixed crashes when generating/deleting symmetry mates and atom clicking. * Added an option (Preferences-Display-Render quality-Use shaders) to enable/disable vertex/fragment shaders for (much) smoother lighting. It currently only handles one light, but does behave correctly with fog, slab and transparency. NB. this option is not saved between sessions (yet). This is not available in the CentOS 4 build. * Movie GUI should be more robust: The combo-box for picking glide frames should work properly and not cause problems if you change type of frame. * Sync to screen refresh. * The Sequence viewer has moved to the Applications menu. * Fixed failure to find sequence alignment executable on OS X. * Text labels fixed in batch mode rendering and in picture definition save. * Zalman stereo no longer needs a resize window hack. * Fullscreen mode. * Many persistent widgets (Geometry, PISA, Movie Editor, Sequence Viewer) are now docked widgets. The Display Table can also be docked, though this is a user option: Preferences-Behaviour-Advanced-Dock display table. Please report problems to ccp...@ysbl.york.ac.uk. Best Wishes, CCP4MG
[ccp4bb] Post-doctoral position
Dear All, A post-doctoral position is available in the research group of Inari Kursula at the Department of Biochemistry, University of Oulu, Finland. The group is mainly working on structural and functional characterization of actin and actin-binding proteins from the malaria parasite. Funding for the position comes from the Sigrid Jusélius foundation and the Academy of Finland and funding for this position is initially guaranteed for two years. We are looking for a highly motivated person with extensive experience in protein expression and purification, biochemical and biophysical characterization, as well as crystallization and structure determination of proteins by X-ray crystallography. Because the group is divided between the University of Oulu, Finland and the Helmholtz Centre for Infection Research on the DESY campus in Hamburg, Germany, the group leader being most of the time in Hamburg, the suitable candidate should be capable of independent planning and conduction of experiments as well as supervising students. The current group in Oulu is formed by one post doc (Marie Curie IIF fellow), one PhD student, and occasional trainees. The successful candidate is expected to be involved in the optimization of expression and purification of several Plasmodium actin-binding proteins, mostly to be produced by co-expression in baculovirus-infected insect cells, and further characterization of the proteins and complexes. The aim is to draw a detailed picture of the actin-based machinery involved in the motility and host-cell invasion of apicomplexan parasites, using a combination of structural biology (in particular X-ray crystallography and SAXS) and modern biophysical methods, such as SPR, ITC, light-scattering, and fluorescence spectroscopy, together with classical actin biochemistry. The University of Oulu is one of the largest universities in Finland, and the Department of Biochemistry hosts about ten research groups and has excellent facilities for protein chemistry and structural biology. In addition, the group has access to all the facilities at the CSSB-HZI at DESY, Hamburg, including ample synchrotron beam time both in Hamburg and elsewhere on Europe synchrotron radiation sources. Applicants should send their CV and the names and contact information of 2-3 referees by e-mail to Inari Kursula (inari.kurs...@helmholtz-hzi.de). More information can be found from http://www.biochem.oulu.fi/tutkimus/ikursula and http://www.desy.de/~inari, and informal inquiries by e-mail are most welcome. The position is to be filled as soon as possible and applications will be considered until 30.11.2010 or until a suitable candidate has been identified. - Inari Kursula, Asst.Prof. Helmholtz Centre for Infection Research and University of Hamburg CSSB-HZI at DESY Notkestrasse 85, Bldg. 25b 22607 Hamburg Germany and Department of Biochemistry University of Oulu Linnanmaa H4 90570 Oulu Finland http://www.desy.de/~inari/ http://www.biochem.oulu.fi/tutkimus/ikursula/ http://cc.oulu.fi/~inkursul/ inari.kurs...@helmholtz-hzi.de, inari.kurs...@oulu.fi +49-(0)40-89986151, +358-(0)8-5531184 -
[ccp4bb] pseudotranslation in C2 space group
Hi, There 1.I have collected two data sets one for the native protein (60Kda) and complex of native with other protein of 8 Kda. The shape of native dataset is cubic while that of the complexed one is triangular. A number of dataset were collected for these two and i successfully indexed them to a spacegroup of C2. 2.While doing molecular replacement for the native data using a monomeric template clear solution with 3 monomers in the asyymetric unit was obtained and structure solved successfully with R/rfee of 19/23 at 2.5A reolution. 3.The molecular replacement of the complexed dataset with the same template gave a solution with 2 monomers in asymmetric unit with a lot of clashes between the two subnuints. when i closely examined the logfile i observed that there was pseudotranslation detected by the program in all of my complex dataset. I run xtiage as well as pointless and truncate which rules out any twinning as well as wrong space group assignment. Pseudotranslation of 18% has been detected by balbes. 4. I also run the Balbes at Murshodov server which gave a solution with 4 monomers in the asymmetric but still showing a lot of clashes in the asymmetric unit (R/Rfree 0.43/0.47) followed by automatic refinemnet with Arp/wARp which gave a model . When i examine the density of the model i saw a lot of clashes in the asymmetric unit but the density are interpretable so that bakbone can be easily modelled. But the R and R free donot goes down from (R/Rfree 0.43/0.47) I have pasted the logfile below from molrep for your convenience. Kindly suggest me how can i proceed with this dataset. That will be very kind of you if you spend some time over my problem. Another question , is it possible that this pseudotranslation is due to the smaller protein of the complex which has slightly changed the crystal packing. ( SDS done on the complex crystals clearly showed the presence of both the proteins). --- Check Patterson for pseudo-translation --- PST_limit : 0.125 of origin peak INFO: pseudo-translation was detected. Origin Patterson peak: P,P/sig : 80563.180 266.237 1 Patterson. peak: p,P/sig : 80560.719 266.228 2 Patterson peak : P,P/sig : 13992.70846.242 3 Patterson peak : P,P/sig : 13992.70846.242 Peak 1: trans.vector /ort/ :60.16498.423 0.000 trans.vector /frac/: 0.500 0.500 0.000 Peak 2: trans.vector /ort/ :31.861 0.000 0.000 trans.vector /frac/: 0.265 0.000 0.000 Peak 3: trans.vector /ort/ :28.30398.423 0.000 trans.vector /frac/: 0.235 0.500 0.000 INFO: translation vector of peak 2 will be used. WARNING: with keyword: PST -- MODE = F , STICK = N Sol_ Space group : C 1 2 1 Sol_ No: 5 Sett: 2 Sol_ Cell: 120.328 196.846 109.285 90.00 113.84 90.00 Sol_--- Rotation function --- Sol_ Radius of gyration : 23.58 Sol_ Radius of integration : 47.16 Sol_ Resmin,Resmax : 48.032.42 WARNING: For this radius integration program uses data included between48.0 and2.71 (angstrom..) --- rfcoef for model --- --- rfcoef for Fobs --- NCS (from Self rotation Function): 1 NCS_model (from Model Self rotation Function): 1 Program will use NCS_model =: 1 Number of RF peaks : 30 thetaphi chialphabeta gamma Rf Rf/sigma Sol_RF 1 106.45 50.401.37 320.211.31 39.410.9325E+05 19.98 Sol_RF 2 0.000.000.000.000.000.000.8668E+05 18.57 Sol_RF 3 158.10 -1.79 120.96 209.61 37.87 33.180.8147E+05 17.46 Sol_RF 422.21 -179.07 120.40 149.19 38.30 327.330.7596E+05 16.28 Sol_RF 5 0.83 144.00 179.87 143.941.66 35.930.4234E+05 9.07 Sol_RF 6 146.73 90.95 73.37 329.03 38.27 327.140.3574E+05 7.66 Sol_RF 7 0.000.00 179.92 97.160.00 82.760.3504E+05 7.51 Sol_RF 834.01 88.19 71.45 29.00 38.12 32.610.3354E+05 7.19 Sol_RF 977.12 174.71 90.84 97.45 87.95 288.040.2136E+05 4.58 Sol_RF 10 134.42 132.297.11 39.815.07 315.220.2089E+05 4.48 Sol_RF 11 152.93 177.57 136.00 21.98 49.92 206.840.1861E+05 3.99 Sol_RF 12 156.31 -169.21 19.45 91.887.78 250.290.1849E+05 3.96 Sol_RF 13 130.28 116.07 92.63 351.98 66.96 299.830.1810E+05 3.88 Sol_RF 14 0.000.00 11.30 11.300.000.000.1808E+05 3.87 Sol_RF 1536.79 -89.11 90.53 219.84 50.36 218.060.1801E+05 3.86 Sol_RF 16 134.90 -102.85 173.11 82.03 90.00 107.720.1761E+05 3.77 Sol_RF 17 106.060.94 54.00 262.92 51.73 81.030.1753E+05 3.76 Sol_RF 18 135.11 85.04 162.00 277.64 88.39 287.56
[ccp4bb] Post Doctoral Research Associate position at Diamond Light Source
Dear CCP4bb We are looking for a highly motivated and skilful Post Doctoral Research Associate to join the MX group at Diamond as member of the I02 beamline team. You will take on a number of ongoing challenging structural biology projects themed around membrane transporter proteins and join our efforts to improve methods for sample handling and data collection. Our target proteins are P-type ATPase and ABC transporters and we benefit from a close collaboration with the Membrane Protein Laboratory at Diamond. We also have a huge interest in continued development of beamline experiments, crystal manipulation, and room temperature data collection. Within Life Sciences at Diamond we also have a range of beamlines dedicated to techniques other than crystallography, and we encourage cross beamline projects which make use of CD, SAXS, and IR spectroscopy, to take advantage of our unique location. We also foresee use of the facilities within the newly opened MRC led Research Complex at Harwell as well as other facilities on site which is a true scientific hub providing numerous enabling facilities. For further information please see http://www.diamond.ac.uk/Home/Jobs/Current/DIA0572-TH.html Application deadline November 12th, 2010. Best wishes Prof. Thomas Sorensen Principal Beamline Scientist I02 Diamond Light Source
Re: [ccp4bb] precipitation after storage
We routinely use a P200 to pipette drops of protein directly into a small Dewar of liquid nitrogen. The protein forms small BB's with a volume of approximately 30 micro-L each. Pipette slowly, allowing the drops to freeze solid before adding the next one. The frozen BB's can be picked up with forceps or a slotted spoon and stored in a cryovial in the -80 freezer. For future experiments, you can thaw only what you need. I have only seen one protein that couldn't recover from this and could only be crystallized prior to freezing. A systematic study of this procedure is described in Deng et al. http://www.ncbi.nlm.nih.gov/pubmed/14684931 --Andrew On 11/5/10 3:40 PM, Eric Karg harvard...@yahoo.com wrote: Dear all, I'm working on a protein which starts to precipitate after 3-4 days of storage at 4 degrees or room temperature. The storage buffer contains 300 mM NaCl because at lower salt concentrations it also tends to precipitate. Different buffers and adding glycerol did not help although this was not done in a systematic way. Has anyone had similar experiences? Any suggestions to overcome this problem? Thanks in advance! Eric -- Andrew M. Gulick, Ph.D. --- (716) 898-8619 Hauptman-Woodward Institute 700 Ellicott St Buffalo, NY 14203 --- Hauptman-Woodward Institute Dept. of Structural Biology, SUNY at Buffalo http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html http://labs.hwi.buffalo.edu/gulick
Re: [ccp4bb] precipitation after storage
A modification of this was done in pcr tubes, and it seemed to work even better: Acta Cryst. (2004). D60, 203-204[ doi:10.1107/S0907444903024491 ] An improved protocol for rapid freezing of protein samples for long-term storage J. Deng, D. R. Davies, G. Wisedchaisri, M. Wu, W. G. J. Hol and C. Mehlin Abstract: Freezing of purified protein drops directly in liquid nitrogen is a convenient technique for the long-term storage of protein samples. Although this enhances reproducibility in follow-up crystallization experiments, some protein samples are not amenable to this technique. It has been discovered that plunging PCR tubes containing protein samples into liquid nitrogen results in more rapid freezing of the samples and can safely preserve some proteins that are damaged by drop-freezing. The PCR-tube method can also be adapted to a PCR-plate freezing method with applications for high-throughput and structural genomics projects. On Mon, Nov 8, 2010 at 8:21 AM, Andrew Gulick gul...@hwi.buffalo.edu wrote: We routinely use a P200 to pipette drops of protein directly into a small Dewar of liquid nitrogen. The protein forms small BB’s with a volume of approximately 30 micro-L each. Pipette slowly, allowing the drops to freeze solid before adding the next one. The frozen BB’s can be picked up with forceps or a slotted spoon and stored in a cryovial in the –80 freezer. For future experiments, you can thaw only what you need. I have only seen one protein that couldn’t recover from this and could only be crystallized prior to freezing. A systematic study of this procedure is described in Deng et al. http://www.ncbi.nlm.nih.gov/pubmed/14684931 --Andrew On 11/5/10 3:40 PM, Eric Karg harvard...@yahoo.com wrote: Dear all, I'm working on a protein which starts to precipitate after 3-4 days of storage at 4 degrees or room temperature. The storage buffer contains 300 mM NaCl because at lower salt concentrations it also tends to precipitate. Different buffers and adding glycerol did not help although this was not done in a systematic way. Has anyone had similar experiences? Any suggestions to overcome this problem? Thanks in advance! Eric -- Andrew M. Gulick, Ph.D. --- (716) 898-8619 Hauptman-Woodward Institute 700 Ellicott St Buffalo, NY 14203 --- Hauptman-Woodward Institute Dept. of Structural Biology, SUNY at Buffalo http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html http://labs.hwi.buffalo.edu/gulick
[ccp4bb] Post-doctoral position available in New York
A post-doctoral position to study cystoskeletal macromolecular assemblies using cryo-electron microscopy is available in our laboratory. For this position the ideal candidate would be interested in solving problems related to protein structure and function and have experience in molecular electron microscopy. Candidates with experience in protein expression and purification with a strong interest in structural biology will also be considered. In our lab we employ a variety of approaches such as site-directed mutagenesis, cryo-electron microscopy and single molecule fluorescence microscopy to investigate cystoskeletal motors at the molecular level (e. g. see: Tan et al., Structure 16: 1732-9, 2008; Asenjo Sosa PNAS 106: 5657-62, 2009).We have access to state of the art facilities for cryo-em work located at the Albert Einstein College of Medicine and at the New York Structural Biology Center that include several cryo-em microscopes (Tecnai 20, Tecnai G2 F20, JEOL 1230, JEOL 2100F, JEOL 3200FSC). Our laboratory is located in the Albert Einstein College of medicine in New York City, which offers excellent opportunities for scientific interaction within the college and with many other scientific institutions in the New York area.Interested candidates please send a letter (or email), CV and reference names to: Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 Office: 718-430-3456 Lab: 718-430-3451 FAX: 718-430-8819 Email: hernando.s...@einstein.yu.edu The Albert Einstein College of Medicine is an equal opportunity employer. -- --- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hernando.s...@einstein.yu.edu --- POST_doctoral_add_2010.pdf Description: Adobe PDF document
[ccp4bb] Postdoctoral Fellow: Computational Systems Biology Postdoctoral Position in Macromolecular Modeling and Protein Structure Prediction
Computational Systems Biology Postdoctoral Position in Macromolecular Modeling and Protein Structure Prediction Center for the Study of Systems Biology at the Georgia Institute of Technology Outstanding Postdoctoral applicants are sought in Computational Systems Biology to work with Professor Jeffrey Skolnick at the Georgia Tech Center for the Study of Systems Biology in the following areas: · Development of algorithms for the prediction of protein tertiary structure using both template based and template free approaches based on both knowledge and physics based force fields. · Development of algorithms for the prediction and refinement of GPCR structures. · Development of approaches to predict RNA-protein interactions. · Application of the above to assist in the structure based annotation of proteomes. · Highly creative, outstanding individuals with a background in biophysics, computational physics, or bioinformatics are sought with the following qualifications: · Demonstrated ability to do high quality research in protein structure prediction, RNA modeling, large scale biological simulations, Brownian Dynamics, bioinformatics, or computational genomics. · A track record of publication in high quality international journals. · Ability to work in a team, yet think independently. · Extensive computer code development experience using languages such as Fortran, C, C++, and/or Perl. To apply please send your CV to: skoln...@gatech.edu.
[ccp4bb] bruker smart and mosflm
I am trying to read Bruker's Smart 6000 images with mosflm and it fails. Based on some limited googlearch I feel that NPIXELB:1 is a relevant information and when these files were processed in HKL (not by me), the relevant detector line says format ccd bruker smart6000 binned. I see from mosflm website that I might be in trouble here although it says that in recent version handling of bruker smart has been improved. In the mosflm crash file I get this From information in the image file, the detector has been recognized as: Bruker SMART If this is incorrect you must supply a DETECTOR keyword So my question is how do I figure out if this particular format is supported or not? Cheers, Ed. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] Nov 15, 2010 deadline- User proposal submission for Collaborative Crystallography at BCSB
Dear Users, The deadline for Jan/Feb 2011 Collaborative Crystallography proposals will be *Nov 15, 2010. * Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; and * Reduced travel costs. To apply, please submit a proposal through the ALS General User proposal review process for beamtime allocation. Proposals are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the CC projects on Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography - How To Apply: To learn more, go to: http://www.als.lbl.gov/als/quickguide/becomealsuser.html To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll down to *Structural Biology beamlines (includes protein SAXS)* and click on New Proposal. Enter your proposal information, with attention to the following details: * For question 3/First choice, select 5.0.1 (Monochromatic); for question 3/Second choice, select 5.0.2 (MAD). * Check box (yes) in response to question (7) Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only) * In question 4, please describe a specific research project with a clear end point. In order to request CC time for Jan/Feb 2011 allocation period, proposals must be submitted by *Nov 15, 2010.* The deadline for CC proposals for the time period Mar/April 2011 will be Jan 15, 2011. Regards, Banumathi Sankaran
Re: [ccp4bb] bruker smart and mosflm
Hi Ed, Bruker used to supply a utility called FRM2FRM that would unwarp their images so that they were readable by Mosflm. You may want to consult them directly; Matt Benning (I believe he's still there) was most helpful when I was having problems with Bruker images a few years ago. HTH, Iain On 11/8/2010 12:01 PM, Ed Pozharski wrote: I am trying to read Bruker's Smart 6000 images with mosflm and it fails. Based on some limited googlearch I feel that NPIXELB:1 is a relevant information and when these files were processed in HKL (not by me), the relevant detector line says format ccd bruker smart6000 binned. I see from mosflm website that I might be in trouble here although it says that in recent version handling of bruker smart has been improved. In the mosflm crash file I get this From information in the image file, the detector has been recognized as: Bruker SMART If this is incorrect you must supply a DETECTOR keyword So my question is how do I figure out if this particular format is supported or not? Cheers, Ed.
