[ccp4bb] Couldn't access the log graph in Aimless
Dear all, I have a problem with opening the log graph in the log file in Aimless with CCP4 suite 6.3.0 (perhaps all the log graphs in all the software). Is anybody know why? Then I try to access the log graph with terminal by typing: loggraph name_aimless.log and the error message pop up: Error in startup script: couldn't load file /home/mauricetam/Documents/Software/ccp4/tcltkplusplus/lib/libBLT24.so: /home/mauricetam/Documents/Software/ccp4/tcltkplusplus/lib/libBLT24.so: wrong ELF class: ELFCLASS32 while executing load $library BLT (procedure LoadBLT line 30) invoked from within LoadBLT 2.4 /home/mauricetam/Documents/Software/ccp4/tcltkplusplus/lib/blt2.4 (package ifneeded script) invoked from within package require BLT (file /home/mauricetam/Documents/Software/ccp4/ccp4-6.3.0/share/ccp4i/bin/loggraph.tcl line 47) invoked from within source [file join $env(CCP4I_TOP) bin loggraph.tcl] (file /home/mauricetam/Documents/Software/ccp4/ccp4-6.3.0/share/ccp4i/bin/loggraph line 5) Regards Heng-Keat
[ccp4bb] PhD position available
A 4-year PhD position is offered at the Biomolecular Sciences and Biotechnology Institute, University of Groningen, the Netherlands. Starting date: position is open. Description The successful PhD candidate will determine X-ray structures of novel cytochrome P450 enzymes, to understand the structural basis of their selectivity and catalytic properties, and to use this insight for developing improved P450 variants. Furthermore, the successful candidate will participate in the activities of the FP7 Marie Curie Initial Training Network called P4FIFTY (http://www.p4fifty.eu), including research collaborations with 8 academic and 2 industrial partners. Qualifications To be eligible, applicants must hold an MSc degree, or comparable, in biophysical chemistry, biochemistry or similar. Experience with protein production/purification, basic molecular biology, X-ray crystallography and biochemical/biophysical characterization of proteins is highly desirable. Applicants should also have good knowledge of English, both written and oral, as the successful candidate will be asked to submit reports and the doctoral thesis in English. The position is offered in the context of a Marie Curie Initial Training Network, and transnational (European) mobility is a key element of eligibility. As such, applications will only be accepted from EU candidates who have spent less than 12 months in the Netherlands within the last three years. Candidates’ eligibility for the post is determined by Marie Curie terms and conditions. Application information Further details of the post and application procedure are available at: http://www.rug.nl/corporate/vacatures/jobOpportunitiesRUG (look for job title: PhD position Crystallography of P450s) Applicants should send: Their Curriculum Vitae A covering letter explaining their motivation for applying and any previous research experience or project work. Two names and contact information for references Please note that, if interested, you will need to apply online through the link above. For more information you can contact Dr. Andy-Mark W. H. Thunnissen, phone: +31-50-3634380; e-mail a.m.w.h.thunnis...@rug.nl
[ccp4bb] two Postdoctoral positions at YSBL
Two Wellcome Trust funded postdoctoral positions are available at York Structural Biology Laboratory, to work with Dr Fred Antson. Both posts are available for 3 years, with potential to extend for a further 2-years. One project focuses on investigating protein-nucleic acid interactions within DNA-translocating molecular motors present in several viruses. This project will involve collaboration with Elena Orlova (Birkbeck College, London), Paulo Tavares and Leonor Oliveira (Unité de Virologie Moléculaire et Structurale, Gif-sur-Yvette), Juan Alonso (Biotecnología Microbiana, Madrid) and Carol Robinson (University of Oxford). The second project will focus on several tRNA-modifying enzymes, in particular, structural and functional studies of human dihydrouridine synthase implicated in lung cancer. This project is in collaboration with Marina Rodnina (Max Planck Institure for Biophysical Chemistry, Goettingen) and Eugene Koonin (NCBI/NIH, Bethesda). Additional information and full details about the application process can be found at: https://jobs.york.ac.uk/wd/plsql/wd_portal.show_job?p_web_site_id=3885p_web_page_id=154693 Fred Antson York Structural Biology LaboratoryTel: +44-(0)1904-328255 Department of Chemistry University of York York YO10 5DD UK
[ccp4bb] Postdoc positions in X-ray crystallography or electron microscopy at Imperial College London
Research Associates: London, United Kingdom Imperial College London Salary: £32,100 - £40,720 per annum Two Research Associate posts are available in the the research group of Professor Paul Freemont (www.msf.bio.ac.uk) in the in the Centre for Structural Biology, at the South Kensington Campus of Imperial College London. Funded by Cancer Research UK and Medical Research Council you will join a group of multi-disciplinary colleagues and collaborators on two unrelated projects. Project one (NS 2012 168 IL) in collaboration with Professor Xiaodong Zhang is aimed at understanding the molecular mechanism and functions of the mammalian AAA ATPase p97 whilst Project two (NS 2012 176 IL) in collaboration with Professor Alain Filloux, will investigate the structure and function of the Type VI secretion system in Pseudomonas aeruginosa. You must hold a PhD in a structural biology or biochemistry discipline or a related discipline, or an equivalent level of professional qualifications and experience. Research experience in a structural biological laboratory environment (covering X-ray crystallography, and/or electron microscopy single particle analysis), and knowledge of protein biochemistry are essential. For informal enquires please contact Professor Paul Freemont (p.freem...@imperial.ac.uk). Our preferred method of application is online via our website http://www3.imperial.ac.uk/employment (please select “Job Search” then enter the job title or vacancy reference – number ( in bold above) including spaces into “Keywords”). Please complete and upload an application form as directed. Closing date for NS 2012 168 IL : 7 September 2012 (Midnight BST) Closing date for NS 2012 176 IL : 17 September 2012 (Midnight BST) *** Professor Paul Freemont Head of Division of Molecular Biosciences Faculty of Natural Sciences Imperial College London South Kensington Campus London SW7 2AZ, UK www.imperial.ac.uk/molecularbiosciences Group: www.msf.bio.ic.ac.uk Co-director of EPSRC Centre for Synthetic Biology and Innovation at Imperial www.imperial.ac.uk/syntheticbiology ***
[ccp4bb] Senior Lecturing Position - University of Huddersfield
Dear all, The University of Huddersfield are advertising for a Senior Lecturing position in Biochemistry. Our X-ray facilities will consist of a new dual source (Mo and Cu), Bruker D8 Venture diffractometer with Photon-100 CMOS detector (to be installed end of 2012). We also have a Bruker Nanostar SAXS. Further details and application forms available on our website http://www.hud.ac.uk/hr/jobs/jobdetail/index.php?jobId=1748 Thanks Richard Dr. Richard J. Bingham PhD. First Year Tutor Senior Lecturer in Biological Science Department of Chemical and Biological Sciences School of Applied Sciences University of Huddersfield Queensgate Huddersfield HD1 3DH United Kingdom Tel 01484472435 Room X1/18 r.j.bing...@hud.ac.ukmailto:r.j.bing...@hud.ac.uk Senior Lecturer in Biochemistry University of Huddersfield -School of Applied Sciences £36,271 - £45,908 Huddersfield Full-time, 1.0 FTE Ref: 6401 The thriving, successful and expanding Department of Chemical Biological Sciences is seeking an enthusiastic individual to play a major role in the development and teaching of undergraduate and postgraduate courses in Biological Sciences and to undertake an active research programme. You should have a research degree and preferably relevant post-doctoral or industrial experience with a good record of publications and the ability to attract research funding. Closing date: 10 September 2012. Interview date: 1 October 2012. Working for Equal Opportunities. Innovative University. Inspiring Employer. Dr. Richard J. Bingham PhD. First Year Tutor Senior Lecturer in Biological Science Department of Chemical and Biological Sciences School of Applied Sciences University of Huddersfield Queensgate Huddersfield HD1 3DH United Kingdom Tel 01484472435 Room X1/18 r.j.bing...@hud.ac.ukmailto:r.j.bing...@hud.ac.uk --- This transmission is confidential and may be legally privileged. If you receive it in error, please notify us immediately by e-mail and remove it from your system. If the content of this e-mail does not relate to the business of the University of Huddersfield, then we do not endorse it and will accept no liability.
[ccp4bb] Strange crystal morphology - needles with a periodic pattern
Hi ccp4bb community, apologies for the off-topic question but I hope someone in the community may have seen something similar before. I'm fighting to optimize some needles that don't currently diffract. After coaxing them into growth large enough to see their shape, I notice they have a funny morphology (photo linked below). Apologies for the blur, the photo is at the zoom limit of our imager; the largest central rod is around 10 um wide. These rods make me think of the WTC One building if it were to be stacked end-on-end, or alternatively, argyle socks. http://imgur.com/5tFun Anyway, so far as I understand, this type of shape is incompatible with the growth of a single crystal, and I wonder what might cause this. They do seem to have diamond-shaped facets with edges, but I can't tell if the facets are flat or have some curvature. In similar conditions, these crystals do splinter quite a bit, and so I might guess that it is a result of some strange amalgam of 1D needles, though the pattern repeats regularly with a period of about 30 um. My two questions are: 1: What might cause this? Could this just be a fluke packing of aligned needles, some effect of lattice distortions, or something else? 2: If it's known, is there anything that might be done to coax these into a better, more prismatic morphology that might diffract? I'm sure the usual strategies about seeding and additives apply, but I wonder if a distorted shape like this might suggest any other avenues of attack. Thanks for your time, Shane Caldwell
[ccp4bb] Phaser and space groups
Hi all, we have been running into a space group issue when we start phaser (2.5.1) through ccp4i since the installation of ccp4-6.3.0: We typically scale data in the point group and then let Phaser go through various space groups. Even though the corresponding line appears in the input file SGALTERNATIVE SELECT LIST SGALTERNATIVE TEST P41 rotation and translation function would only run in the space group provided by the mtz file. Obviously it does not matter for the rotation function. As a work around one can edit the input file (run view com file), by replacing the two lines mentioned above with SPACEGROUP P41 This is a bit inconvenient though. Any ideas what is going wrong with the standard way? Cheers, Jan -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com
[ccp4bb] Changing HETATM to ATOM record
Dear all Is there any tool in CCP4 that can change all HETATM records in PDB file to ATOM? I need the metals to be defined as ATOM for calculation of its normal mode with elNémo. Thank you.
Re: [ccp4bb] Changing HETATM to ATOM record
Hi, Something like this may do the trick: sed 's/HETATM/ATOM /' current.pdb new.pdb Cheers Rob On 20 Aug 2012, at 16:14, Theresa Hsu wrote: Dear all Is there any tool in CCP4 that can change all HETATM records in PDB file to ATOM? I need the metals to be defined as ATOM for calculation of its normal mode with elNémo. Thank you.
Re: [ccp4bb] Phaser and space groups
Hi, As of last week, this is a known bug (defined as one where I got around to adding it to the list on our Phaser Wiki). It has been fixed in the latest nightly builds of Phenix, and a new executable will be released through CCP4 in a few weeks, coordinated with the next stable release of Phenix. It only happens under very specific circumstances, i.e. when you say SGALTERNATIVE SELECT LIST and then give a list with only one element. We didn't think this would happen much because we thought that, if people know which space group they should be using, they will put the correct space group in the MTZ file. If you don't know the correct space group, it's pretty easy to list all of the possibilities in one job and then you don't run into this bug. The new version of Phaser is more clever than the old one about choosing the correct space group (it used to make such decisions prematurely, but now waits until the choice is unambiguous), so there shouldn't be a real incentive to submitting separate jobs for the possible space groups. Thanks for reporting it, and sorry for the trouble! Randy Read On 20 Aug 2012, at 16:06, Jan Abendroth wrote: Hi all, we have been running into a space group issue when we start phaser (2.5.1) through ccp4i since the installation of ccp4-6.3.0: We typically scale data in the point group and then let Phaser go through various space groups. Even though the corresponding line appears in the input file SGALTERNATIVE SELECT LIST SGALTERNATIVE TEST P41 rotation and translation function would only run in the space group provided by the mtz file. Obviously it does not matter for the rotation function. As a work around one can edit the input file (run view com file), by replacing the two lines mentioned above with SPACEGROUP P41 This is a bit inconvenient though. Any ideas what is going wrong with the standard way? Cheers, Jan -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] Changing HETATM to ATOM record
Unix command line: echo | pdbset XYZIN old.pdb XYZOUT new.pdb or pdbset XYZIN old.pdb XYZOUT new.pdb then Ctrl/D (or Ctrl/Z in Windows/DOS). otherwise default settings for pdbset in ccp4i. pdbset does all kinds of PDB file manipulations, including this one. Arguably changing HETATM - ATOM should be an option, not the default, since HETATM is the correct keyword for anything except the standard amino-acids. -- Ian On 20 August 2012 16:14, Theresa Hsu theresah...@live.com wrote: Dear all Is there any tool in CCP4 that can change all HETATM records in PDB file to ATOM? I need the metals to be defined as ATOM for calculation of its normal mode with elNémo. Thank you.
Re: [ccp4bb] Evaluating crystallogarphic experiment
Thanks for all the replies {off list}.
Now it's wait and hope that this crystallization experiment is succesful.
Re: [ccp4bb] Suggestion for storage buffer for protein
Hi Christine, I'm just now catching up on some of your older posts, so this may be too late too help. For Fab crystallization, my successful protein stabilization buffer contained 20-50 mM MES pH 6.0 or 6.5 with the minimum possible amount of salt to stabilize the protein - 50 mM NaCl, perhaps. Low ionic strength seems to be useful for Fab crystallization, though I have seen 2.0 M ammonium sulfate work once. Best, Anna On Fri, May 4, 2012 at 12:37 PM, Harman, Christine christine.har...@fda.hhs.gov wrote: Hi All, I was wondering if any of you could recommend a buffer to store my Fab fragment for crystallization trials. My Fab is currently stored in 0.1M Sodium Acetate pH5, 150mM NaCl and I have had some success with crystallization hits (three conditions that have actually single crystals); however reproducing these seemingly rare events again has been a problem. I am doing another preparation and was thinking of trying a new buffer to store my Fab in for crystallization trials. I have not determined the precise pI of my Fab but it is predicted to be ~8-8.4 based on the sequence. Any suggestions would be greatly appreciated. Thanks, Christine
