Re: [ccp4bb] Confused with pirate::Refine_HL_coeff::operator() function
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jiawei Wang, I suppose the programmer assumed that line 694 is reached at least once during the loop, despite the if-clause around it. But even if this were not the case, many C++ compilers will initialise f2 to zero when it is declared although I don't think the standard guarantees this. Regards, Tim On 01/18/2013 04:02 AM, Jiawei Wang wrote: Hi, all: Please look at the attached figure. In the function Refine_HL_coeff::operator(), the variable f2 was declared on the line 684, and it was assigned to specific Miller indices on the line 694. Once the iteration (690-718) was terminated on the line 718, f2 could be any value. However, on the line 737, f2 was used again without pointing to any specific Miller indices. Could anybody explain the reason for that, or it's a bug? Best, Jiawei Wang - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQ+Q67UxlJ7aRr7hoRAsdAAKDPKVtqzW3Fkrxg9Wdvhe4/2i7jfgCgkCB9 e1+Z50ivoQPyIJ4ZUhwBNhA= =4Trt -END PGP SIGNATURE-
[ccp4bb] Instruct Biennial Meeting 22-24th May - Registration Open
Dear all, Registration for the first Instruct Biennial Structural Biology Meeting taking place on the 22-24th May, 2013, at EMBL Heidelberg Advance Training Centre is now open. Registration for the conference is free. The meeting will showcase integrative structural biology and its impact on biological research and development. Confirmed speakers include: So Iwata, Elena Conti, Tim Springer, Carol Robinson, David Eisenberg, Dinshaw Patel, Roger Sunahara, Thomas Muller Reichert and Wolfgang Baumeister. The talks will represent recent structural biology highlights, emerging methods and technologies and results of biomedical importance. A special session, jointly organised with Euro-Bioimaging, will focus on the bridge between structural and cell biology provided by recent developments in electron, light and X-ray microscopy. The position of Instruct in the wider context of integrated European infrastructure will also be presented. Young scientists interested in gaining a broader understanding of structural biology and its community are especially encouraged to attend. Four abstracts from participants will be chosen to give talks at the meeting. For more details, and to register, visit http://www.structuralbiology.eu/content/instruct-biennial-structural-biology-meeting Best wishes, The Instruct Operations Team * * Dr. Martyn Winn * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * Tel: +44 1925 603455 (DL) or +44 1235 567865 (RcaH) * E-mail: martyn.w...@stfc.ac.uk Skype: martyn.winn * -- Scanned by iCritical.
[ccp4bb] Group Leader Position@ EMBL/CSSB, Hamburg
Dear colleagues, I am writing to inform you that we are currently advertising for a Group Leader position at EMBL Hamburg and the future Center for Structural Systems Biology (CSSB) on the DESY campus in Hamburg, Germany. EMBL is a partner of the future CSSB which aims to promote highly interdisciplinary and collaborative research projects between all partners. The successful candidate will be expected to have experience and research interests in *Membrane Protein Crystallography*, and medically relevant research fields - preferably infection biology. In particular, research interests should include: -innovative use of synchrotron radiation in structural biology -complementary 'hybrid' structural biology approaches -interest in Free Electron Laser applications (optional) -plans for complementary functional experiments The deadline for applications is the *17th March 2013*. For more information, please go to: http://www.embl-hamburg.de/aboutus/jobs/searchjobs/index.php?newlang=1newms=srsearchregion=668 Kind regards, Margret on behalf of Matthias Wilmanns
Re: [ccp4bb] Protein-DNA crystallisation
Dear CCP4 I wish to crystalise a transcription factor in complex with DNA. Are there any good papers you can recommend on protein-DNA crystallisation? Also any helpful tips on protein:DNA ratios, protein concentrations or buffer conditions that have worked for any of you would be most helpful Thanks Careina --- 1) Adjust DNA parameters before protein DNA plays a critical role in crystallization since it is often the source of crystal contacts. Use a ratio for protein to DNA of 1:1.2-5 2) Start with 10-11 base pairs of DNA Increase 1-2 bases at a time, usually stopping at 21 bp. The idea is that a helix forms every 10.5 base pairs and forms a pseudo-continuous helix. 3) Sticky ends The sticky ends do not have to be complementary. Blunt ends can work, but this would not be one of the first variables to change. 4) Screening Expect all the normal fun of protein screening. I would favor PEG or MPD in screens (Natrix) rather than high salt screens. The high salt can disrupt the charged interaction between the protein and DNA. 5) Run a gel If you are unsure if you have protein-DNA complex formation 6) Concentrate your protein-DNA before crystallization trials If precipitation is occurring, consider running DLS to help determine at what concentrations precipitation is occurring References: http://mcl1.ncifcrf.gov/nihxray/Tips-and-Tricks_Crystallization_Protein-DNA_updated.pdf http://bstr521.biostr.washington.edu/PDF/2011%20Protein-DNA%20complexesV06.pdf I hope that helps in getting you started, take care! Sean Seaver P212121 http://store.p212121.com/
[ccp4bb] Golden Jubilee of Ramachandran Plot
http://eventheodd.blogspot.in/2013/01/golden-jubilee-of-ramachandran-plot.html Golden Jubilee of Ramachandran Plot http://eventheodd.blogspot.in/2013/01/golden-jubilee-of-ramachandran-plot.html Exactly fifty years from now i.e. in the year 1963, G. N. Ramachandran et. al published breakthrough original research in Journal of Molecular Biology. Ramachandran plot still remains a touchstone for protein form and structure (example, in validating a homology models). This plot is remarkable because it came ahead of time (it was proposed in 1963 when there were no computers, mechanical calculators were the cutting edge of technology) ... -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
[ccp4bb] Postdoctoral posts as RCaH and Oxford
FIVE POSTDOCTORAL POSTS IN STRUCTURAL AND MOLECULAR BIOLOGY: RESEARCH COMPLEX AT HARWELL (RCAH) AND WEATHERALL INSTITUTE OF MOLECULAR MEDICINE (WIMM) WITH DEPARTMENT OF CHEMISTRY, UNIVERSITY OF OXFORD. Applications are invited for Postdoctoral Scientists (posts 1-3) for three years in an exciting new research programme to discover and develop small molecule inhibitors of mutant RAS for treatment of cancer. This new chemical biology drug discovery programme has co-investigators based at the Weatherall Institute of Molecular Medicine, the Research Complex at Harwell (RCaH) and the Department of Chemistry, Oxford, and is funded by the Wellcome Trust Seeding Drug Discovery Initiative. The aim of the project is to discover small-molecule drugs that inhibit protein-protein interactions involving the RAS family of proteins for treatment of cancer. The project will adopt a highly innovative strategy using single domain antibody fragments as tools for identification of drug-like molecules. Post 1 is for a structural biologist with a PhD in structural biology. Experience with solving structures using X-ray diffraction, crystallography of protein-ligand complexes, co-crystallisation and crystal soaking methods are essential. Experience with surface plasmon resonance and small molecule library screening will be advantageous. The post will be based in the laboratory of Professor Simon Phillips http://www.rc-harwell.ac.uk/directors.html at RCaH (adjacent to the Diamond Synchrotron). Informal enquiries may be made by email to simon.phill...@rc-harwell.ac.ukmailto:simon.phill...@rc-harwell.ac.uk and terence.rabbi...@imm.ox.ac.ukmailto:terence.rabbi...@imm.ox.ac.uk. Applications for this vacancy are to be made online. To apply for this role and for further details, including a job description and selection criteria, please use:- https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=106083 The closing date for this position is noon on Friday 08 March 2013. Please quote reference 106083. Posts 2 and 3 are suitable for molecular biologists with a PhD in molecular biology. Experience with recombinant protein production and purification, DNA transfection of mammalian cells, complex genetic engineering and site directed mutagenesis are essential. Experience with signal transduction cell biology, small molecule library screening and structural biology will be advantageous. The posts will be based in the laboratory of Professor Terry Rabbitts http://www.imm.ox.ac.uk/wimm-research/molhaem/terry_rabbitts at the Weatherall Institute of Molecular Medicine. Informal enquiries may be made by email to terence.rabbi...@imm.ox.ac.ukmailto:terence.rabbi...@imm.ox.ac.uk. Applications online at: https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=106082 The closing date for these positions is midday on Friday 08 March 2013. Please quote reference 106082. Applications are also invited for two postdoctoral positions (Posts 4 and 5) in a new programme, funded by Leukaemia and Lymphoma Research, to discover and develop small molecule inhibitors of oncogenic proteins for the treatment of leukaemia/lymphoma. The posts will be available for 3 years in the laboratory of Professor Terry Rabbitts http://www.imm.ox.ac.uk/wimm-research/molhaem/terry_rabbitts. The aim of this project is to discover small-molecule drugs that inhibit protein-protein interactions involving transcription factor multi-protein complexes in leukaemia and lymphoma. The approach will involve novel strategies using single domain antibody fragments and peptide aptamers, as tools for the identification of drug-like molecules to lead the development for treatment of cancer. The programme involves structural determination of leukaemia proteins together with screening and characterization of small molecule inhibitors of protein-protein interactions. In particular, the project will use the structure of single antibody domains as templates for drug lead development. Posts 4 and 5 are for molecular biologists with a PhD in structural biology, experience with recombinant protein production purification and with solving structures using X-ray diffraction. Experience with surface plasmon resonance, AlphaScreen and other methods for small molecule screening and NMR are desirable. Informal enquiries may be made to Professor Terry Rabbitts at terence.rabbi...@imm.ox.ac.ukmailto:terence.rabbi...@imm.ox.ac.uk. Applications online at: https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=106000 The closing date for these positions is noon on Friday 08 February 2013. Please quote reference 106000.
[ccp4bb] Register now for the CCP-BioSim Conference: Frontiers of Biomolecular Simulation
Dear All, Registration is now open for the second annual meeting of CCP-BioSim Frontiers of Biomolecular Simulation at the University of Nottingham, Monday 25th to Wednesday 27th March 2013. The meeting is open to all - registration provides FREE membership of CCP-BioSim. We have an impressive list of invited speakers: Alessio Ciulli (Cambridge), Gianni De Fabritiis (Barcelona), Philippe Hünenberger (ETH Zurich), Ruth Nussinov (Tel Aviv/NCI), Lars Schaefer (Frankfurt), Nigel Scrutton (Manchester), and Joanna Trylska (Warsaw). Thanks to support from EPSRC and MGMS, we have been able to keep costs low; the registration fee: £50/75 (students/non-students) includes refreshments and conference dinner. On-site accommodation is available separately. If you are interested in presenting a short talk and/or poster REGISTER NOW - DEADLINE IS THE 21ST JANUARY. There are bursaries from the Molecular Graphics and Modelling Society for selected junior researchers. For full details and to register, see: http://www.ccpbiosim.ac.uk * * Dr. Martyn Winn * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * Tel: +44 1925 603455 (DL) or +44 1235 567865 (RcaH) * E-mail: martyn.w...@stfc.ac.uk Skype: martyn.winn * -- Scanned by iCritical.
[ccp4bb] CCP4 Update 014
Dear CCP4 Users A CCP4 update has just been released, consisting of the following changes. All systems: * Ctruncate: Introduced DNA/RNA reference curve; uses flat prior on request, or when have tNCS or twinning * Othercell: Various bug fixes * PISA, QtPISA: Stability fixes and generation of Remark 350 in no-complex situations * PDBCur: Finish gracefully, rather than terminate, when atom selection is empty * PDB_Merge: Various bug fixes * Xia2: Correction to Ctruncate wrapper Linux and Mac only: *) * Aimless: Various bug fixes * Pointless: Correction for XDS input * Scala: Corrected output for CC(1/2) *) Corresponding changes for Windows have been already included in update No 13 Windows only: * Phaser.ensembler: Corrected path to syminfo.lib If you do not currently receive updates, consider re-installing your CCP4 setup using the latest binary packages, which now have CCP4 Update manager (ccp4um) integrated. Note that auto-updates will work correctly only with CCP4 release 6.3.0, therefore upgrade if necessary. Please report any bugs to c...@stfc.ac.ukmailto:c...@stfc.ac.uk Many thanks for using CCP4. Andrey Lebedev -- Scanned by iCritical.
