[ccp4bb] Reminder: Announcement of the Workshop Diffraction Data Collection Using Synchrotron Radiation
This is a reminder of the announcement of the Data Collection Workshop, which will take place at the BESSY II synchrotron in Berlin from June 13-15, 2013. There is only about 10 days left to the deadline. For details concerning the program, please see: http://www.helmholtz-berlin.de/bessy-mx-workshop/ Manfred Weiss Uwe Mueller We would hereby like to announce the 4th edition of the workshop Diffraction Data Collection Using Synchrotron Radiation, which will take place from June 13-15, 2013 at the BESSY II storage ring of the Helmholtz- Zentrum Berlin for Materials and Energy (HZB) in Berlin. This workshop is the successor to three previous successful workshops, which took place in 2007, 2009 and 2011. It is sponsored by the German Society for Crystallography (DGK) and organised by the DGK Working Group 1 (Biological Structures) in cooperation with Dr. Manfred Weiss and Dr. Uwe Mueller. The workshop comprises a series of basic lectures on the topic and two extended practical sessions. It is aimed at PhD students in Biological Crystallography with little or no experience in diffraction data collection at a synchrotron. The practical sessions will take place at the MX beamlines located at the electron storage ring BESSY II. The workshop fee is 60 EUR for DGK-members and 75 EUR for non-members. This fee covers all conference material as well as board and lodging for two nights on the campus in Berlin-Adlershof. For more information please visit the web page http://www.helmholtz-berlin.de/bessy-mx-workshop/ Registration is now open. Since the number of students will have to be limited to 20 in order to ensure that the practical sessions run efficiently, we expect that the workshop will fill up quickly. Participants are also expected to present a poster on their own work. As previously, the best poster will be awarded with an attractive prize. ## Manfred Weiss Uwe Mueller -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin für Materialien und Energie Macromolecular Crystallography (HZB-MX) Albert-Einstein-Str. 15 D-12489 Berlin GERMANY Fon: +49-30-806213149 Fax: +49-30-806214975 Web: http://www.helmholtz-berlin.de/bessy-mx Email: mswe...@helmholtz-berlin.de -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin für Materialien und Energie Macromolecular Crystallography (HZB-MX) Albert-Einstein-Str. 15 D-12489 Berlin GERMANY Fon: +49-30-806213149 Fax: +49-30-806214975 Web: http://www.helmholtz-berlin.de/bessy-mx Email: mswe...@helmholtz-berlin.de Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de
Re: [ccp4bb] new phaser and threads
Hi Francois, add the keyword JOBS N to your scripts. If it still uses more than N threads, this is possibly a bug. BW, Gabor On Apr 4 2013, Francois Berenger wrote: Hello, Is there a way to tell the new phaser to not use more than N threads when running? I have a problem with it overloading some cluster nodes. Thanks a lot, F.
[ccp4bb] COOT usage for structure comparison
Hello everybody, I have a question about structures comparison in coot 0.7 After aligment I pick up one residue and see only atom name, residue number and chain identifier in status bar. Is there any way to see exact name of molecule ? Example: structures with pdb 3pps and 2q9o were loaded and aligned. After that I pick up one atom and see that this atom belongs to 2q9o, chain a and so on. Thank you in advance, -- Eugene Osipov Junior Research Scientist Laboratory of Enzyme Engineering A.N. Bach Institute of Biochemistry Russian Academy of Sciences Leninsky pr. 33, 119071 Moscow, Russia e-mail: e.m.osi...@gmail.com
Re: [ccp4bb] COOT usage for structure comparison
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear --, you also see the molecule ID in the status bar which matches the ID within the Display Manager Window which in turn shows the name of the structure file you loaded. Best, Tim On 04/04/2013 10:24 AM, Evgeny Osipov wrote: Hello everybody, I have a question about structures comparison in coot 0.7 After aligment I pick up one residue and see only atom name, residue number and chain identifier in status bar. Is there any way to see exact name of molecule ? Example: structures with pdb 3pps and 2q9o were loaded and aligned. After that I pick up one atom and see that this atom belongs to 2q9o, chain a and so on. Thank you in advance, - -- - -- 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/ iD8DBQFRXTnqUxlJ7aRr7hoRAnbuAKD3rihYeILBXPHR+zqS8hG2jatF/wCgrykN GGxrfPvl/pWiQtqa4nz4DhM= =bJCA -END PGP SIGNATURE-
Re: [ccp4bb] COOT usage for structure comparison
On 04/04/2013 04:29 AM, Tim Gruene wrote: Dear --, Are we, the ccp4bb community, recently on the hunt to find new and exciting ways to make sure people stop asking questions? Gentleman from Moscow has clearly disclosed his full name and affiliation, but perhaps I am wrong and subtle criticism of his signature-formatting skills is highly relevant. Feel free to call me Julian from now on :) Cheers, Ed. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] COOT usage for structure comparison
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Ed, I guess your criticism is adequate - I'll stop doing this. My apologies to Eugene. Best, Tim On 04/04/2013 02:43 PM, Ed Pozharski wrote: On 04/04/2013 04:29 AM, Tim Gruene wrote: Dear --, Are we, the ccp4bb community, recently on the hunt to find new and exciting ways to make sure people stop asking questions? Gentleman from Moscow has clearly disclosed his full name and affiliation, but perhaps I am wrong and subtle criticism of his signature-formatting skills is highly relevant. Feel free to call me Julian from now on :) Cheers, Ed. - -- - -- 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/ iD8DBQFRXX9hUxlJ7aRr7hoRAoQOAJ9G9paVwHygxrwOUvYZ1sNpoYhlygCg4Z+n FGU/U7+xE7is5iem8LRME/E= =K6GE -END PGP SIGNATURE-
[ccp4bb] pKa and electrostatic affinity
Dear colleagues: I was wondering if you could kindly share your thoughts and help me understand the relationship between pKa and affinity of a protein for a ligand. Are these two properties related? Specifically, does a lysine with a pKa of 8.5 have a greater affinity for a negatively charged ligand than a lysine with a pKa of 10.5 for the same ligand at physiological pH? Any comments would be highly appreciated. Deepak
Re: [ccp4bb] pKa and electrostatic affinity
A good starting place: Biophys J. 1996 Oct;71(4):2049-55. Evaluation of linked protonation effects in protein binding reactions using isothermal titration calorimetry. Baker BM, Murphy KP. Abstract A theoretical development in the evaluation of proton linkage in protein binding reactions by isothermal titration calorimetry (ITC) is presented. For a system in which binding is linked to protonation of an ionizable group on a protein, we show that by performing experiments as a function of pH in buffers with varying ionization enthalpy, one can determine the pK(a)'s of the group responsible for the proton linkage in the free and the liganded states, the protonation enthalpy for this group in these states, as well as the intrinsic energetics for ligand binding (delta H(o), delta S(o), and delta C(p)). Determination of intrinsic energetics in this fashion allows for comparison with energetics calculated empirically from structural information. It is shown that in addition to variation of the ligand binding constant with pH, the observed binding enthalpy and heat capacity change can undergo extreme deviations from their intrinsic values, depending upon pH and buffer conditions. PMID: 8889179 [PubMed - indexed for MEDLINE] PMCID: PMC1233671 On Apr 4, 2013, at 8:56 AM, Deepak Oswal wrote: Dear colleagues: I was wondering if you could kindly share your thoughts and help me understand the relationship between pKa and affinity of a protein for a ligand. Are these two properties related? Specifically, does a lysine with a pKa of 8.5 have a greater affinity for a negatively charged ligand than a lysine with a pKa of 10.5 for the same ligand at physiological pH? Any comments would be highly appreciated. Deepak
[ccp4bb] ICSG 2013 Abstract Deadline April 30, 2013: International Conference on Structural Genomics - Structural Life Science
Dear Colleagues, We hope that you are planning to attend the International Conference on Structural Genomics 2013, which will be held in Sapporo, Hokkaido, Japan, July 29th – August 1st, 2013. ICSG2013-SLS is intended to provide an overview for the most recent developments in Structural Genomics and its impact on research in biology, medicine and disease, and to foster international collaboration among researchers. Five oral presentations will be chosen from the posters, and three poster prizes will also be awarded! Please submit your abstracts by April 30, 2013. You can see all the details of the conference at: http://www.c-linkage.co.jp/ICSG2013 The scientific topics covered in ICSG2013-SLS include the wider life science research fields with particular attention to drug discovery (small molecules and biopharmaceuticals), biotechnology and industrial issues while keeping strength in the high-throughput technologies and integration of hybrid methods. These technologies are now leading to the new field of “Structural Life Science”. In order to widen the opportunity to young and enthusiastic fellows to study more, we have organized several satellite workshops before ICSG2013- SLS (during the day on July 29, 2013). The topics will include “Small molecule screening”, “Automation of X-ray Structure Determination”, “Cell-free Protein Production”, “Automated NMR methods”, Eukaryotic expression, “Interaction analyses and Bioinformatics”. We hope you also find the satellite workshops are informative and productive. The conference will be held in Keio Plaza Hotel Sapporo, in walking distance of Hokkaido University's main campus and Sapporo station. The summer in Sapporo is a great time to stay and enjoy the cool summer night of Japan. ICSG2-13-SLS is partially supported by the Grant-in-Aid for Scientific Research on Innovative Areas; “Structural Cell Biology”, “Intrinsically Disordered Protein” and “Transient Macromolecular Complexes”, from Ministry of Education, Culture, Sports, Science and Technology (MEXT) . We are looking forward to welcoming you to Sapporo in the summer of 2013. Sincerely yours, Katsumi Maenaka, Ph.D. Chair, International Conference on Structural Genomics 2013 -Structural Life Science- (ICSG2013-SLS) Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Japan Soichi Wakatsuki Chair of Program Committee, ICSG2013-SLS Photon Science, SLAC National Accelerator Laboratory Department of Structural Biology School of Medicine Stanford University The International Structural Genomics Organization Executive Committee Shigeyuki Yokoyama Dino Moras Joel Sussman Jennifer Martin Aled Edwards Tom Terwilliger
[ccp4bb] positions open in Dublin, Ireland
Applications from potential PhD students, post-doctoral fellows, and research technicians are invited for the protein X-ray crystallography group at Trinity College Dublin, Ireland. The projects are diverse and involve the crystallization of bacterial/cellular protein complexes associated with membrane trafficking, as well as viral/cellular complexes that antagonize innate immunity. More information and a publication list can be found on the web pages below. Proficiency in at least two of molecular biology, protein production and crystallographic methods is required for these positions. The lab is located in the center of Dublin, which is a multi-cultural and vibrant city that is well connected to Europe and the USA. Please email a cover letter, CV, and contact information for three references to: Amir Khan School of Biochemistry and Immunology Trinity College Dublin amir.k...@tcd.iemailto:amir.k...@tcd.ie http://www.tcd.ie/Biochemistry/research/a_khan/index.php
[ccp4bb] CCP4 Update 021
Dear CCP4 Users A CCP4 update has just been released, consisting of the following changes. * QtRView: corrected Prosmart result page; enabled incorporation of web-links into citation section If you do not currently receive updates, consider re-installing your CCP4 setup using the latest binary packages, which now have the 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.
[ccp4bb] Building ideal B DNA model in Coot
Hi everyone, I met a problem when trying to build ideal DNA model in Coot. The calculated DNA looks less than 10.5 bp/ turn, probably is about 10 bp/ turn. Is there a way for me to change the pitch to make it 10.5 bp/turn in Coot? Thanks for your kind help! Sincerely, Frank
