Re: [ccp4bb] where to get jre 1.5_22 for mac osx 10.6
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Subbu, are you sure you require jre 1.5? The Coeus download site says: Coeus 4.5 requires Java Runtime Environment 1.6 and **If you are using an older system (Mac, PC, UNIX, Linux or Solaris) that requires Java 1.5, please use this link which to me sounds like the main download should be installable on your Mac. Maybe try a Mac OS X updata, java update and get the latest installer for Coeus. Best, Tim On 09/08/2012 01:40 AM, Ramasubbu, Narayanan wrote: All: Sorry for the non-CCP4 question. But please help!! I have to install jre 1.5_22 on my mac to have the COEUS (MIT software premium). My computer already has java 1.6 How to install the old version. If this old is not on the computer, then the install commands do not work. Thanks a lot Subbu - -- - -- 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/ iD8DBQFQTbDIUxlJ7aRr7hoRAly1AKCQ3lggattmu/Cw1KUJQ7YC5SXEYQCg2rBw 8be1j4SudYperXCPx5TUy6s= =hblU -END PGP SIGNATURE-
[ccp4bb] Final announcement: EMBO Global Exchange Lecture Course: Structural and biophysical methods for biological macromolecules in solution
Structural and biophysical methods for biological macromolecules in solution EMBO Global Exchange Lecture Course 29 November-6 December 2012 Hyderabad, India http://events.embo.org/12-macromolecule/index.html The main objective of the Course is to teach the young PhD students and postdocs from all areas of biology the methods applicable to study biological macromolecules in solution. We aim at a comprehensive coverage of the field including the major structural and biophysical techniques employed for the characterization of high and low resolution structure and structural transitions, macromolecular complex formation, protein folding and stability, protein-protein and protein-ligand interactions and enzymatic mechanisms. The Course will include lectures on small-angle X-ray and neutron scattering (SAXS/SANS), nuclear magnetic resonance (NMR), static and dynamic light scattering (SLS/DLS), analytical ultracentrifugation (AUC), surface plasmon resonance (SPR), differential and isothermal calorimetry (DSC/ITC) and spectroscopic approaches. Bioinformatic tools to analyze protein-protein interactions will also be considered, and the joint use of the solution characterization methods with the major non-solution structural techniques, macromolecular crystallography (MX), electron microscopy (EM), mass spectrometry (MS) and with the in situ methods will be covered. Special attention will be paid to interdisciplinary approaches, where the synergistic use of complementary techniques leads to a comprehensive description of macromolecular systems. From the Indian side, the Course will be co-organized by the Centre for Cellular and Molecular Biology (CCMB), Hyderabad, and the Tata Institute of Fundamental Research (TIFR), Mumbai. The course will be held at CCMB in Hyderabad immediately following an International meeting on biology (25-27 November 2012), commemorating 25 years of moving into the current CCMB RD complex. A maximum of 40 participants will be selected to attend the course. No registration fee will be requested from the academic participants. Applicants from industry are expected to pay a 1000 Euro fee. The Course is oriented towards applicants active in structural biology, mostly late Ph.D. students and early post-docs but more senior scientists, depending on circumstances, could also participate. Students working in India or Indian students working abroad will be given preference but all applications are welcome at http://events.embo.org/12-macromolecule/application.html Application deadline for the Course: September, 17th, 2012 -- Clement Blanchet, Ph.D. EMBL Hamburg Building 25A Notkestrasse 85 22603 Hamburg Germany Tel: +49 40 89902-128 E-mail: clement.blanc...@embl-hamburg.de
[ccp4bb] MX BAG training at Diamond
To all Diamond MX BAG Users, Diamond Light Source will be holding the next training day for MX BAG Users on Wednesday 24th October 2012. The aim of the day is to provide BAG users with sufficient training to be able to operate any of the Diamond MX beamlines efficiently and get the most benefit from their beamtime. It is essential that each BAG sends at least one representative per calendar year. Sessions include: -Automation In Data Analysis and Remote access -Mini-Kappa Goniometer -Sample Humidity Control (HC1) -Microbeam Crystallography -In Situ Diffraction -New GDA Client and ISPyB Registration is free-of-charge with lunch provided on the 24th October and accommodation and dinner for the night of the 23rd October. Travelling expenses within the UK will also be provided. The training is targeted at all BAG members and is not limited to students and post docs. Individuals wishing to register should register here: http://www.diamond.ac.uk/Home/Events/MX-BAG-training/Registration.html Early registration is recommended as places are limited to twenty and registration deadline is on 1st October. Best wishes, Jitka Waterman Dr Jitka Waterman Industrial Liaison Scientist Diamond Light Source Ltd Diamond House Harwell Science and Innovation Campus Didcot, Oxfordshire OX11 0DE United Kingdom E: jitka.water...@diamond.ac.uk www.diamond.ac.uk/industry -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
[ccp4bb] Post-Doc position at Diamond Light Source
Dear all - see below for a postdoc position available immediately at Diamond - don't hesitate to contact me directly for more information. Application details can be found on the Diamond web pages (http://www.diamond.ac.uk/Home/Jobs/Current/DIA0766_TH.html) Martin === Post-Doctoral Research Associate - Macromolecular Crystallography Job Reference DIA0766/TH Post Type Full time / 3 year fixed term Division Science Salary information £28,409 - £35,629; starting salary, dependent on assessment of previous relevant experience and qualifications Application deadline 5th October 2012 Date of interviews TBC Duties Diamond Light Source is the UK's national synchrotron science facility. Located at Harwell Science Innovation Campus in Oxfordshire, we enable world-leading research across a wide range of scientific disciplines and industrial applications.. We are looking for a highly motivated and experienced structural biologist at the Post Doctoral Research Associate level to join a multidisciplinary collaboration formed by groups located at the central laser facility within the Research complex at Harwell, Diamond and the Universities of Strathcylde and Nottingham. The post will be based within the group of Martin Walsh at Diamond. The aim of the project is to combine X-ray crystallography, time resolved 2D-IR spectroscopy and biochemical techniques to study the structure and function of targeted bacterial sensors of nitric oxide. The project will involve elements of biochemistry, structural biology and infrared spectroscopy, including time resolved and multidimensional methods. Expertise in all areas is not required, though a strong background in cloning and overproduction of proteins for structural studies is advantageous. The successful candidate will join ongoing collaborative projects in place between Strathclyde, Diamond, Nottingham and the Research Complex at Harwell that aim to investigate the mechanisms of protein systems from a multidisciplinary perspective. Regular interactions with Strathclyde and the Research Complex are envisaged. As such the project will suit an ambitious and motivated candidate with a strong commitment to multidisciplinary research. Qualifications and Experience: Essential * PhD in biochemistry or related disciplines; or equivalent qualification or experience; * Experience in cloning and recombinant expression of proteins for structural studies * Sound understanding of methods, systems and approaches relating to macromolecular crystallography; * Good laboratory research skills; * Good interpersonal, communication and presentational skills; * Good problem solving skills; * Ability to plan and carry out a research project; * Ability to interact effectively with staff at all levels; * Ability to work on own initiative and take personal responsibility for delivery of work; * Must be available to travel occasionally within the UK and abroad, including overnight absences. Qualifications and Experience: Desirable * Expertise in single crystal protein structure solution * Experience or knowledge of synchrotrons and diffraction experiments; Further Information * Candidates are encouraged to contact Dr. Martin Walsh (martin.wa...@diamond.ac.ukmailto:martin.wa...@diamond.ac.uk) for further details on the responsibilities and research associated with the post. Applying for employment For further details on applying for employment at Diamond, please visit our 'Application Form'http://www.diamond.ac.uk/Home/Jobs/Apply/Form.html page. -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
[ccp4bb] Job opening for a structural biologist to join the “Biocrystallography and Structural Biology of Therapeutic Targets” group at the Institute for the Biology and Chemistry of Proteins, Lyon in
A 2 year postdoctoral position with support from the French National Research Agency (ANR) is available at the Institut de Biologie et Chimie des Protéines, a mixed CNRS and University of Lyon 1 research institute in Lyon, to study the human cytosolic 5’-nucleotidase II. This enzyme plays an important role in the regulation of intracellular nucleotide pools, and due to this regulatory activity, it is partly responsible for the failure of some cancer treatments involving cytotoxic nucleoside analogues. With the aim of increasing the efficiency of these anti-cancer agents currently used in the clinic, our studies involve a multidisciplinary approach, which combines molecular and structural biology along with classical biochemical procedures, bioinformatics and chemical synthesis. The project is therefore conducted within a research consortium gathering cellular-, molecular- and structural biologists but also biochemists and chemists. A Ph.D. in biochemistry or biophysics, and a solid experience in protein expression, purification and X-ray structure determination are required. Background knowledge in Small Angle X-ray Scattering techniques is an advantage. Salary is according to the CNRS guidelines. Lyon is one of the major cities in France and is ideally located in the centre of Europe within two hours of Paris, the Alps and the Mediterranean. It has a strong cultural and intellectual tradition, is widely known as the gastronomic centre of France, and the old town is a UNESCO World Heritage site. The position is immediately available and interested candidates should send their CV, a letter of interest and contact information for 3 referees to Dr. Nushin Aghajari; n.aghaj...@ibcp.fr
Re: [ccp4bb] where to get jre 1.5_22 for mac osx 10.6
Installing Java 1.5 on Snow Leopard http://chxor.chxo.com/post/183013153/installing-java-1-5-on-snow-leopard From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ramasubbu, Narayanan Sent: Friday, September 07, 2012 6:41 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] where to get jre 1.5_22 for mac osx 10.6 All: Sorry for the non-CCP4 question. But please help!! I have to install jre 1.5_22 on my mac to have the COEUS (MIT software premium). My computer already has java 1.6 How to install the old version. If this old is not on the computer, then the install commands do not work. Thanks a lot Subbu
[ccp4bb] comparing differences across multiple structures of the same protein
I am trying to compare structures of the same protein in the apo form and when bound to several different ligands. There are differences, but they are subtle and I am unsure whether they are actually significant or just do to coordinate error or something similar. Is there a theoretical minimum (in Angstroms maybe?) that a side chain or secondary structure element needs to be displaced by between structures to be considered to be real? This may depend on resolution/B-factors as well? Phenix reports overall coordinate error for each structure, but this must vary for at least a bit for certain amino acid residues just like B-factors do.
Re: [ccp4bb] comparing differences across multiple structures of the same protein
I believe that the definition of significant for crystallographic data should be based on the difference map. If a shift of that magnitude causes a feature to appear in the map, then the crystal data is driving the shift. If you can have a shift that large, for the particular atoms in question, and the difference map remains flat then the crystal data doesn't care. A refinement program will move an atom for lots of reasons in addition to the diffraction data, sometimes for no reason at all (simulated annealing, for example). The difference map is a pure expression of the will of the diffraction data. The most sensitive calculation is the F(holo)-F(apo) map, but this requires isomorphous crystals. It might be possible to paste into the holo model a couple residues from the apo model, refine all parameters except the position of these atoms, and see if the Fo-Fc map objects. Remember, a lysine on the surface can probably be built in twenty different conformations and the difference map flat in every case while a couple atoms elsewhere could have a shift of 0.1 A that lights up the map. There are no generic cut-offs or thresholds that work. Dale Tronrud On 9/10/2012 9:01 PM, Michael Murphy wrote: I am trying to compare structures of the same protein in the apo form and when bound to several different ligands. There are differences, but they are subtle and I am unsure whether they are actually significant or just do to coordinate error or something similar. Is there a theoretical minimum (in Angstroms maybe?) that a side chain or secondary structure element needs to be displaced by between structures to be considered to be real? This may depend on resolution/B-factors as well? Phenix reports overall coordinate error for each structure, but this must vary for at least a bit for certain amino acid residues just like B-factors do.
[ccp4bb] Same protein showing different SG
Dear All, Recently I collected one data set for the protein having SG P222 with a= 36.8, b= 44.7, c= 78.4(reported with compound). I crystallized the protein with same kind of other compound. The diffraction was up to 2.3A. But I am facing problem during indexing. I tried with SGP222 (as reported) but the cell dimension was showing a= 41.5, b= 96.3, c= 112.7 and distortion index around 9.83% whereas for SGP2 its showing a= 96.3, b= 41.5, c= 112.7 with distortion index 0.03%. All spots are taken nicely (Denzo). But with P222 predicted spots are completely different than the real one. So I processed it in P2. Surprisingly when I put the reported SGP222 and cell dimensions during scaling (scalepack), for the same data integrated in P2 (just for curiosity), it is showing better data statistics than P2. Anybody experienced this situation? Am I doing any mistake during indexing? Asking for the suggestions. Thanks in advance. Regards, Dipankar Aurigene Discovery Technologies Limited, #39-40 KIADB Industrial Area, Electronic City, Phase II, Hosur Road, Bangalore- 560 100, India Cell: +91-9538631469 | Office Ph : +91 80-66204422 (Extn: 398) | Email ID: dipanka...@aurigene.commailto:dipanka...@aurigene.com This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information.If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.Any unauthorized review, use, disclosure, dissemination, forwarding,printing or copying of this email or any action taken in reliance on this e-mail is strictly prohibited and may be unlawful. Visit us at http://www.aurigene.com
