[ccp4bb] Announcement: Molecular Graphics Software CueMol version 2.2
Dear All, I'm sorry for off-topic posting. We are pleased to announce the molecular graphics program CueMol version 2.2. http://www.cuemol.org/en/ CueMol is an open-source computer program for the macromolecular structure visualization, especially for the sophisticated publication-quality molecular graphics, with the user-friendly GUI. Main features: - Open source software, distributed under GPLv3 (for non-commercial purposes) - Supported platforms: Windows , MacOS X, and Linux (source code distribution only). - Advanced GUI: -- Tab-based molecular views -- Support for multi-molecular scenes -- Copypaste of objects (across different scenes) -- Support for the complete undo/redo operations (with respect to each scene) - Supported data formats: -- Molecular coordinates in PDB -- Electron density map in X-PLOR/CNS (ascii), CCP4 MTZ and MAP formats -- Molecular surface (MSMS format) -- APBS electrostatic potential map (OpenDX format) - Store and restore of the scene in XML-based format - Supported display: -- Basic molecular display functions (ball-and-stick model, CPK model, etc) -- Cartoon model display with tunable interpolation smoothness -- Edge rendering (with more tunable parameters than PyMOL's one) -- Solvent-excluded molecular surface (including the generation of the cross-section) -- Electron density rendering using GPU shader (mesh and volume rendering) -- Geometric object (solid/dashed lines) - Animation functions: -- Simple spin -- Camera motion -- Display fade in/out -- Structure morphing - Inter-operation with external programs -- Electrostatic potential calculation using APBS and PDB2PQR -- Rendering using POV-Ray -- Movie creation using FFmpeg Upcoming features: - Scripting by python and other script languages - Reading of PyMOL session file (pse format) Sincerely, Ryuichiro Ishitani -- Department of Biological Sciences Graduate School of Science The University of Tokyo Associate Professor, Ryuichiro Ishitani, PhD 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 E-mail: ishit...@bs.s.u-tokyo.ac.jp Tel: +81-3-5841-4394 FAX: +81-3-5841-8057 --
[ccp4bb] Reminder - CCP4 Study Weekend 2015 - Early bird registration and Standard Student bursary deadline is 24th November 2014
The CCP4 Study Weekend (7 - 9 January 2015) East Midlands Conference Centre, University of Nottingham Wednesday 7 - MX User Meeting Thursday 8 / Friday 9 - CCP4 Study Weekend Advances in Experimental Phasing We cordially invite you to participate in the 2015 CCP4 Study Weekend at the the East Midlands Conference Centre, University of Nottingham. The annual CCP4 Study Weekend is a chance to shake off the post-New Year torpor, and work hard and play hard with your fellow crystallographers. Once again, we have put together an exciting scientific programme for the Thursday and Friday, either side of the traditional conference dinner. Please also check out the satellite meetings which may be of interest. The Study Weekend is a chance to catch up with old friends, but is also a chance to meet the CCP4 staff who will be there to present and demonstrate the latest software and to answer questions - please say hello! This year, the topic for the Study Weekend is Advances in Experimental Phasing. In keeping with previous CCP4 meetings, the lectures will focus on the presentation and discussion of advanced methods and techniques developed and used by the leaders in the field. Scientific Organisers Thomas Schneider - EMBL Hamburg (Germany) Airlie McCoy - University of Cambridge (UK) Further details of the program and the registration are at http://www.ccp4.ac.uk/events/CCP4_2015 Please note that we have a limited number of standard student bursaries available to any students to help with the cost of attending the Study Weekend. The deadline for applicants looking to avail of these bursaries is the 24th of November, 2014, so please get your application in before then. Please note that Early Bird registration closes on 24th November after which the cost of registration goes up! Terms and Conditions apply. Please read the cancellation policy before applying. -- Scanned by iCritical.
[ccp4bb] Open postdoc positions in research and scientific software development (EMBL Hamburg, Lamzin)
Dear colleagues, I would like to make you aware of two open positions in the Lamzin group at the EMBL in Hamburg. We are looking for two enthusiastic postdoctoral fellows in research and scientific software development: 1) The post holder will play a key role in the development of the ARP/wARP software for crystallographic structure determination and the building of macromolecular models in 3D electron density maps generated from X-ray diffraction. http://www.embl-hamburg.de/aboutus/jobs/searchjobs/index.php?newlang=1ref=HH_00072back=%2Faboutus%2Fjobs%2Fsearchjobs%2Findex.php%3Floc%3D3%26list%3D1 2) The post holder will be involved in the development of novel software approaches for free electron laser data interpretation beyond phase retrieval and imaging, towards refined models and their validation. http://www.embl-hamburg.de/aboutus/jobs/searchjobs/index.php?newlang=1ref=HH_00073back=%2Faboutus%2Fjobs%2Fsearchjobs%2Findex.php%3Floc%3D3%26list%3D1 The deadline for applications is 7 December 2014. Please apply online through www.embl.org/jobs http://ig14.i-grasp.com//fe/tpl_embl01.asp?newms=apid=53190aid=15470. Further information may be obtained from Victor Lamzin, victor[at]embl-hamburg.de Best regards Philipp -- -- Dr Philipp Heuser Senior Technical Officer EMBL-Hamburg c/o Building 25A, DESY Notkestrasse 85 22603 Hamburg phone: +49 40 89902 128 fax: +49 40 89902 149 mail:philipp.heu...@embl-hamburg.de web: www.philipp-heuser.de --
[ccp4bb] Career Development Fellow Birkbeck University of London
Birkbeck, University of London has a long tradition in structural biology going back to JD Bernal. As part of the institute for Structural Molecular Biology http://www.ismb.lon.ac.uk/ under Prof Gabriel Waksman FRS, it remains a leading centre in the UK for structural biology. The college is using part of its Wellcome Institutional Strategic Support Fund to hire up to 3 two year career development fellows. This is to allow an early career researcher to develop an idea, including collecting preliminary data, to the stage where they would be competitive for a Wellcome or other funding body early career researchers. The application should include an outline of the research plans as well as a description of previous experience. The advert can be found at http://jobs.bbk.ac.uk/fe/tpl_birkbeckcollege01.asp?s=4A515F4E5A565B1Ajobid=55528,9858157887key=85249108c=525423345221pagestamp=sexomqdrzqtzrakcse The deadline is 10th December 2014. Informal enquires can be made to Prof Waksman g.waks...@mail.cryst.bbk.ac.uk -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door
[ccp4bb] The phase problem
Dear all, I would like to known if someone could help me with some idea about the phase problem. I am a beginner in crystallography and the first time I tryed to solve the structure by Molrep, amore, mr. Bump and I didnt find anything for molecular replacement. Thus, currently I've tried to soak heavy-atom ( Hg, Pt, I, Pb) and the diffraction was good, the results in XDS didnt show so good. I didnt look the heavy atom in density. I appreciate any suggestion and ideas what I could do. Best regards, -- Giulliana Rangel Mestranda PPG-Biotecnologia UNIFESP Laboratório de Biologia Estrutural Tel.: (12) 3309-9698 Rua Talim 330, Vila Nair CEP 12231-280 São José dos Campos - SP
Re: [ccp4bb] The phase problem
Screen for heavy atoms with native gel. Run protein with variety of heavy atoms. If you see a discreet shift in the native gel, then you will get derivative. If you don't see a shift, don't bother soaking. It's worked for me every time. Also, ammonium sulfate will mess up your heavy atoms, so if that's in your condition, you need to substitute AmSulf with LiSO4 in your soak. Nick On Wed, Nov 5, 2014 at 2:20 PM, Giulliana Rangel giulliana.ran...@gmail.com wrote: Dear all, I would like to known if someone could help me with some idea about the phase problem. I am a beginner in crystallography and the first time I tryed to solve the structure by Molrep, amore, mr. Bump and I didnt find anything for molecular replacement. Thus, currently I've tried to soak heavy-atom ( Hg, Pt, I, Pb) and the diffraction was good, the results in XDS didnt show so good. I didnt look the heavy atom in density. I appreciate any suggestion and ideas what I could do. Best regards, -- Giulliana Rangel Mestranda PPG-Biotecnologia UNIFESP Laboratório de Biologia Estrutural Tel.: (12) 3309-9698 Rua Talim 330, Vila Nair CEP 12231-280 São José dos Campos - SP -- [This e-mail message may contain privileged, confidential and/or proprietary information of H3 Biomedicine. If you believe that it has been sent to you in error, please contact the sender immediately and delete the message including any attachments, without copying, using, or distributing any of the information contained therein. This e-mail message should not be interpreted to include a digital or electronic signature that can be used to authenticate an agreement, contract or other legal document, nor to reflect an intention to be bound to any legally-binding agreement or contract.]
Re: [ccp4bb] The phase problem
Hi Giuliana, if your crystal diffracts to 3 Å or better and you have at least one Cys/Met per 25 residues, put it on the home source and collect until the sulfur signal rises above the noise. Then solve by SAD. http://www3.imperial.ac.uk/xraycrystallography/learning/sulfur_sad Andreas On 05/11/2014 7:20, Giulliana Rangel wrote: Dear all, I would like to known if someone could help me with some idea about the phase problem. I am a beginner in crystallography and the first time I tryed to solve the structure by Molrep, amore, mr. Bump and I didnt find anything for molecular replacement. Thus, currently I've tried to soak heavy-atom ( Hg, Pt, I, Pb) and the diffraction was good, the results in XDS didnt show so good. I didnt look the heavy atom in density. I appreciate any suggestion and ideas what I could do. Best regards, -- Giulliana Rangel Mestranda PPG-Biotecnologia UNIFESP Laboratório de Biologia Estrutural Tel.: (12) 3309-9698 Rua Talim 330, Vila Nair CEP 12231-280 São José dos Campos - SP -- Andreas Förster X-ray Crystallograhpy Facility Manager Centre for Structural Biology Imperial College London
Re: [ccp4bb] The phase problem
Hi Giulliana, I would (re)check for issues during the assignment of the space group prior to MR. Many people in the list can help you with this if you provide additional information regarding your data. In case you have a structure that can not be solved by MR, I would give a chance for the so-called quick cryo soaking. There are many successful histories of phasing with this approach. Some references that might be useful: http://scripts.iucr.org/cgi-bin/paper?gr0995 (*Acta Cryst.* (2000). D*56*, 232-237) http://scripts.iucr.org/cgi-bin/paper?dz5043 (*Acta Cryst.* (2005). D*61*, 1022-1030) http://www.sciencedirect.com/science/article/pii/S0959440X0200372X (Current Opinion in Structural Biology,Volume 12, Issue 5, 1 October 2002, Pages 674–678) HTH, -Alessandro [ ]s --alessandro 2014-11-05 17:20 GMT-02:00 Giulliana Rangel giulliana.ran...@gmail.com: Dear all, I would like to known if someone could help me with some idea about the phase problem. I am a beginner in crystallography and the first time I tryed to solve the structure by Molrep, amore, mr. Bump and I didnt find anything for molecular replacement. Thus, currently I've tried to soak heavy-atom ( Hg, Pt, I, Pb) and the diffraction was good, the results in XDS didnt show so good. I didnt look the heavy atom in density. I appreciate any suggestion and ideas what I could do. Best regards, -- Giulliana Rangel Mestranda PPG-Biotecnologia UNIFESP Laboratório de Biologia Estrutural Tel.: (12) 3309-9698 Rua Talim 330, Vila Nair CEP 12231-280 São José dos Campos - SP
