Re: [ccp4bb] 2Theta data set solving problem
Dear Navin, Maybe a little more explanation: the merging of different runs is done by the scaling program. There is nothing special with different 2theta angles, the only thing is that the scaling program should know about it for applying absorption corrections etc. This is handled automatically and should not require user intervention. For XSCALE you can read in multiple HKL files, for scala/aimless, as Tim pointed out, you first have to combine the different mtz files into one. Scale/aimless should also automatically detect the different runs. Best, Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: Tuesday, April 09, 2013 6:37 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] 2Theta data set solving problem -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Navin, what happens when you read them both into pointless, followed by aimless? Once processed, the data should scale irrespective of the 2theta. If they don't they might be indexed differently, but pointless would fix this. Best, Tim On 04/09/2013 06:15 PM, navin narayanan wrote: hello everybody, Thank you for all your suggestions. I am able to process the 2 data sets separately. But the problem is that I dont have an idea as to how can i merge the 2 data sets with different 2theta values. On Tue, Apr 9, 2013 at 5:48 PM, herman.schreu...@sanofi.com wrote: ** Dear Navin, As others have pointed out, it is not clear where your problem exactly lies: Are you not able to process the 2theta=20° run, or are you not able to merge it with the 2theta=0° run? Anyways, I and others have had similar problems with merging high and low resolution runs, see a very recent thread below: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg30764.html In my case, Scala would fail with low redundancy data or when there are too few reflections in common between both runs. What worked for me is to process with XDS and scale with XSCALE. For this you can use the autoProc procedure of global phasing, or teh Xia2 pipeline which seems to be part of CCP4. Using one of these pipelines will probably also solve your problem if you are not able to process the swing-out run. Good luck! Herman -- *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *navin narayanan *Sent:* Tuesday, April 09, 2013 1:49 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] 2Theta data set solving problem Hello everybody, We have a diffraction data set from home source with 2theta at 20deg. But we are not able to solve the data set using CCP4 suite. The software is picking up only the lower resolution data but not the higher resolution data points. Also we are not able to merge data two sets, one with 2theta at 0deg and the other with 2theta at 20deg. Is there anyway to solve the data. Any help will be truly appreciated. Thank you in advance. Navin V Narayanan - -- 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/ iD8DBQFRZEO4UxlJ7aRr7hoRAv02AKC9ty1xv0Qq6Pd0dwjOpd9uM1Va9QCgyz6e ipQwR9GT3DW8EyvSqIt0MY8= =nxDA -END PGP SIGNATURE-
[ccp4bb] Post-Doctoral Research Fellow - University of Sussex
A Cancer Research UK-funded Postdoctoral Research Fellow position is immediately available in the laboratory of Professor Laurence Pearl FRS and Dr Antony Oliver, to study the structural basis for the assembly and specificity of multi-protein complexes involved in the recognition and repair of DNA damage, and DNA damage signalling. The internationally renowned MRC Genome Damage and Stability Centre and the School of Life Sciences are very well equipped for all aspects of modern structural biology, with state-of-the-art laboratories for molecular biology, recombinant expression in bacterial and eukaryotic hosts, biochemistry, biophysics and X-ray crystallography. Excellent synchrotron access (~ 2 days/month) is also available through rolling beam-allocation programmes at both the Diamond Light Source and ESRF. Applicants must have a PhD, and extensive experience in recombinant expression and protein purification. Previous experience of crystallization and X-ray crystallography would be a distinct advantage. The post-holder will be responsible for expression, purification, crystallization and structure determination of protein-protein and protein-DNA complexes, plus downstream biochemical and biophysical characterisation. The Genome Damage and Stability Centre is an internationally renowned Institute carrying out research on the response of cells to DNA damage, genome instability and its relationship to human disease. We provide a stimulating and supportive environment and our expertise covers a range of experimental systems. Further information about our research can be obtained by visiting our website at: http://www.sussex.ac.uk/gdsc Fixed term for three years, full time. Salary range: starting at £30,424 and rising to £36,298 per annum, commensurate with level of experience. Closing date for applications: 17 May 2013 Expected start date: 1st June 2013 or as soon as possible thereafter. === Please note that previous applicants for Job Reference 768, advertised in August 2012, should not reapply. Full information and instructions for APPLICANTS can also be found at the following URL: http://www.sussex.ac.uk/aboutus/jobs/090 WORD format Application Form: http://www.sussex.ac.uk/humanresources/documents/acadnw.doc PDF format Application Form: http://www.sussex.ac.uk/humanresources/documents/acadnw.pdf Application forms should be completed and sent via e-mail to: lifescirecruitm...@sussex.ac.uk When emailing your application please use the following format in the 'subject' line: (post reference number / post title / your name). If you are applying for more than one post advertised by the University, please send a separate email and application form for each post. Please attach your completed application form and any other documents directly to the email rather than using a web-based upload / weblink service (e.g. SkyDrive) otherwise we may not receive your application due to incompatibility with our email software. Alternatively, completed applications forms may be posted to: Human Resources Division, Sussex House, University of Sussex, Falmer, Brighton, BN1 9RH. Applications should be received by midnight on the closing date. INFORMAL enquiries ONLY may be made to Professor Pearl: laurence.pe...@sussex.ac.uk, or Dr Oliver: antony.oli...@sussex.ac.uk
[ccp4bb] Postdoc Position - Berkeley
Lawrence Berkeley Laboratory Postdoctoral Researcher Job ID: 75785 Division: Physical Biosciences Date Opened: 4/9/2013 Summary: A postdoctoral position is available to work on developing new methods for macromolecular structure determination and refinement with the PHENIX software system. To learn more about Phenix visit: http://www.phenix-online.org Duties: Development and implementation of computational algorithms for structure determination using crystallography. Including methods for the assessment of crystallographic data quality, improved methods for minimization of target functions, algorithms for the automated parameterization of structure refinement, new target functions for the refinement of structures, and enhanced structure deposition tools. Qualifications: Ph.D. in computational crystallography or a related field. Demonstrated experience with computational methods development. Publications in macromolecular crystallography or closely related field. Familiarity with software development tools such as C++, C and scripting languages such as Python. Strong programming and mathematical skills. Solid interpersonal skills and the ability to work in a team environment are critical. Ability to communicate with a broad range of researchers. Note that this is a multi-year position that is renewed annually on the basis on performance and continued funding. Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 13 Nobel Prize recipients over the past 75 years, and 57 present members of the National Academy of Sciences. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov. To apply visit https://lbl.taleo.net/careersection/2/jobsearch.ftl?lang=en and search for the job number 75785 or visit: https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=enjob=75785 -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ] --
Re: [ccp4bb] 2013年4月9日 16:39:16 自动保存莞
Hi Quanju, Pymol is good as it will show you polar contacts (h-bonds and electrostatic interactions/salt bridges). However pi-stacking and pi-cation interactions comes with experience to some extent i.e. being able to recognise them. Coot will help as it shows polar contacts as well as “close contacts”. You can tailor the parameters for “close contacts to assist you in identifying other interactions say up to 4 Angstrom. My instinct still leads to experience. Have a look at a medicinal chemistry text book as a start e.g. Patrick, “An introduction to medicinal chemistry” although from memory there isn’t much on pi stacking. Also keep in mind there are numerous (3) modes of pi stacking; stacked, edge to face as well as triangulated interactions between three rings. For pi-cation, it is somewhat simpler to look at specific amino acids (Arg/Lys) in your protein active site interacting with an aromatic ring (within 4 Angstrom roughly). Hope this helps J From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of xiangquanju Sent: Tuesday, 9 April 2013 8:51 p.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] 2013年4月9日 16:39:16 自动保存草稿 Hello everybody, i am a freshman in structural biology. Right now i encountered two questions and need help from all of you: 1) from the paper, i saw there are three different interactions between the ligand and the residue:(i) hydrogen bonding, (ii) π�Cπ stacking and (iii) cation�Cπ interactions, how can i determine which kind of interaction did happen in my protein. i had chencked that there are no hydrogen bonds between the ligand and the residue. 2) my protein is dimeric in the crystal, when i want to find the polar contacts of one residue (pymol) and found that this residue has differnet polar contacts in the two monomer. Is this acceptable? Thanks in advance! quanju
[ccp4bb] CCP4 Update victim of own success
Hello All, I downloaded a crispy new version of CCP4 and ran update until the update update script disappeared. Is the reason that CCP4 has reached its final update? James
Re: [ccp4bb] CCP4 Update victim of own success
No, it got renamed to ccp4um :) That should have been written in update descriptions, was it not? Eugene On 11 Apr 2013, at 03:54, James Stroud wrote: Hello All, I downloaded a crispy new version of CCP4 and ran update until the update update script disappeared. Is the reason that CCP4 has reached its final update? James -- Scanned by iCritical.
Re: [ccp4bb] CCP4 Update victim of own success
On Apr 10, 2013, at 9:30 PM, eugene.krissi...@stfc.ac.uk eugene.krissi...@stfc.ac.uk wrote:No, it got renamed to ccp4um :) That should have been written in update descriptions, was it not?There was only one mention of "ccp4um" that I could find in all update descriptions that I found (6.3.0-020). I only figured out what information was trying to be communicated because of your message (see attachment).JamesOn 11 Apr 2013, at 03:54, James Stroud wrote:Hello All,I downloaded a crispy new version of CCP4 and ran update until the update update script disappeared. Is the reason that CCP4 has reached its final update?James
