Re: [ccp4bb] On maps and doubts
Dear Israel, I wonder why you do not see anything in your Fo-Fc (mFo-DFc?) maps, since the limit for a (n+1) * mFo - n * DFc map, when n approaches inifinity, is the mFo-DFc difference map. There is nothing wrong in going further like with 4mFo-3DFc maps, but you should bear in mind that they are becoming more and more difference map-like and less and less regular maps. What I think is happening is that since you added your ribosomal factor to preformed crystals, you have incomplete occupancy, say the factor bound only to 50% or less of the ribosomes. This means that you have to go down in contour level from the 3 sigma which is the default for difference maps to maybe 1.5 or even 1 sigma. If the factor is bound indeed at lower level you will see relatively nice density, if nothing is there, you will see only noise. To prove a conformational change at a single residue, I would just leave it out and refine. Since the refinement program has no reason to bias either conformation, the result should be unbiased. However, in the case of partial occupancy, the resulting map will be a superposition of both conformations. Also to reduce model bias, you might want to try the Buster program. Best regards, Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Israel Sanchez Sent: Thursday, October 04, 2012 9:17 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] On maps and doubts Hello everyone, I would like to share my experience with one dataset and request some advice on which is the best way to prove a conformational change seen in a density map. The first issue arose when we were looking for an extra ribosomal factor added to a crystalized ribosome. After careful data collection and refinement (I/sigma last shell 1.2, 3.1A and CC1/2 around 22%) the sigma-A-weighted maps 2mFo-DFc and Fo-Fc does not show any clear difference density that we could interpret as the expected factor. Interestingly, a computed map with coefficients 3mFo-2DFc started to show some features that clearly could be explained as a fragment of the factor. The density improved even more with a B-sharpened map. We have seen this behavior before and I was wondering if someone else is using this kind of maps and may could explain the reason behind this density improvement. Is it a crazy idea to go even higher like 4mFo-3DFc? The second query has to do with which is the best way to prove that a conformational change is present in an specific residue (in this case and RNA base) in your structure. To my knowledge, a classic omit map with simulated annealing would do the job regarding removing the model bias. Actually, I found an interesting alternative in PHENIX called a Kick map, were a series of maps computed from a ramdoinised set of models yields a averaged map ideally free from model bias. Does anyone has a preference for any of those schemes? Are there more alternative to prove a conformational change in a model phased with a molecular replacement solution? Thank you very much in advance. -- Israel Sanchez Fernandez PhD Ramakrishnan-lab MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK
[ccp4bb] off topic: PDB data mining
Dear all, I have a question about Protein Data Bank. Does anyone know how to search for structures based on molecular weight. For example, I want to get a list of all the enzymes (molecular weight, say, 10kD), is it possible to manage it? Thank you in advance! -- Tiantian ** LIFE LIBERTY AND THE PURSUIT OF HAPPINESS **
Re: [ccp4bb] off topic: PDB data mining
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear, the advanced interface of www.pdb.org allows to search within a MW-range. Alternatively you can also specify a chain length. Best, Tim On 10/05/2012 10:01 AM, ChenTiantian wrote: Dear all, I have a question about Protein Data Bank. Does anyone know how to search for structures based on molecular weight. For example, I want to get a list of all the enzymes (molecular weight, say, 10kD), is it possible to manage it? 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/ iD8DBQFQbpjXUxlJ7aRr7hoRAp7eAKDWhqNm6ul/iz1BDMquIADPgANu8ACaAoVU AiL8OgaXKHZd/DCaCeLFrfY= =NUJV -END PGP SIGNATURE-
[ccp4bb] Post Doc - Membrane Protein Nanocrystallography
Project Title: Membrane Protein Nanocrystallography Post Doc Location: AstraZeneca Mölndal, Sweden Description of Opportunity: We have an exciting opportunity for a Ph.D. scientist to join the Discovery Sciences department, a global organisation supporting all innovative Medicines Units (iMeds) within AstraZeneca. The project Membrane Protein Nanocrystallography (NanoMem) is part of the Marie Curie Initial Training Network funded by the European Commission and is a close collaboration between ten different laboratories in Europe from both Universities and Industries. The aim is to exploit synchrotron based micro-focus X-ray beams to address challenging diffraction studies from small membrane protein crystals and the revolutionary new possibilities created by the Xray Free Electron lasers which combine ultrafast X-ray pulses with high brilliance focussing capabilities. NanoMem will exploit the new scientific opportunities created by these technical capabilities through close collaboration between structural biologists, beamline engineers, software developers and industrial partners like AstraZeneca and others. NanoMem is an interdisciplinary training network incorporating membrane protein crystallisation, microcrystal and nanocrystal preparation and handling technologies, microfocus diffraction, software development, structure based drug design and serial femtosecond crystallography. The postdoc is expected to contribute to the overall objectives of the Marie Curie Initial Training Network NanoMem through networking, secondments and joint experiments with the other partners involved. The role's major responsibilities Develop and explore approaches to prepare small well diffracting membrane protein crystals Show strong initiative in developing ideas and bringing them forward to functional use within AstraZeneca and within the NanoMem network Communicate results both within AstraZeneca, the NanoMem Collaboration and externally at meetings and through publications Develop skills in and understanding of the drug discovery process Work collaboratively with other experts within Discovery Sciences, the iMED organisation and within the NanoMem network Minimum experience A recent PhD in one or more of the following areas: Biochemistry focussing on membrane proteins Structural Biology with an interest in membrane protein Preferred experience/requirements Experience working with membrane protein expression and purification Experience in crystallization/X-ray crystallography Ability to design and carry out research independently Strong written and oral communication skills Motivation to work in a multidisciplinary and international environment is fundamental to this position For this position the eligible researcher must not have lived in Sweden more than 12 months for the last three years More Information / Main Supervisors: AZ: Margareta Ek, Ph.D. Associate Principal Scientist, Structure Biophysics, Discovery Sciences. margareta.e...@astrazeneca.com Arjan Snijder,Ph. D. Associate Principal Scientist, Reagents and Assay Development, Discovery Sciences. arjan.snij...@astrazeneca.com Apply online no later than November 14, 2012. To find the ad, search for job number: MOL00VP at http://www.astrazeneca.se/karriar/ledig-tjnstervacancies/job-search--en Please refer to the job number and the title in all correspondence. _ Patrik Johansson Associate Principal Scientist AstraZeneca, RD | Discovery Sciences Pepparedsleden 1, 43183 Mölndal, SWEDEN P +46 31 70 64570, F +46 31 77 63792 -- Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful.
[ccp4bb] Test [My apologies]
My apologies to all for this apparent spam, but one of my colleagues signed up for the CCP4BB recently and despite Ronan Keegan checking that his account has been activated, he has not been receiving CCP4B email. I'm trying to help him track down the problem with this email. This message (including any attachments) may contain confidential, proprietary, privileged and/or private information. The information is intended to be for the use of the individual or entity designated above. If you are not the intended recipient of this message, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or other use of this message or any attachments by an individual or entity other than the intended recipient is prohibited.
[ccp4bb] Postdoctoral Fellow in Mooers Laboratory
Postdoctoral Fellow in Mooers Laboratory Dept. of Biochemistry Molecular Biology College of Medicine University of Oklahoma Health Sciences Center (OUHSC) Oklahoma City, OK, USA A post-doctoral fellow position is available in structural (X-ray diffraction and SAXS) and biophysical studies of RNA. The projects are NIH funded. Previous experience in RNA biochemistry and thermal stability studies would be advantageous. Recent graduates with a strong background in protein purification, RNA purification, or both and an interest in learning crystallography are also encouraged to apply. Job Requirements: --- The position requires a Ph.D. at time of hire with prior experience in RNA or protein biochemistry, molecular biology, and/or biophysical methods. The candidate must have clear oral and written communication skills in the English language and the desire to work as part of a highly motivated team. Applications should be received by December 1, 2012 for full consideration. Interested individuals send to blaine-moo...@ouhsc.edu (1) a cover letter that includes research interests and future goals, (2) a CV that includes a list of publications and presentations and a list of experimental expertise and skills relevant to this position, and (3) contact information (including e-mail addresses) for three references able to assess your scientific abilities, experience, and potential. OUHSC is an Equal Opportunity/Affirmative Action Employer. OUHSC does background checks on all final candidates.
[ccp4bb] 3D Molecules on Android - iMolview App
Dear All, iMolview (http://www.molsoft.com/iMolview.html) is an App that enables you to view protein, DNA, chemicals, and molecular documents on mobile devices in *3D.* We received many requests from CCP4 mailing list members for an Android version. We released the *Android **version *today and it is now available for download on Google Play Store and it is *free*. _Download Sites_ Android Download (Google Play) - https://play.google.com/store/apps/details?id=com.molsoft.imolview iPad/iPhone Download (Apple Store) - http://itunes.apple.com/us/app/imolview-lite/id543731121?mt=8 We have also released a new version of our free desktop molecular viewer ICM-Browser (http://www.molsoft.com/icm_browser.html ) and the ActiveICM plugin ( http://www.molsoft.com/activeicm.html ) for viewing fully interactive molecules in PowerPoint (Windows) and web browsers. Also, if you would like to join us at our next Protein Structure and Drug Discovery workshop we teach how to make fully interactive 3D molecular documents in ICM and more... please see http://www.molsoft.com/trainingreg.html iMolview is under active development and we welcome your feedback and feature requests. Thanks, -- Andrew Orry Ph.D. MolSoft LLC Senior Research Scientist 11199 Sorrento Valley Road, S209 San Diego CA 92121 USA Tel: 858-625-2000 x108 Fax: 828-625-2888 -- www.molsoft.com www.twitter.com/molsoft
