[ccp4bb] 3 PhD and 4 Postdoc positions at MPI Heidelberg
The Department of Biomolecular Mechanisms at the Max Planck Institute for Medical Research in Heidelberg invites people interested in the structure and dynamics of macromolecular switches and assemblies to apply for doctoral degree (Ph.D.) positions (reference number 13/2008) and postdoctoral positions (reference number 14/2008) Our department is an international and interdisciplinary team of four closely interacting groups. Our main research topics are: mRNA processing, chaperone-assisted and unassisted protein folding, and the detailed mechanisms of enzyme-catalysed reactions involving flavin or haem cofactors. We offer a unique environment of top-level scientific research and state-of-the-art technology. For further information, see the groups’ web pages at http://wbmm.mpimf-heidelberg.mpg.de/groups. The stimulating and productive environment provides young scientists with an ideal starting-point for further career steps. Heidelberg is one of the top centres for biomedical research in Germany, and graduate students have access to several different Ph.D. programmes. Candidates should have knowledge of and interest in one or more of the fields mentioned (with respect to either the research topic or the techniques employed), an outstanding track record and excellent skills in spoken and written English. Candidates should send their formal application before February 28, 2009 to bmm.recruitm...@mpimfheidelberg.mpg.de with the reference number given in the subject line. The e-mail should contain a single PDF including - a brief letter, preferably indicating which of the department’s groups would be preferred - a Curriculum Vitae - a full list of publications (if applicable) - a description of past and present research activities (1 page) and - the names and addresses of referees (two for Ph.D. applicants or three for postdoctoral applicants).
Re: [ccp4bb] Molecular replacement using a partial molecular replacement solution
Hi Mo, Phaser sometimes rejects solutions because of clashes in the crystal packing, which may be due to differences between the search model and the target molecule. I would certainly recommend to play around with the PACK keyword to see whether Phaser will find solutions if more clashes are allowed. Best regards, Herman From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Mo Wong Sent: Monday, January 19, 2009 5:37 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Molecular replacement using a partial molecular replacement solution Hello, My problem: I have poorly phased 3.5A data which suggests 6 molecules per ASU, and using MolRep with the experimental phases (search for model in the map) I have good solutions 3 of them. There is a lot of empty electron density which needs to be filled with more copies of the molecule. I have looked for NCS operators as I know this will improve the map and help with model fitting (the Self Rot function suggests I have at least 2-fold symmetry), but no luck yet. My current focus is on using the 3-molecule partial solution as a starting point, but since I'm not getting anywhere fast, I though I'd post to the bulletin board. Can someone please either point me to a MolRep script that allows me to fix the known solutions, use the experimental phases, and search for (3?) more copies of the model, or tell if there is something wrong with the following Phaser scripts below (is it necessary to apply an operator to the MolRep solution before reading into Phaser?). Thanks! # phaser eof MODE MR_FRF HKLIN overall_best_denmod_map_coeffs.mtz LABIN F = FP SIGF = SIGFP ENSEMBLE trimer PDBFILE trimer.pdb IDENTITY 0.25 ENSEMBLE monomer PDBFILE monomer.pdb IDENTITY 0.25 COMPOSITION PROTEIN SEQUENCE trimer.seq NUM 1 COMPOSITION PROTEIN SEQUENCE monomer.seq NUM 3 SOLU 6DIM ENSE trimer EULER 0 0 0 FRAC 0 0 0 SEARCH ENSEMBLE monomer NUM 1 ROOT AUTO_monomer eof # phaser eof MODE MR_FTF HKLIN overall_best_denmod_map_coeffs.mtz LABIN F = FP SIGF = SIGFP ENSEMBLE trimer PDBFILE trimer.pdb IDENTITY 0.25 ENSEMBLE monomer PDBFILE monomer.pdb IDENTITY 0.25 COMPOSITION PROTEIN SEQUENCE trimer.seq NUM 1 COMPOSITION PROTEIN SEQUENCE monomer.seq NUM 3 @AUTO_monomer.rlist ROOT AUTO_monomer2 eof #
Re: [ccp4bb] Replacement for arp_waters?
Dear David, You can use ARP/wARP 7.0.1 (www.arp-warp.org), which should be better than old arp_waters. Either the ARP/wARP GUI module 'ARP solvent' or a command line script auto_solvent.sh Best regards, Victor David J. Schuller wrote: I note that in CCP4 6.1.0, arp_waters has been deprecated. Is there a program in the suite which fills the role formerly filled by arp_waters, of automatically adding waters? Cheers, - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
[ccp4bb] fragments meeting in march
There might be people who are interested in this but have not seen it advertised: there is still place available at a not-too-expensive fragment-based drug design meeting organised by the Royal Society of Chemistry. It takes place March 4th and 5th at our place (AstraZeneca, Alderley Park, Cheshire UK). Further details (programme, pdf of final circular) are available via www.confsec.co.uk Richard Pauptit Associate Director and Principal Scientist Cell, Protein, Structural Sciences AstraZeneca 50S36, Mereside, Alderley Park Macclesfield SK10 4TG Cheshire, UK. email: richard.paup...@astrazeneca.com tel: +44 1625 516135 -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 15 Stanhope Gate, London W1K 1LN. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged 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 unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies.
[ccp4bb] Polarizing filter
We are looking to buy a polarizing filter for our Leica stereomicroscope that we use to observe crystals. However, I am a little confused about the types of filters that are available from photography stores; specifically there are linear and circular polarizers. I would guess that what I need is a linear polarizing filter that can rotate, though these are harder to find than the circular polarizers that seem to be more common for general photography. Any advice? Thanks, Terje --- Terje Dokland, PhD Associate Professor Department of Microbiology University of Alabama at Birmingham 845 19th St South, BBRB 311 Birmingham, AL 35294 Tel:(205) 996 4502 Fax:(205) 996 2667 Do. Or do not. There is no try. -- Master Yoda
Re: [ccp4bb] Polarizing filter
Edmunds Optics and Prinz sell linear polarizers of nearly any thread type/combination, as well as unmounted. Probably cheaper than Leica. Perhaps search the Edmunds site http://www.edmundoptics.com/onlinecatalog/browse.cfm?categoryid=166 BR From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Terje Dokland Sent: Wednesday, January 21, 2009 9:16 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Polarizing filter We are looking to buy a polarizing filter for our Leica stereomicroscope that we use to observe crystals. However, I am a little confused about the types of filters that are available from photography stores; specifically there are linear and circular polarizers. I would guess that what I need is a linear polarizing filter that can rotate, though these are harder to find than the circular polarizers that seem to be more common for general photography. Any advice? Thanks, Terje --- Terje Dokland, PhD Associate Professor Department of Microbiology University of Alabama at Birmingham 845 19th St South, BBRB 311 Birmingham, AL 35294 Tel: (205) 996 4502 Fax:(205) 996 2667 Do. Or do not. There is no try. -- Master Yoda
Re: [ccp4bb] temperature after 30 minutes using microscopes ?
CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK wrote on 01/21/2009 05:50:13 PM: Hi there, *warning, reading beyond this line might expose you to non CCP4 related topics* anybody out there who could do the following experiment: Turn on your microscope and measure the temperature after 30 minutes where you would place your precious crystal tray. Okay. Start: 71.9 F Finish: 73.1 F Temperature measured with thermocouple Scotch-taped to the center of the microscope stage, underneath an empty 96-well plate. Room thermostat set to 70. In particular I'm interested in LED versus Halogen driven models. My light source is halogen, but it's coupled to the microscope through a fiber optic light pipe. I know from experience that the older model scopes with the bulb right in the base get quite warm after they've been on for a while. I'm pretty sure my fiber optic setup can be retrofitted to most microscopes... - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
Re: [ccp4bb] temperature after 30 minutes using microscopes ?
Jurgen, From your question I assume that you are having problems with the warming up of the crystal tray due to the microscope light. Did you consider the use of an external cold light source like the KL1500 LCD? I do not feel anything warming up. Which microscope are you using? The LED systems I have tried are not bright enough. Try them before you buy. Suggestion - request a demo to your supplier. Cheers, Joao João M. Dias, Ph. D. Ollmann Saphire Lab The Scripps Research Institute 10550 North Torrey Pines Rd. IMM-2 La Jolla, CA 92037 USA tel (858)784-8925 http://www.scripps.edu/~jmdias/ On Jan 21, 2009, at 2:50 PM, Jürgen Bosch wrote: Hi there, *warning, reading beyond this line might expose you to non CCP4 related topics* anybody out there who could do the following experiment: Turn on your microscope and measure the temperature after 30 minutes where you would place your precious crystal tray. In particular I'm interested in LED versus Halogen driven models. Is there anybody out there who would like to comment on LED driven microscopes for our purposes ? Thanks, Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Biochemistry and Molecular Biology, W8708 615 North Wolfe Street Baltimore, MD 21205 Phone: +1-410-614-4742 Fax: +1-410-955-3655
Re: [ccp4bb] Polarizing filter
Hi Terje, I think the circular polarizers are really linear polarizers with a 1/4-wave retarder (which make the polarized light circular again) sticked to the back. The reason for them selling the CPs these days is because that digital cameras will have problem metering with LPs. But for human eyes, both should work if you use it properly - meaning looking from the 1/4-wave plate side. And if you are using another one for generating the polarized light, you should make sure the polarizer side is facing the sample, and the 1/4-wave plate side is facing the light source. (a) If you place it so that the polarizer side faces the light source (this is the normal photographic setup): normal circular light---|- polarizer-|-linearly polarized light-|-1/4-wave plate-|-circularized light again. (b)If you place it so that the 1/4 retarder is facing the light source: light---|-1/4wave plate-|-circular light-|-polarizer-|-linearly polarized light As you can see, with setup (b) you can generate polarized light, while with (a) you can filter the light to only let light with certain polarized angle to pass through. Normally the CP filters you get from photographic stores has the polarizer side facing outside, and the 1/4-wave plate facing the camera. If you are not sure, you can use a mirror to check it: put the filter between you and the mirror, look through the filter, if it looks transparent, then the polarizer side is facing the mirror, if the light looks significantly darkened, then the polarizer side is facing you. There is a youtube video that shows it: http://ca.youtube.com/watch?v=6lVIo9C0NDA Zhijie - Original Message - From: Terje Dokland To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, January 21, 2009 12:16 PM Subject: [ccp4bb] Polarizing filter We are looking to buy a polarizing filter for our Leica stereomicroscope that we use to observe crystals. However, I am a little confused about the types of filters that are available from photography stores; specifically there are linear and circular polarizers. I would guess that what I need is a linear polarizing filter that can rotate, though these are harder to find than the circular polarizers that seem to be more common for general photography. Any advice? Thanks, Terje --- Terje Dokland, PhD Associate Professor Department of Microbiology University of Alabama at Birmingham 845 19th St South, BBRB 311 Birmingham, AL 35294 Tel: (205) 996 4502 Fax: (205) 996 2667 Do. Or do not. There is no try. -- Master Yoda
Re: [ccp4bb] temperature after 30 minutes using microscopes ?
Dear Jürgen, Unless you have to spend your money on a microscope immedeately, it is best to evaluate demo instruments from different vendors on site at the same time. All vendors will give you a demo instrument for a few hours to several days. The new Olympus LED instruments are excellent on paper, brighter than the halogen lamps, and produce virtually no heat detectable by hand. However, the new LED-containing base produces a diffuse light on the sample, compared to the focused beam of the old halogen lamp bases. In my opinion, the performance of the LED-containing base is the same or better of a halogen lamp-containing base in the highly oblique and dark field modes. In the bright field mode, the diffuse illumination of the LED base results in flattening of the object. Perhaps, our Olympus demo instrument (with a LED base) had flaws, but it performed worse than an older generation Nikon instrument (halogen lamp) with an objective of a smaller aperture. Petr - Petr Leiman École Polytechnique Fédérale de Lausanne (EPFL) Cubotron/BSP-415 CH-1015 Lausanne Switzerland - Original Message - From: Jürgen Bosch jubo...@jhsph.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, January 21, 2009 11:50 PM Subject: [ccp4bb] temperature after 30 minutes using microscopes ? Hi there, *warning, reading beyond this line might expose you to non CCP4 related topics* anybody out there who could do the following experiment: Turn on your microscope and measure the temperature after 30 minutes where you would place your precious crystal tray. In particular I'm interested in LED versus Halogen driven models. Is there anybody out there who would like to comment on LED driven microscopes for our purposes ? Thanks, Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Biochemistry and Molecular Biology, W8708 615 North Wolfe Street Baltimore, MD 21205 Phone: +1-410-614-4742 Fax: +1-410-955-3655
Re: [ccp4bb] temperature after 30 minutes using microscopes ?
Here are some numbers Matthew.Franklin: Okay. Start: 71.9 F Finish: 73.1 F Temperature measured with thermocouple Scotch-taped to the center of the microscope stage, underneath an empty 96-well plate. Room thermostat set to 70. I should have mentioned that I was thinking about fiberoptics and not the halogen light directly under the tray. Still I always had the impression that there's a significant temperature difference when using the fiberoptics for a long time e.g when mounting crystals. The microscope in question is a Zeiss and the $ difference between LED halogen is about 2.5K in favour of the LED system. I have seen the LED version and it seemed good to me - but I have not looked at crystal trays of course. I'll post a summary in a few days. Thanks for all your replies so far, Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Biochemistry and Molecular Biology, W8708 615 North Wolfe Street Baltimore, MD 21205 Phone: +1-410-614-4742 Fax: +1-410-955-3655
Re: [ccp4bb] temperature after 30 minutes using microscopes ?
We have tested the Zeiss LED plate with hanging and sitting drop trays and found it it unsuitable for looking at crystals. The reason is the really low contrast with this kind of diffuse illumination. Obviously, contrast is generated by refraction at crystal/mother liquor interfaces and this effect diminishes with diffuse light coming from a range of incidence angles. Clemens Zitat von Jürgen Bosch jubo...@jhsph.edu: Here are some numbers Matthew.Franklin: Okay. Start: 71.9 F Finish: 73.1 F Temperature measured with thermocouple Scotch-taped to the center of the microscope stage, underneath an empty 96-well plate. Room thermostat set to 70. I should have mentioned that I was thinking about fiberoptics and not the halogen light directly under the tray. Still I always had the impression that there's a significant temperature difference when using the fiberoptics for a long time e.g when mounting crystals. The microscope in question is a Zeiss and the $ difference between LED halogen is about 2.5K in favour of the LED system. I have seen the LED version and it seemed good to me - but I have not looked at crystal trays of course. I'll post a summary in a few days. Thanks for all your replies so far, Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Biochemistry and Molecular Biology, W8708 615 North Wolfe Street Baltimore, MD 21205 Phone: +1-410-614-4742 Fax: +1-410-955-3655
