[ccp4bb] Two PhD two postdoc positions in protein structure prediction
Two PhD. and two postdoc positions are available in the field of 3D protein structure prediction at the Bioinformatics Center (http://www.binf.ku.dk), Department of Molecular Biology, University of Copenhagen, Denmark. The positions (funded by the Danish Council for Strategic Research) are part of a project that aims at simulating protein dynamics on long time scales with coarse grained models, and is in close collaboration with Novozymes A/S. The projects are built around probabilistic models of protein structure (see PLoS Comput. Biol., 2006, vol. 2, issue 9, e131), Monte Carlo simulations (see Eur. Phys. J. B, 2002, 29, 481-484) and estimation of force fields (see Phys. Rev. E, 2004, vol 70:030903). Candidates must have experience in physics, mathematics, computer science, bioinformatics, or a related relevant subject. Candidates ideally have programming experience in C or C++. Knowledge of Python is a plus. For more info, see: http://www.binf.ku.dk/JobsNABIIT_0507 http://www.binf.ku.dk/Job4Apr17 Best regards, Thomas Hamelryck Group leader Structural Bioinformatics Bioinformatics center Institute of Molecular Biology University of Copenhagen Ole Maaloes Vej 5 DK-2200 Copenhagen N Denmark http://www.binf.ku.dk/User:Thomas_Hamelryck http://www.binf.ku.dk/Protein_structure
Re: [ccp4bb] scala and cell dimensions
I dont know but I would check whether there is some residual P422 info somewhere.. Eleanor Jan Abendroth wrote: Hi mosflm experts, last week's problem with mosflm solved, another one appearing. Scala fails with the error message below. These are ~10AA data. Scala finishes in p422, however dies in p222... Any ideas? Cheers Jan ~ scala.log Run(s):1 * Wavelength and cell extracted from Batch headers, with rms variation: * Wavelength: 1.541800 Cell:125.750 126.277 158.322 90.00090.00090.000 * rms0.00 rms 0.000 0.000 0.000 0.000 0.000 0.000 ERROR: cell deviates too much from constraint Relative length error0.000 Angle error 0.00 Cell constraints: Scala: *** Error in batch cell dimensions ***
Re: [ccp4bb] How to determine ligand binding from diffraction pat tern?
There are several scenarios and it is hard to generalise. Certainties are: 1) The better your data the easier it is to see a ligand. At 3A it can be hard to model a blob, but it is usually straightforward at 2A. It is harder if your data is twinned etc.. 2) There is a lot of unnecessary and confusing molecular replacement done. If your ligand data is reasonably isomorphous ( similar cell and space group) then the berst procedure is to start from your known structure and do rigid body refinement first to correct for any small changes of cell. If you do a full blown MR run you are very likely to get a solution on a different origin - this is formally correct but makes it hard to overlap the maps! I often merge the 2 data sets and do a Scaleit check to see how the differences seem.. 3) It is a good idea to inspect the ligand map AND the apo map at the same time to see what has changed around the active site - it isnt only ligand you are insterested in - have side chains or waters moved? 4) If desperate, it can help to do an Fobs_lig -Fobs_apo if they are isomorphous enough - Eleanor Schubert, Carsten [PRDUS] wrote: Aha Dr. Palm Tough to generalize this, but if the ligand is weak or the site only partially occupied you need to refine almost to completion. Since you seem to be doing something akin to fragment screening I can only pass on my experience. I had plenty of cases where the Rfree was ~35 after a rigid body refinement and the ligand density was practically indistinguishable from bound water. Refinement to an Rfree of ~25 with waterpicking/pruning resulted in clear enough density to place the ligand. This is probably overkill for very tight binders but necessary for weak binders. phenix works pretty well for this since one can do rigid body refinement, individual positional refinement and B-refinement all in one shot. Ciao Carsten -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of Palm Sent: Tuesday, May 29, 2007 4:25 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] How to determine ligand binding from diffraction pattern? I would like to expand on the question and answer below and compare your experiences: Looking for ligands in many different soaks / cocrystals of your protein of interest, you still should do molecular replacement and a bit of refinement. I agree with Steve, but how much refinement is necessary and enough? We have a specific case with a 24 kDa protein crystallizing in P6522 with resolution of 2.5 - 3 A, which should be comparable to most cases. The ligands have 10 - 20 non-hydrogen atoms (most of the time we don't know, we are actually screening for them). How far should we refine to see if we have only water molecules or a ligand bound - to an Rfree of 0.45 or 0.40 or 0.35? greetings Gottfried Dear all, Is there a simple way to determine whether ligand is bound or not by comparing the diffraction patterns between ligand-free (structure known) and ligand-soaked protein crystals? I would like to solve the ligand bound protein structure, but before I do so, I have to find out if the ligand is actually bound. Thank you very much! Best, Joe Having done this a few hundred times, I would strongly suggest that you just collect the data and solve the structure. Since you already have the apo structure solved, then it really isn't that much work to do an MR solution on the complex. Be aware that quite frequently there is enough non-isomorphism to necessitate partial refinement of the complex structure before recognizable density will appear for the ligand. The definitive answer can only be obtained with a full data set, so go for it. Good luck- Steve === WEB-Mailer der Uni-Greifswald ( http://www.uni-greifswald.de/ ) ===
Re: [ccp4bb] How to determine ligand binding from diffraction pattern?
We have a specific case with a 24 kDa protein crystallizing in P6522 with resolution of 2.5 - 3 A, which should be comparable to most cases. The ligands have 10 - 20 non-hydrogen atoms (most of the time we don't know, we are actually screening for them). How far should we refine to see if we have only water molecules or a ligand bound - to an Rfree of 0.45 or 0.40 or 0.35? greetings Gottfried In my opinion, this is not easy to reduce to a single number since there are too many variables. True resolution and quality of the data, the actual non-isomorphism (and in particular conformational changes), B-factor of the ligand, etc. The coy answer would be enough refinement to convince yourself that it is or isn't there, but in all seriousness, it does boil down to a judgment call on when you have reached the point of diminishing returns. I think the problem is particularly complex with the fragment screening work you describe, since you may or may not know where the ligands are actually binding. Tricky stuff indeed. Steve -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. --
Re: [ccp4bb] How to determine ligand binding from diffraction pat tern?
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Eleanor Dodson Sent: 30 May 2007 10:16 To: Schubert, Carsten [PRDUS] Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] How to determine ligand binding from diffraction pat tern? 2) There is a lot of unnecessary and confusing molecular replacement done. If your ligand data is reasonably isomorphous ( similar cell and space group) then the berst procedure is to start from your known structure and do rigid body refinement first to correct for any small changes of cell. If you do a full blown MR run you are very likely to get a solution on a different origin - this is formally correct but makes it hard to overlap the maps! Often, even with soaked ligands the cell dimension changes are not small, e.g. I've seen up to 10%, and in many cases RB refinement simply doesn't work, even if you cut the resolution to say 4 Ang (which you would hope should increase the radius of convergence). But it's indeed totally unnecessary, and for the reasons you mention actually undesirable to do a full MR search. With Phaser for example in 'Brute Force' mode you can do 'ROTATE AROUND EULER 0 0 0 RANGE r' and 'TRANSLATE AROUND ORTHOGONAL POINT 0 0 0 RANGE d' (e.g. r = 10 deg, d = 5 Ang should normally do the trick). This does a limited search around the origin (and is also much quicker than a full BF search!!). -- Ian Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
[ccp4bb] Swiss Light Source - Beamline Scientist Position
*We are looking for a Beamline Scientist for the Swiss Light Source* The Paul Scherrer Institut is a centre for multi-disciplinary research and one of the world’s leading user laboratories. With its 1200 employees it exists as an autonomous institution within the Swiss ETH domain, and concentrates its activities on solid-state research and material sciences, elementary particle and astrophysics, energy and environmental research as well as on biology and medicine. The Swiss Light Source (SLS) is one of the most advanced radiation sources worldwide. The SLS operates two state-of-the-art undulator beam lines for protein crystallography. The Macromolecular Crystallography group is involved in several aspects of protein crystallography including the design and construction of new beamline components as well as various structural biology projects. We are looking for a Beamline Scientist for beamline X10SA of the SLS. Your tasks You will be responsible for the operation, and the further development and automa- tion of the undulator beamline X10SA at the SLS, in close collaboration with the MX-group. The position offers the opportunity to develop an independent scientific research programme in the field of protein crystallographic methods development including the supervision of PhD students and postdocs. The infrastructure of the PSI structural biology group will be available for you to pursue your own crystallo- graphic research projects. Your profile You hold a Ph.D. degree in biology or (bio-) chemistry, and have several years of experience in either protein crystallography or related beamline instrumentation. Knowledge of spectroscopic techniques is a plus. If you are a good team player with fine communication skills and sense of responsibility, this position will offers a great opportunity for you to develop your research career in an exciting and highly multi- disciplinary environment. We are looking forward to your application. For further information please contact Dr. Clemens Schulze-Briese, Tel. +41 56 310 45 33, e-Mail [EMAIL PROTECTED] Please send your application to: Paul Scherrer Institut, Human Resources, Mrs. Elke Baumann, ref. code 6112-01, 5232 Villigen PSI, Switzerland. Further job opportunities: www.psi.ch -- Dr. Clemens Schulze-Briese - [EMAIL PROTECTED] --- Swiss Light Source at Paul Scherrer Institut CH-5232 Villigen PSI - http://sls.web.psi.ch Phone +41 56 310 4533 - Fax -5292 - Secretary -3178
[ccp4bb] I vs. 2theta plot, image processing
1) Some data collection and image processing files have the options to show the intensity distribution over a user-defined line in the image. Does any program allow one to trace a line from the beam center to the detector edge and save this intensity distribution to a file, so one could have I vs. 2theta data (or even a I vs. pixel data file, which could be easily converted to a I vs. 2theta file given the experimental setup)? 2) Is there a program which could convert image files from common 2D detectors (Mar345, MarCCD, RaxisII...) to a text file with the intensity on each pixel so one could easily write programs to do things such as in (1)? 3) If the answer to 2 is No, you should learn how to handle binary files and image data formats, is there a tutorial on how to do this (I would prefer C/C++, but Fortran is OK), or some well-documented open source code I could study? Thanks, Lucas Bleicher __ Fale com seus amigos de graça com o novo Yahoo! Messenger http://br.messenger.yahoo.com/
[ccp4bb] C-termini in protein-protein interaction
Dear all, I am looking for examples of protein-protein interaction through C-termini to form a multimer. Could anyone please help me find these or perhaps guide me towards haw to look for them? Thank you, Oleg - Oleg A. Zadvornyy, mailto:[EMAIL PROTECTED] Montana State University Chemistry and Biochemistry Department 108 Gains Hall Bozeman, MT 59717 Tel: 406-994-7213 Fax: 406-994-7212
[ccp4bb] Delphi question
Hi All, I'm trying to install Delphi on the MacOS PPC. The distributed package has a delphiMacOSX. However, when trying to run the program I get the error: dyld: Library not loaded: /opt/ibmcmp/lib/libxlomp_ser.dylib Reasong: Image not found Obviously, I'm missing something here as the directory /opt/ibmcp/lib does not exist!! The makefile does not have any indication for that directory! I have no idea why I see this error and how to remove it! I'd be appreciated if anyone has an experience in installing Delphi on the MacOS would guide me through the installation. P.S. Hope this non-ccp4 question does not bother you guys! thanks, Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., Uinversity Park Pennsylvania State University, PA16802 Tel. (814)863-8703 Fax. (814)865-7927 --
Re: [ccp4bb] Delphi question
On May 30, 2007, at 5:22 PM, Ibrahim M. Moustafa wrote: dyld: Library not loaded: /opt/ibmcmp/lib/libxlomp_ser.dylib Reasong: Image not found Obviously, I'm missing something here as the directory /opt/ibmcp/ lib does not exist!! The binary was built using the IBM compilers using OpenMP. You used to be able to download the libraries from IBM's website, but I can't see them there anymore. If you need, I can send the libraries to you. If you have the library on your system, but installed elsewhere you can just point the DYLD_LIBRARY_PATH to that location: bash: export DYLD_LIBRARY_PATH:/path/to/library/folder csh/tcsh: setenv DYLD_LIBRARY_PATH /path/to/library/folder * Shameless Plug * You can also use APBS (within Pymol or on the command line) to perform electrostatics calculations. We have pre-built binaries that you can download that don't have the external dependencies. Regards, Dave David W. Gohara, Ph.D. Center for Computational Biology Washington University School of Medicine http://www.macresearch.org http://gohara.wustl.edu 314-362-1583 (phone) 617-216-8616 (cell)
Re: [ccp4bb] Delphi question
Hello Ibrahim, from the name of the library I would guess it belongs to the IBM compiler. Since you probably don't want to install it only to run Delphi (because it costs quite a bit), you would have to contact the authors of Delphi to recompile their program. Many compilers come with a switch to make the binary independent of the actual compiler libraries, and even though I don't have access to the IBM compilers I guess that this is possible for those, too. Tim On Thursday 31 May 2007 08:22, Ibrahim M. Moustafa wrote: Hi All, I'm trying to install Delphi on the MacOS PPC. The distributed package has a delphiMacOSX. However, when trying to run the program I get the error: dyld: Library not loaded: /opt/ibmcmp/lib/libxlomp_ser.dylib Reasong: Image not found Obviously, I'm missing something here as the directory /opt/ibmcp/lib does not exist!! The makefile does not have any indication for that directory! I have no idea why I see this error and how to remove it! I'd be appreciated if anyone has an experience in installing Delphi on the MacOS would guide me through the installation. P.S. Hope this non-ccp4 question does not bother you guys! thanks, Ibrahim --- --- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., Uinversity Park Pennsylvania State University, PA16802 Tel. (814)863-8703 Fax. (814)865-7927 --- --- -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia pgprmQpiu0XOQ.pgp Description: PGP signature
Re: [ccp4bb] Is anomalous signal a different wavelength?
==Original message text=== On Wed, 30 May 2007 6:51:09 pm CDT Ethan Merritt wrote: On Wednesday 30 May 2007 16:24, Jacob Keller wrote: I have been wondering recently whether the anomalous component of a diffraction pattern is of a different wavelength from the regular diffraction pattern. The diffraction pattern satisfies Bragg's Law. If the input radiation is monochromatic, then the diffraction pattern shows a spot wherever that wavelength satisfies Bragg's Law for some set of planes in the crystal. In the presence of anomalous scattering, some of the incident radiation is absorbed rather than diffracted. The absorbed photon may then be re-emitted via X-ray fluorescence, as you mention. That emitted photon goes off in some random direction and does not contribute to the main Bragg diffraction pattern. In principle it could produce a diffraction pattern of its own as it travels through the rest of the crystal, but the diffraction pattern from a single photon will not be measurable in practice. Although I am no authority on this matter, the way I think of resonant scattering is scattering which is phase-shifted from the protein scattering by a certain absolute amount, due to a resonance event which takes a certain amount of time. Is this a correct model? If so, the question would be whether this resonance event saps energy from the incident light--then the emitted light from the heavy atoms would be of lesser energy. If this were true, then the heavy atoms would indeed be sending out a diffraction pattern of their own, which would be, I believe, at just slightly higher scattering angles and somewhat different Bragg conditions due to their lesser energy. Were you saying that there was some resonant scattering from the heavy atoms which was the same wavelength as the incident light, and some which was different? Thanks for your response, Jacob Keller *** Jacob Keller Northwestern University 6541 N. Francisco #3 Chicago IL 60645 (847)467-4049 [EMAIL PROTECTED] ***
