[ccp4bb] Postdoctoral positions in membrane protein crystallography
Two postdoctoral positions in membrane protein crystallography at the Stockholm Center for Biomembrane Research The Center for Biomembrane Research (CBR), located at Stockholm University, is a newly formed strategic research center funded by the Swedish Foundation for Strategic Research and headed by Prof. Gunnar von Heijne. CBR provides a unique setting for membrane protein research. It presently encompasses over 15 research groups performing world-class biomembrane research using both theoretical and experimental approaches, and spans from basic biochemistry and molecular biology to methods development, proteomics, bioinformatics and structural biology. Interaction with industry and society is also actively pursued. The collective competence is extraordinarily multifaceted and presents an ideal environment for collaborative studies and cooperation. The protein X-ray crystallographic activity at CBR is presently being established. The general goal is to increase the amount of high-resolution structural information available for membrane proteins of outstanding medical and scientific interest and to use this information in the design of further experiments to obtain an in-depth functional understanding. We seek two talented postdocs with expertise in membrane protein expression, purification and crystallization. Ideally the applicant should be able to start work in Stockholm during the fall of 2007 or early 2008. The successful applicants will join a newly established team to take on this challenging task in a very stimulating environment and will participate in all stages of structure determination, from expression and purification to crystallization and crystallography. For more information, please contact: Dr. Martin Högbom[EMAIL PROTECTED] www.cbr.su.se
[ccp4bb] Filament lifetime on Rigaku Micromax007
Dear Colleagues, During more than three years of operation, I have recorded considerable difference in filament lifetimes on my Micromax007: roughly in the range 500-2000hrs. Some of this may be accounted for by poor manufacture and Rigaku have, in the past, noticed this problem and replaced some filaments. For the last three filaments fitted, two have lasted about 500hrs and the third about 2000hrs. These filaments were replacements. My generator running protocol has been constant throughout. Interestingly, the filaments show no visible sign of wear or damage (even the 2000hr one) and are only changed when the generator starts to shut down on OL or FC limits. I recall earlier Rigaku generators that would give 2000hrs when well maintained and they ran at 5.4KW compared to the 800W of the Micromax. I would be grateful for any comments or suggestions from other Micromax operators. Sincerely, Pat Bryant Dr Pat Bryant Senior Experimental Officer Macromolecular Crystallography Core Facility Faculty of Life Sciences Michael Smith Building The University of Manchester Oxford Road Manchester M13 9PT, UK Phone: +44-161-275-5090/5658 Fax: +44-161-275-1505 email: [EMAIL PROTECTED] Intranet:http://www.intranet.ls,manchester.ac.uk/facilities/research/xraycrystallography Internet:http://www.ls.manchester.ac.uk/research/facilities/xray
Re: [ccp4bb] software to calculate VDW interactions between small molecule and protein
CONTACT from the CCP4 suite can do this - have a look at the documentation and examples. Tadeusz mathias [EMAIL PROTECTED] Sent by: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK 27-Feb-2007 18:43 Please respond to mathias [EMAIL PROTECTED] To CCP4BB@JISCMAIL.AC.UK cc Subject [ccp4bb] software to calculate VDW interactions between small molecule and protein Dear all, Can anyone of you guys recommend free software, or any open access internet server, to calculate VDW interactions of small molecules binding to protein. The only information I need is an output file which lists all amino acids of the target protein which make VDW interactions with the binding small molecule. Thank you very much for your help and recommendations, Mathias --- This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. ---
Re: [ccp4bb] Filament lifetime on Rigaku Micromax007
Dear Pat, I too am shocked by the extra-long lifetimes the current batch of MM filaments have. I've had filaments in both our instruments (a M007 and an M007 hf) since August and they are still going strong. Not long ago I would replace a filament before it blew if I knew there was an important data collection scheduled on the same instrument. It used to be 12 - 16 weeks on average, on this occassion it's over 30 weeks for each filament. Good to see we are getting our money's worth ;) Mark _ Dr Mark Agacan Scientific Officer, Division of Biological Chemistry and Molecular Microbiology, Wellcome Trust Biocentre, College of Life Sciences, Dow St., University of Dundee, Dundee, DD1 5EH Tel: +44 1382 388751 Fax: +44 1382 345764 _ Patrick Bryant [EMAIL PROTECTED] 28/02/07 1:18 PM Dear Colleagues, During more than three years of operation, I have recorded considerable difference in filament lifetimes on my Micromax007: roughly in the range 500-2000hrs. Some of this may be accounted for by poor manufacture and Rigaku have, in the past, noticed this problem and replaced some filaments. For the last three filaments fitted, two have lasted about 500hrs and the third about 2000hrs. These filaments were replacements. My generator running protocol has been constant throughout. Interestingly, the filaments show no visible sign of wear or damage (even the 2000hr one) and are only changed when the generator starts to shut down on OL or FC limits. I recall earlier Rigaku generators that would give 2000hrs when well maintained and they ran at 5.4KW compared to the 800W of the Micromax. I would be grateful for any comments or suggestions from other Micromax operators. Sincerely, Pat Bryant Dr Pat Bryant Senior Experimental Officer Macromolecular Crystallography Core Facility Faculty of Life Sciences Michael Smith Building The University of Manchester Oxford Road Manchester M13 9PT, UK Phone: +44-161-275-5090/5658 Fax: +44-161-275-1505 email: [EMAIL PROTECTED] Intranet:http://www.intranet.ls,manchester.ac.uk/facilities/research/xraycrystallography Internet:http://www.ls.manchester.ac.uk/research/facilities/xray
Re: [ccp4bb] process SeMet labelled data
Dear all, I have a data set at 2.2A, of the selenomethionene labelled protein.How should I process the data. Properly
Re: [ccp4bb] process SeMet labelled data
Anastassis Perrakis wrote: On Feb 28, 2007, at 14:37, shivesh kumar wrote: Dear all, I have a data set at 2.2A, of the selenomethionene labelled protein.How should I process the data. Carefully ! Thanx for the help. Shivesh Tassos i am sure what tassos really meant was Very Carefully ! jon -- Dr. Jonathan M. Grimes, Royal Society Research Fellow University Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: [EMAIL PROTECTED], Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547
[ccp4bb] video zueras do tooby
video zueras do tooby video de pessoas famosas em cada situaçao!!! clika o lik p/ ver o video se nao der disite a url em outra janela --http://h1.ripway.com/videozueras/52609-videozueiras.rar
Re: [ccp4bb] process SeMet labelled data
On Feb 28, 2007, at 14:37, shivesh kumar wrote: Dear all, I have a data set at 2.2A, of the selenomethionene labelled protein.How should I process the data. Some hopefully useful remarks (fairly random and not complete and exhaustive): 1. make sure to mask out the backstop and beamstop holder correctly. Although various integration software claims to do this fairly automatic it is always better to do a good job on this. 2. check the rejected reflections (at the scaling/merging step): is there some system in those rejections? The two files produced by SCALA (ROGUES and a xmgr file that plots the detector position of rejected reflections) are very helpful. It can show ice-rings, bad beamstop-masking (see point 1) etc. 3. heavy atom detection/phasing software will also write out some helpful information about outliers: if there are some suspicious messages (e.g. warnings in autoSHARP) they usually point back to problems in data processing (see point 1). 4. if you collected several datasets/wavelengths: you can give those to SCALA for some 'local scaling'. This will also show you those really helpful CC(Dano) plots. But be careful with absorption correction: all datasets/sweeps need to be indexed identically. 5. always remember what your first reaction was when looking at the images: 'great' images should give you good statistics further down the pipeline. But if 'awfull' images give you good statistics I would be suspicious ... 6. unless you really know what's going on: stick with program defaults. Usually the developers have a very good idea why the program is doing things in a specific way. Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
[ccp4bb] Solubility of ligands
Dear all, I have a small library of In-silico screened compounds to test for activity and for crystallization trials with our protein of interest. We only have about 10 mg/ml of each compound. As there is no available experimental information about solubility of these compounds, I have no choice but to try different solvents. The first solvent to try will be DMSO (100%) to make the highest stock concentration of each compound. My question to those who passed through similar experience is: Assuming some of the compounds turned to be insoluble in DMSO, which is possible, how to completely recover the compounds from DMSO before trying another solvent. Will spinning and leaving the tube open over the bench be enough to get rid of the solvent or what people usually do in that case? What is the recommended solvent to try next? Is there a standard protocol to follow for the case we have?? thanks in advance for those who are willing to share their experience. regards, Ibrahim Ibrahim M.Moustafa, Ph.D. Pennsylvania State University Biochemistry Molecular Biology Dept. 201 Althouse Lab. University Park, PA16802 Tel (814) 863 8703 Fax (814) 865 7927
Re: [ccp4bb] process SeMet labelled data
why don't you just send all your images to the ccp4bb, then we'll process them, solve the structure and publish it for you. And we might put you in the acknowledgements, if you are lucky. Mark On 28 Feb 2007, at 16:35, Jonathan Grimes wrote: Anastassis Perrakis wrote: On Feb 28, 2007, at 14:37, shivesh kumar wrote: Dear all, I have a data set at 2.2A, of the selenomethionene labelled protein.How should I process the data. Carefully ! Thanx for the help. Shivesh Tassos i am sure what tassos really meant was Very Carefully ! jon -- Dr. Jonathan M. Grimes, Royal Society Research Fellow University Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: [EMAIL PROTECTED], Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 Mark J. van Raaij Dpto de Bioquímica, Facultad de Farmacia and Unidad de Rayos X, Edificio CACTUS Universidad de Santiago 15782 Santiago de Compostela Spain http://web.usc.es/~vanraaij/
Re: [ccp4bb] video zueras do tooby
hahaha! brazilian humour - always cracks me up! for those of you whose portuguese is a bit rusty, let me provide a quick and dirty translation: video de pessoas famosas em cada situa?ao!!! videos of famous pessaries in situation comedy clika o lik p/ ver o video se nao der disite a url em outra janela click and lick on the video and let your nose decide the url of the outer janela priceless! --bixo do coco (previously known as o fenomeno) ** Gerard J. Kleywegt [Research Fellow of the Royal Swedish Academy of Sciences] Dept. of Cell Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED] ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. **
Re: [ccp4bb] Solubility of ligands
Hi all, Thanks for those who replied so far. I can see that the solubility issue is not that problematic for the crystallization work (as Kendall mentioned). I recall that some people on the board reported in a different thread that they tried the solid powder in the crystallization drop and it worked! The biggest concern is with the planned activity assay! For that, I think I need to get a clear solution with known concentration of the compound to be tested. P.S. Just a correction, I meant we have 10 mg of each compounds. The compounds received as powder. At 11:28 AM 2/28/2007, you wrote: Dear all, I have a small library of In-silico screened compounds to test for activity and for crystallization trials with our protein of interest. We only have about 10 mg/ml of each compound. As there is no available experimental information about solubility of these compounds, I have no choice but to try different solvents. The first solvent to try will be DMSO (100%) to make the highest stock concentration of each compound. My question to those who passed through similar experience is: Assuming some of the compounds turned to be insoluble in DMSO, which is possible, how to completely recover the compounds from DMSO before trying another solvent. Will spinning and leaving the tube open over the bench be enough to get rid of the solvent or what people usually do in that case? What is the recommended solvent to try next? Is there a standard protocol to follow for the case we have?? thanks in advance for those who are willing to share their experience. regards, Ibrahim Ibrahim M.Moustafa, Ph.D. Pennsylvania State University Biochemistry Molecular Biology Dept. 201 Althouse Lab. University Park, PA16802 Tel (814) 863 8703 Fax (814) 865 7927 Ibrahim M.Moustafa, Ph.D. Pennsylvania State University Biochemistry Molecular Biology Dept. 201 Althouse Lab. University Park, PA16802 Tel (814) 863 8703 Fax (814) 865 7927
[ccp4bb] questions on SF likelihood
Hi, I've managed to do a pretty good job of confusing myself in my latest attempt to understand the likelihood stuff, and was hoping that I could get some pointers as to what I'm misunderstanding. 1. How does one determine the amplitude and phase to use from a given likelihood surface? Some of the papers I've read refer to using the centroid; others seem to be talking about using the location of the maxima. Is there any guidance for when you'd use one instead of the other, or is this one of those try both and see which works best situations? 2. How do you get the HL coefficients out of a likelihood surface? The only way I could think of to do this would be to pick up the likelihood values over the full phaser circle for a constant amplitude, and fit a 2-term fourier series to the ln of those values. But this approach feels more like a work-around than anything else (and would lead to the same point in complex space having two difference likelihoods for a centric reflection), so I'm fairly sure there's a better way to do this (although I don't have any ideas what that would be). SigmaA weights might be a possibility, but as far as I know they wouldn't work for all cases (MAD and SAS don't have native amplitude measurements). Thanks in advance for any help, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
[ccp4bb] Cannot running NTA to purify the protein having His-tag?
Dear CCP4 users, I'm purifying a kind of protease having His-tag. The protein is expressed in insect cells and broken by sonication. I used NTA resin to purify this protein. Buffer A is 50mM phosphate buffer pH 7.5 and 300mM NaCl. Buffer B is 50mM phosphate buffer pH 7.5, 300 mM NaCl and 300 mM Imidazole. However, all proteins cannot bind to NTA resin. My protein is eluted in Flow-through. I also check the NTA resin with the control His-tag. The western blot also shows that my protein has His-tag. Do you have any ideas about my problem? I'm really appreciate all of your advices how to solve this. Thank you very much! My best regards, TriNgo Sungkyunkwan University
Re: [ccp4bb] Oxford Xcalibur Vs Rigaku micromax
Sankar We had an Oxford Diffraction PX system, with the same goniometer and detector as the Nova, for 3 years until last Fall when we upgraded to the Nova. We also have 3 other Xcalibur instruments with the same goniometer and control systems. All four diffractometers have performed reliably with very little downtime, the oldest now being nearly 6 years old, and with very little maintainance. The Nova itself has worked well, and has stayed in alignment since it was installed 6 months ago. You can see a few more details at www.crystal.vt.edu. I do not have experience of the micromax. Obtaining a valid comparison between any two diffractometers is difficult. I can only suggest that you do what the rest of us do, and that is take some of your typical crystals and some of your poorer crystals around and try them out on each of the instruments that you are considering. Ross Angel At 12:27 AM 2/28/2007, Sankar Narayanan Manicka wrote: Hi, Our lab is planning to buy an X-ray machine for protein crystallography. Which system would be best for home source, Oxford diffraction system Xcalibur Nova or a MSC/Rigaku MicroMax-002. sincerely, sankar -- Sankar narayanan Manicka[EMAIL PROTECTED] C/o Prof. S. Krishnaswamy +91 452 245 9931 - tel School of Biotechnology +91 452 245 9105 - fax Madurai 625 021 +91 94860 88613 - cell TAMIL NADU INDIA http://www.mkuniversity.org/biotech_school.htm l Ross Angel Research Professor in Crystallography Crystallography Laboratory Tel: 540-231-7974 Dept. GeosciencesFax: 540-231-3386 Virginia Tech Blacksburg VA 24060-0420 USA http://www.crystal.vt.edu/crystal/
Re: [ccp4bb] Oxford Xcalibur Vs Rigaku micromax
Well since Jim answered I must do also!! Bruker, together with Incoatec, has on the market a new Incoatec Microfocus Source with novel QUAZAR multilayer optics which in my understanding is significantly brighter than the other systems referred to. This source is very interesting as it is air cooled - no need for plumbing. All these models are excellent for their performance compared to the older style 5.4 kw 300 micron focus generators and are small footprint, simple systems. They do not equal the brightness of the current microfocus rotating anode generators (eg Bruker MICROSTAR ULTRA) which have greatly surpassed the older style 300 micron systems. We try to give you new technology to help you do excellent science. All the best Sue Byram Susan K. Byram Business Manager Crystallographic Systems Bruker AXS Inc. 5465 East Cheryl Parkway Madison, WI 53711 USA Toll-free tel.: (800) 234-XRAY Tel.: (608) 276-3041 Fax:(608) 276-3006 e-mail: [EMAIL PROTECTED] WWW:http://www.bruker-axs.com please note my current email address. The old one [EMAIL PROTECTED] no longer functions. -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Jim Pflugrath Sent: Wednesday, February 28, 2007 11:36 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Oxford Xcalibur Vs Rigaku micromax Of course, the Rigaku system would be the best. Jim On Wed, 28 Feb 2007, Sankar Narayanan Manicka wrote: Hi, Our lab is planning to buy an X-ray machine for protein crystallography. Which system would be best for home source, Oxford diffraction system Xcalibur Nova or a MSC/Rigaku MicroMax-002. sincerely, sankar -- Sankar narayanan Manicka [EMAIL PROTECTED] C/o Prof. S. Krishnaswamy +91 452 245 9931 - tel School of Biotechnology +91 452 245 9105 - fax Madurai 625 021 +91 94860 88613 - cell TAMIL NADU INDIA http://www.mkuniversity.org/biotech_school.htm l
[ccp4bb] R-free error in highest resolution bin
When using Refmac how does one find/calculate R-free error in the highest resolution bin?
Re: [ccp4bb] R-free error in highest resolution bin
On Wednesday 28 February 2007 11:08, John Bruning wrote: When using Refmac how does one find/calculate R-free error in the highest resolution bin? R and Rfree by shell are in the data-harvesting output file What is R-free error? -- Ethan A MerrittCourier Deliveries: 1959 NE Pacific Dept of Biochemistry Health Sciences Building University of Washington - Seattle WA 98195-7742
[ccp4bb] homology modeling----good bond lengths, bad angles
Hi CCP4 community! I have constructed a homology model of a deletion variant of a protein whose structure has already been solved. These deletions are 3-4 amino acid in length and are in a loop that connects two helices. The model structures look good with respect to bond lengths in the aforementioned loop region but the bond angles (especially Phi and Psi) are very distorted. Ramachandran plot suggests the same and some of the amino acids flanking the loop are now in the disallowed region. I thought one way to avoid this is to delete one amino acid at a time and construct the model and use the previous model as the template to construct the next model. This is not working very well in fixing the wrong angles. I was wondering if 1) Anybody out there knows good homology modeling software. I used SWISS model and CPH model to create my models. I have heard about prime but right now am waiting to get the software . 2) Is there a way I can fix the angles if I perform an energy minimization of the model. Suggestions are appreciated. Thanks, Anagha.
