Re: [ccp4bb] Freezing crystal
Dear Theresa Cryo-cooling the crystals straight out of their drops or after brief incubations in crystal stabilization solutions containing 2M ammonium sulfate may be the way to go. Here is a copy/paste piece from Kyndt et al (2007) Biochemistry 46, 95-105. All the best Savvas Aliquots (0.5 í L) of the seed suspension (diluted 1:100 in stabilization buffer) were introduced into a series of fresh hanging drops (containing 4 í L of protein sample and 4 í L of reservoir solution) that had been equilibrated for 24 h over reservoirs containing 3 M ammonium sulfate and 20 mM sodium phosphate, pH 5.4- 6.2. Single crystals with bipyramidal morphology grew after 1 week to a final size of 0.150 mm 0.150 mm 0.100 mm. To prepare crystals for data collection under cryogenic conditions (100 K), crystals were flash-cooled by plunging them directly from their native drops into liquid nitrogen. A series of cryocooling conditions using a variety of cryoprotecting reagents such as glycerol, sucrose, PEG 400, and paratone indicated that only crystals flash-cooled by plunging them directly from their native drops into liquid nitrogen produced diffraction of acceptable quality. On 05 Feb 2012, at 23:49, Theresa H. Hsu wrote: Hi all Is there a list of conditions to be tried *first* for cryoprotectant? My crystals diffract at room temperature capillary but no in 30% PEG 400. Crystals are from 2 M ammonium sulfate. Thank you. Theresa
[ccp4bb] Soaking Kinase Crystals with ATP analogues
Dear all, Thanks a lot for good suggestions on this topic. To answer some of the questions: The apo strucuture has not been solved; the crystals dissolved upon soaking (my term 'crack' was not accurate); and I have not tried co-crystallization. A brief summerization here: 1) Soak/Co-crystallization with ADP + Aluminium fluoride/beryllium fluorid (Thank you Gregory and Pascal) or just ADP (Thanks Sofia). 2) Try other ATP analogues (ATP gammaS, AMP PCP). (Thank you Nat) 3) Soak the crystals with lower concentration, shorter time, slow addition (Thank you Thierry, Artem and Francis) 4) Try other crystal forms if available. I actually tried two other crystal forms and one of them survived soaking overnight. If the analogues got there this would be really good. (Thanks Boaz!) 5) Pay attention to the mother liqour used in soaking. Cryo protectant could help (thanks Pius); High sulphate, phosphate, di/tri-carboxylic acid can be a problem; high concentration of ATP can acidify the mother liquor (thanks Pascal). 6) Try inhibitors (Thanks Alex but I do not have any yet) 7) On the protein side, try mutant that does not hydrolyze ATP (I do have one mutant but was not giving crystal. Cheers Filiz) 8) Cross-linking the crystals using glutaraldehyde before soaking (very good point Ed). Best regards, Dianfan
[ccp4bb] Computational Systems Biology Postdoctoral Position in Translational Computational Systems Biology
Computational Systems Biology Postdoctoral Position in Translational Computational Systems Biology Outstanding Postdoctoral applicants are sought in Computational Systems Biology to work with Professor Jeffrey Skolnick at the Georgia Tech Center for the Study of Systems Biology in the following areas: • Identification and validation of off-targets of FDA approved drugs across the entire human proteome. • Application of novel algorithms to identify FDA approved drugs and lead molecules for the treatment of epilepsy. • Application of novel algorithms for the identification of metabolites with novel therapeutic properties. • Development of text mining tools to help prioritize putative drugs for therapeutic application. Highly creative, outstanding individuals with a background in systems biology, biochemistry, genetics, cell biology, bioinformatics, and/or computational systems biology are sought with the following qualifications: • Experience in aspects of drug discovery/metabolomics is highly desirable. • A track record of publication in high quality, international journals. • Ability to work in a team, yet think independently. • Extensive experience in the application of bioinformatics tools. To apply, please email your CV to: skoln...@gatech.edu
[ccp4bb] Computational Systems Biology Postdoctoral Position in Methods Development
Computational Systems Biology Postdoctoral Position in Methods Development Postdoctoral applicants are sought in Computational Systems Biology to work with Professor Jeffrey Skolnick. Specific areas include the development and application of novel algorithms for the: • Protein biochemical function prediction • Proteome scale virtual ligand screening • Prediction of off target uses of all FDA approved drugs • Structure prediction of all membrane protein families followed by virtual ligand screening • Prediction of protein-protein, protein-DNA interactions and protein-RNA interactions • Development of multiscale modeling approaches for the simulation of virtual cells Highly creative and outstanding individuals are sought with the following qualifications: • Extensive experience in developing computer code in languages such as Fortran, C, C++, Perl. • Previous experience doing international quality research in structural modeling, virtual ligand screening, large scale biological simulations, Brownian or Stokesian Dynamics, bioinformatics, or computational genomics would be major advantages. • A track record of publication in high quality, international journals. • Ability to work in a team, yet think independently. To apply, please email your CV to: skoln...@gatech.edu
[ccp4bb] Postdoc in Novel Technique Development at Diamond Light Source
Dear All This is rather off topic for the CCP4 BB but I would like to draw people's attention to developments currently taking place at diamond. We require a postdoctoral scientist to join an exciting and innovative project to develop methods associated with the soft X-ray imaging of vitrified, intact biological cells. The successful scientist will join a team of people involved in the development of the techniques associated with the soft X-ray cryo transmission X-ray microscope (cryo-TXM) for biology beamline B24, a beamline currently in the design and construction phase at Diamond Light Source. As part of the Beamline B24 project a standalone soft X-ray microscope capable of imaging cells to a resolution of 50nm which will ultimately become the beamline end station has been purchased in order to enable the work to progress in advance of beamline completion in 2014. http://www.diamond.ac.uk/Home/Jobs/Current/DIA0689_TH.html If interested please feel free to contact me to find out more! Additionally, if anyone is interested in the potential scientific impact this new technique might have in structural biology then please get in touch as well!! All the best, Liz Dr. Liz Duke Principal Beamline Scientist Diamond Light Source Harwell Science and Innovation Campus Chilton, Didcot Oxon OX11 0DE UK Tel. +44 (0) 1235 778057 Mob. +44 (0)7920 138148
[ccp4bb] Postdoctoral position at Institut Pasteur Paris
A postdoctoral position is available in the Laboratory of Molecular Mechanisms of Membrane Transport at the Institut Pasteur in Paris (France) to study excitatory neurotransmitter transporters. Our work focuses on the structural, energetic and dynamic components of the function of these membrane proteins. To this end, we use X-ray crystallography, calorimetry, fluorescence spectroscopy and electrophysiology. The lab is in the department of Structural Biology and Chemistry, which hosts state-of-the-art X-ray Crystallography and Biophysics core facilities, and a highly collaborative environment ( http://www.pasteur.fr/ip/easysite/pasteur/en/research/scientific-departments/structural-biology-and-chemistry ). The candidates should have a strong interest in membrane transport proteins and be willing to take on a challenging multidisciplinary research project. Experience in some of the following areas is expected: molecular biology, protein purification, protein biochemistry, crystallography or electrophysiology. Preference will be given to candidates with less than 2 years of experience after obtaining the Ph.D. The application should contain a single PDF document including: - Letter of intention stating the scientific interests, technical skills, and previous experience of the candidate. - C.V. including date and field of (expected) graduation and list of publications. - The contact information of at least two references. Please, send your electronic application to: nre...@pasteur.fr Nico Reyes, Ph.D. G5 Unit Molecular Mechanisms of Membrane Transport Department of Structural Biology and Chemistry Institut Pasteur
Re: [ccp4bb] off-topic:schematic representations for secondary structure
Aline does also read a dssp file and print the schematic representation above. Probably this is also possible with STRAP. I am not sure which program exactly the pdb use for their diagrams. Regards Christian Am Samstag 04 Februar 2012 12:11:09 schrieb Vellieux Frederic: I believe Procheck generates drawings such as those. It generates PostScript files, and if you need to have (eg) jpg files, a PostScript interpreter, screen capture and there you are (Gimp to select only the areas you're interested in) HTH, Fred. WENHE ZHONG wrote: Dear memebers, Thank you all firsit for the helps on my previous post about sequence alignment. They are really useful! Apologize for the off-topic question again. I usually use DSSP method to calculate the secondary structures on my sovled structures. I saw a nice schematic representation for secondary structure from PDB database website (please see the attached figure). Does anyone know whether there is a program to draw these schematics? Thank you. King regards, Wenhe
Re: [ccp4bb] Freezing crystal
On Sun, 2012-02-05 at 22:49 +, Theresa H. Hsu wrote: Crystals are from 2 M ammonium sulfate. begin \personal_bias Sodium malonate is your friend http://scripts.iucr.org/cgi-bin/paper?fw5004 end -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
[ccp4bb] sftools expand
Hello, here is a question about the EXPAND command in SFTOOLS, specifically its effect on a free reflection flag. Do the flag values get copied to newly generated reflections based on symmetry, for example in the case of a P622 - P6 expansion? many thanks, Wolfram Tempel
Re: [ccp4bb] sftools expand
On 12-02-06 08:37 AM, wtempel wrote: Hello, here is a question about the EXPAND command in SFTOOLS, specifically its effect on a free reflection flag. Do the flag values get copied to newly generated reflections based on symmetry, for example in the case of a P622 - P6 expansion? many thanks, Wolfram Tempel During expansion all data columns get copied as is, so Rfree flags will be as well (the only exception are phase columns which are adjusted as necessary when there are translational components to the crystallographic symmetry). Bart
[ccp4bb] tcl tk RHEL 6.2
I just installed ccp4 6.2.0 on a new RHEL6.2 system and I get this error. Anyone know how to fix this? I installed tcl and tk into the system but ccp4 seems to want to use its own version. [xray@paprika ~/Desktop]$ /home/xray/ccp4/ccp4-6.2.0/ccp4-6.2.0/bin/ccp4i: /home/xray/ccp4/ccp4-6.2.0/tcltkplusplus/bin/wish: /lib/ld-linux.so.2: bad ELF interpreter: No such file or directory /home/xray/ccp4/ccp4-6.2.0/ccp4-6.2.0/bin/ccp4i: line 4: /home/xray/ccp4/ccp4-6.2.0/tcltkplusplus/bin/wish: Success thanks kas -- Kenneth A. Satyshur, M.S.,Ph.D. Associate Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207 attachment: satyshur.vcf
Re: [ccp4bb] Freezing crystal
When using oil on protein crystal mounts I suggest: 1. once the crystal is under oil, remove as much adhered solution from the crystal surface. 2. if there are any volatile components in your drop condition, presaturate the oil with that solvent. 3. consider using perfluoropolyether since it has a much lower viscosity than ParatoneN, has a very low vapor pressure (used in turbo molecular and diffusion pumps) and is immiscible with just about everything. And remember that some membrane bound crystals will dissolve in oil. Kris Kris F. Tesh, Ph. D. Department of Biology and Biochemistry University of Houston From: Tommi Kajander tommi.kajan...@helsinki.fi To: CCP4BB@JISCMAIL.AC.UK Sent: Mon, February 6, 2012 1:04:13 AM Subject: Re: [ccp4bb] Freezing crystal if you use oil do direct dry Paratone-N, with paraffin oil is not as good. Li-salts should work also - i would almos imgaine you can freeze directly from so high (NH4)2SO4 conc. but perhaps not. little bit (10%) glycerol probably does it also.. Tommi On Feb 6, 2012, at 12:55 AM, Vineet Gaur wrote: Hi Theresa, Once I had crystals in 3.5 M Amm. Sulfate. I used Paraffin oil and Paraton-N-oil (in 1:1 ratio). I also used 30% Xylatol. Best, Vineet On Sun, Feb 5, 2012 at 5:49 PM, Theresa H. Hsu theresah...@live.com wrote: Hi all Is there a list of conditions to be tried *first* for cryoprotectant? My crystals diffract at room temperature capillary but no in 30% PEG 400. Crystals are from 2 M ammonium sulfate. Thank you. Theresa
Re: [ccp4bb] Freezing crystal
Theresa, Several suggestions that have been given are excellent advice: Li salts suggested by Tommi Kajander is what I would use in particular: 80% saturated lithium sulfate. This should work. I would be very surprised if it does not. Malonate as suggested by Sean Seaver is another great idea, but difficult to prepare see ccp4bb by Doug Ohlendorf : Malonic acid is dissolved in water and then pH adjusted to the desired value with NaOH. Caution: dissolving malonic acid is highly exothermic. Do it slowly, in a hood. In general terms what needs to be considered is that when one introduces a cryoprotectant it is important to match the precipitating power of the precipitant. If you just add glycerol, as suggested by some, you will tend to dissolve your crystals with respect to 2M ammonium sulfate. Ideally in a balanced cryoprotectant the mild solubility enhancing effect of the glycols should be counteracted by the addition of MPD or DMSO that can act as precipitants. Therefore, an approach using a complex mixture of glycols and cryoprecipitants should yield improved results. I have assembled a kit initially for my own personal use that creates mixtures respecting these principles. CEA Saclay has licenced it to Molecular Dimensions. The details of the components, the mixtures and their use are freely available: http://www.moleculardimensions.com/applications/upload/CryoProtX.pdf - for the product flyer and: http://www.moleculardimensions.com/shopdisplayproducts.asp?id=201cat=CryoKits - to get more info and order the product. What I prefer about Lithium sulfate compared with malonate is that I just transfer the crystals in the 80% saturated Li2SO4 without bothering about the pH (no buffer) and it works. You may want to transfer with a capillary rather than a loop to avoid shocking the crystals, but for the rest it should give good results. Enrico. On Sun, 05 Feb 2012 23:49:25 +0100, Theresa H. Hsu theresah...@live.com wrote: Hi all Is there a list of conditions to be tried *first* for cryoprotectant? My crystals diffract at room temperature capillary but no in 30% PEG 400. Crystals are from 2 M ammonium sulfate. Thank you. Theresa -- Enrico A. Stura D.Phil. (Oxon) ,Tel: 33 (0)1 69 08 4302 Office Room 19, Bat.152, Tel: 33 (0)1 69 08 9449Lab LTMB, SIMOPRO, IBiTec-S, CE Saclay, 91191 Gif-sur-Yvette, FRANCE http://www-dsv.cea.fr/en/institutes/institute-of-biology-and-technology-saclay-ibitec-s/unites-de-recherche/department-of-molecular-engineering-of-proteins-simopro/molecular-toxinology-and-biotechnology-laboratory-ltmb/crystallogenesis-e.-stura http://www.chem.gla.ac.uk/protein/mirror/stura/index2.html e-mail: est...@cea.fr Fax: 33 (0)1 69 08 90 71
Re: [ccp4bb] protein structure for high schoolers
6-Feb-2012 Dear Marilyn Have you looked at Proteopedia [www.proteopedia.orghttp://www.proteopedia.org], see e.g. http://proteopedia.org/w/DNA http://proteopedia.org/w/Forms_of_DNA http://www.proteopedia.org/w/HIV-1_protease http://www.proteopedia.org/w/Proton_Channels and many more. n.b. How the green links cause the 3D Jmol images to change so as to reflect what the test says. Pls let me know what you think of these pages. best regards, Joel On 21 Jan 2012, at 00:11, Yoder, Marilyn wrote: Hi, I’ve given a couple talks/demos to HS students. As much as I love enzymes, I found it more effective to show structures of proteins binding to other biological molecules (not just other proteins). I typically show phosphatidylinositol binding protein (PITP) bound to phosphatidylcholine, simply because that is a structure I solved and am comfortable with. I think DNA binding proteins would also be effective. p53 might be a good candidate, especially because of its association with cancer – that will get their attention. I used pymol, it was easy to install on the teachers computer, then they could easily use it after I left. Regards, Marilyn Marilyn D. Yoder Division of Cell Biology Biophysics School of Biological Sciences University of Missouri-Kansas City 5007 Rockhill Rd. Kansas City, MO 64110 Phone: 816-235-1986 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of James Whittle Sent: Friday, January 20, 2012 3:41 PM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] protein structure for high schoolers Hi- I am trying to help my former chemistry teacher set up a demonstration of protein structure for her class. I'd like to include electron density maps, and maybe show an enzyme active site. Are there suggestions from the BB on the easiest way to do this? Would pymol be the program of choice, or is there a simpler program that could show electron density? Has anyone already created such a demonstration they could and have advice on it? James
Re: [ccp4bb] tcl tk RHEL 6.2
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear kas, The error message (bad ELF interpreter) suggests a mismatch between a 64bit library and a 32bit binary (or vice versa), i.e. your system may lack compatibility libraries to run 32bit programs. These are usually available for linux distributions. Try to install them and try again. The second line looks like the command actually did find what it was looking for and not fail. Does ccp4i run on this system? Regards, Tim On 02/06/2012 05:17 PM, Kenneth A. Satyshur wrote: I just installed ccp4 6.2.0 on a new RHEL6.2 system and I get this error. Anyone know how to fix this? I installed tcl and tk into the system but ccp4 seems to want to use its own version. [xray@paprika ~/Desktop]$ /home/xray/ccp4/ccp4-6.2.0/ccp4-6.2.0/bin/ccp4i: /home/xray/ccp4/ccp4-6.2.0/tcltkplusplus/bin/wish: /lib/ld-linux.so.2: bad ELF interpreter: No such file or directory /home/xray/ccp4/ccp4-6.2.0/ccp4-6.2.0/bin/ccp4i: line 4: /home/xray/ccp4/ccp4-6.2.0/tcltkplusplus/bin/wish: Success thanks kas -- Kenneth A. Satyshur, M.S.,Ph.D. Associate Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207 - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPMAcKUxlJ7aRr7hoRAuRWAJ9/mNyMeUs42RPj4AqVHoxcINFMlACeNjFj do35CHVvenjDXYJYPQCILwY= =JB6J -END PGP SIGNATURE-
[ccp4bb] SAXS workshop
Hello If I am not wrong, there was one posting related with SASX workshop where we can also bring own samples. Does someone have that information? Please send me the link. Thanks a lot Amit
Re: [ccp4bb] SAXS workshop
http://www.embl-hamburg.de/training/events/2012/SAXS/ -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Luthra,Amit Sent: 06 February 2012 17:27 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] SAXS workshop Hello If I am not wrong, there was one posting related with SASX workshop where we can also bring own samples. Does someone have that information? Please send me the link. Thanks a lot Amit
Re: [ccp4bb] tcl tk RHEL 6.2
Your 64bit system does not have the 32bit LSB libraries installed. Install the packages redhat-lsb.i686 and redhat-lsb-graphics.i686 using yum as follows: yum install redhat-lsb.i686 redhat-lsb-graphics.i686 -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kenneth A. Satyshur Sent: February-06-12 10:17 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] tcl tk RHEL 6.2 I just installed ccp4 6.2.0 on a new RHEL6.2 system and I get this error. Anyone know how to fix this? I installed tcl and tk into the system but ccp4 seems to want to use its own version. [xray@paprika ~/Desktop]$ /home/xray/ccp4/ccp4-6.2.0/ccp4- 6.2.0/bin/ccp4i: /home/xray/ccp4/ccp4-6.2.0/tcltkplusplus/bin/wish: /lib/ld- linux.so.2: bad ELF interpreter: No such file or directory /home/xray/ccp4/ccp4-6.2.0/ccp4-6.2.0/bin/ccp4i: line 4: /home/xray/ccp4/ccp4-6.2.0/tcltkplusplus/bin/wish: Success thanks kas -- Kenneth A. Satyshur, M.S.,Ph.D. Associate Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207
Re: [ccp4bb] Freezing crystal
Dear Theresa, Gary Gilliland's paper on cryosalts would seem to be useful for your problem. http://scripts.iucr.org/cgi-bin/paper?en0028 Also, I have used 15% glycerol in a synthetic mother liquor to effectively freeze crystals grown in 2M Ammonium Sulfate. Another method that Jim Pflugrath teaches is to use ordinary table sugar (sucrose) dissolved in the reservoir solution to cryoprotect your crystal. A webinar is located on the rigaku website here: http://www.msc.com/protein/webinar-001.html Also, Hampton Research has a good list of tips in the Tech Support portion of their webpage. www.hamptonresearch.com Whichever you choose, good luck with your crystals! Bryan -- 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. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Theresa H. Hsu Sent: Sunday, February 05, 2012 5:49 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Freezing crystal Hi all Is there a list of conditions to be tried *first* for cryoprotectant? My crystals diffract at room temperature capillary but no in 30% PEG 400. Crystals are from 2 M ammonium sulfate. Thank you. Theresa
Re: [ccp4bb] SAXS workshop
On 02/06/12 12:26, Luthra,Amit wrote: Hello If I am not wrong, there was one posting related with SASX workshop where we can also bring own samples. Does someone have that information? Please send me the link. Thanks a lot Amit http://www.chess.cornell.edu/BioSAXS%20course/index.htm Getting Started in Biological Small-Angle X-ray Solution Scattering Feb 24-26, 2012 Students will have the opportunity to collect data on CHESS beamlines using protein standards and/or their own samples. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] SAXS workshop
And here's one from Brookhaven -- app. deadline is three weeks away: http://workshops.ps.bnl.gov/default.aspx?w=SAXSMar2012 http://www.chess.cornell.edu/BioSAXS%20course/index.htm Getting Started in Biological Small-Angle X-ray Solution Scattering Feb 24-26, 2012 Students will have the opportunity to collect data on CHESS beamlines using protein standards and/or their own samples. -- = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] Summer Internship at Merck for Ph.D. students
All, We have a summer internship opening at Merck (see below for the details) for graduate students in the Global Structural Chemistry/X-ray crystallography/Biomolecular NMR group at either its Kenilworth, NJ or West Point, PA sites. Internships will begin in early June 2012, and will run for 10-12 weeks.If you are interested please visit our career site at www.merck.com/careershttp://www.merck.com/careers to create a profile and submit your resume for requisition #CHE003379. Sincerely, Corey -- Job Description X-ray Crystallography/BioNMR Summer Internship 2012 - PhD:CHE003379 Description Merck is a global health care leader with a diversified portfolio of prescription medicines, vaccines and consumer health products, as well as animal health products. Today, we are building a new kind of healthcare company - one that is ready to help create a healthier future for all of us. Our ability to excel depends on the integrity, knowledge, imagination, skill, diversity and teamwork of people like you. To this end, we strive to create an environment of mutual respect, encouragement and teamwork. As part of our global team, you'll have the opportunity to collaborate with talented and dedicated colleagues while developing and expanding your career. Merck Research Labs will be offering 2012 summer internships in the Global Structural Chemistry group (X-ray crystallography or Biomolecular NMR) at either its Kenilworth, NJ or West Point, PA sites. Internships will begin in early June 2012, and will run for 9-11 weeks. A suitable candidate has a science background with interest in the use of X-ray crystallography and/or Biomolecular NMR in drug discovery. Not required, but a plus, would be experience in one or more of the areas of protein crystallization, X-ray theory, X-ray crystallography or Biomolecular NMR. Preference will be given to candidates having a strong math and/or physical science background with expertise in computers and computer programming. Candidates will gain firsthand experience in modern drug discovery, and will also make valuable contacts within the industry. **Please note when applying for this position, the candidate MUST upload a cover letter or a personal statement letter and a copy of your unofficial transcript along with your resume. Qualifications Required: * Currently pursuing a Ph.D. in Biomolecular NMR, X-ray crystallography, Computational Chemistry, Biophysics or a related field * Applicants must be available for full-time employment for 9 - 11 weeks during the months of June - August 2012. Preferred: * Experience in one or more of the areas of protein crystallization, X-ray theory, X-ray crystallography or Biomolecular NMR * Strong math and/or physical science background with expertise in computers and computer programming * Science background with an interest in computers and drug discovery Our employees are the key to our company's success. We demonstrate our commitment to our employees by offering a competitive and valuable rewards program. Merck's benefits are designed to support the wide range of goals, needs and lifestyles of our employees, and many of the people that matter the most in their lives. To be considered for this position, please visit our career site at www.merck.com/careershttp://www.merck.com/careers to create a profile and submit your resume for requisition #CHE003379. Merck is an equal opportunity employer, M/F/D/V - proudly embracing diversity in all of its manifestations. 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 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] Freezing crystal
Hi all Thanks for all the suggestions which I will try soon. How do the crystallization condition (PEG vs. salts like ammonium sulfate) affect the croyprotectant condition? Do factors like presence of low concentration of high molecular weight PEG ( 2000) mean PEG is better? Do buffers and salts in protein also important? Trying to rationalize it :) Theresa
[ccp4bb] CASP Roll: Call for novel fold and membrane protein targets to help improve structure modeling methods
Dear colleagues, As many of you know, the CASP community experiments have been running once every two years since 1994, collecting information on soon to be solved structures from the experimental community, and passing on sequence data to the structure modeling community so that blind predictions of structure can be collected and assessed (1). Over that period CASP has seen enormous progress in the quality of modeled structures (2), but many problems remain. The regular CASP experiments collect target information for a three month season every two years, and in that period, thanks especially to the structural genomics community, can acquire over 100 targets, sufficient to evaluate the state of the art for most types of template based modeling. There are some classes of target, specifically proteins with novel folds and membrane proteins, where there are not enough structures solved in three months to provide sufficient information so the methods can be fully evaluated. As a consequence, progress is slowed. To address this problem, with the encouragement of the modeling community, CASP has launched a rolling mechanism, where we accept targets in these categories at any time. Of course for that to work we rely on you, the experimentalists, to provide suitable targets! So we are asking that you tell us about structures in these categories that are about to be solved whenever they come up. For those of you who have not provided targets to CASP before, the procedure is simple – there is a web page for submitting targets, and a very experienced staff to deal with any queries. We don’t need the structure in advance of its release by the PDB, and if we are notified early enough (a minimum of three weeks before release, more is better) there need be no delay in structure release. If you have a suitable target now, we are up and running with 50+ prediction teams already submitting models, and would love to have your targets. Most important, the modeling community is now in continuous need of your assistance, so please get in touch whenever an opportunity arises in the future, and help improve modeling methods. Thanks, CASP organizing committee John Moult, IBBR, University of Maryland, USA Krzysztof Fidelis, University of California, Davis, USA Andriy Kryshtafovych, University of California, Davis, USA Torsten Schwede, University of Basel SIB, Switzerland Anna Tramontano, University of Rome, Italy Get in touch: c...@predictioncenter.org More information: http://www.predictioncenter.org/casprol/ CASP Roll targets so far: http://www.predictioncenter.org/casprol/targetlist.cgi Submit a target: http://www.predictioncenter.org/casprol/targets_submission.cgi 1. Critical assessment of methods of protein structure prediction (CASP)--round IX. Moult J, Fidelis K, Kryshtafovych A, Tramontano A. Proteins. 2011;79 Suppl 10:1-5. doi: 10.1002/prot.23200. Epub 2011 Oct 14. 2. CASP9 results compared to those of previous CASP experiments. Kryshtafovych A, Fidelis K, Moult J. Proteins. 2011;79 Suppl 10:196-207. doi: 10.1002/prot.23182. Epub 2011 Oct 14.
[ccp4bb] shape complementarity between protein and DNA surface
Dear All For calculation of the shape complementarity index using the Sc program between a protein and DNA surface, does anybody have a modified radii.lib file that includes information about DNA atoms? Also, is there any reference that has information regarding the atomic radii of DNA atoms? thanks Deepak
Re: [ccp4bb] Freezing crystal
Hi Theresa, What works well for me, is to use like with like, e.g. to use salts or salt-like cryoprotectants for salt conditions (e.g. malonate, li-sulfate, sucrose/xylitol for ammonium sulfate conditions) and glycerol, low mw PEG etc. for PEG and other alcohol conditions. I have very bad experiences using glycerol with ammonium sulfate conditions. Of course, the pH of the cryo-solution should be the same as of the crystallization conditions to avoid a pH shock. As mentioned, oils which do not mix at all with the reservoir solution could be tried in both cases. In many cases it helps to increase the salt/peg concentration in the cryoprotectant solution, since under crystallization conditions there is often an equilibrium between protein in solution and in the crystal. By increasing the salt/peg concentration, the protein will no longer be soluble and stay in the crystal. Also often some of the water is pulled from the crystal lattice, resulting in a tighter packing, which is more robust versus soaking and which may diffract better (dehydration effect). Good luck! Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Theresa H. Hsu Sent: Monday, February 06, 2012 11:00 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Freezing crystal Hi all Thanks for all the suggestions which I will try soon. How do the crystallization condition (PEG vs. salts like ammonium sulfate) affect the croyprotectant condition? Do factors like presence of low concentration of high molecular weight PEG ( 2000) mean PEG is better? Do buffers and salts in protein also important? Trying to rationalize it :) Theresa
