[ccp4bb] Research Scientist Position - Vertex Pharmaceuticals (Europe) Ltd. - Oxford, UK
Vertex Pharmaceuticals (Europe) Ltd has an immediate opening for a talented protein crystallographer in the Crystallography Group at our UK site (Abingdon, Oxfordshire). Candidates should have a PhD with productive post-doctoral/industrial employment experience in protein crystallography. The major role of the person will be to provide x-ray support to small molecule drug discovery and development by solving structures of protein-ligand complexes for structure-based drug design. The position requires a broad background in protein crystallography and a solid understanding of biophysics and its application in drug discovery projects. Specifically, the required skills include the ability to design protein constructs for crystallization trials; protein crystallization using various techniques; data collection using a laboratory source and at the synchrotron; structure determination by molecular replacement, MIR and MAD; computing experience with a variety of crystallographic programs; the ability to interpret and communicate structural information. In addition, candidates should have a solid basic knowledge of chemistry and/or biochemistry. Excellent communication skills are required as is a strong ability to work in a team. Previous experience in the pharmaceutical industry would be considered an asset. In return, you can look forward to an impressive benefits package that includes 28 days holiday, employee stock purchase plan and group stakeholder pension. As you would expect, we are highly health-aware, so you will also be eligible for private medical, dental and optical insurance as well as life insurance. Plus you can take advantage of our work place nursery and gym membership. If you are innovative and focused on achieving success within a collaborative environment, please visit our website. To find out more information and apply, please visit http://bs.serving-sys.com/BurstingPipe/adServer.bs?cn=tfc=20mc=clickpli=6175807PluID=0ord=[timestamp] The Science of Possibility. Closing date for applications is 28 February 2013. Vertex creates new possibilities in medicine. Our team discovers, develops and commercialises innovative therapies so people with serious diseases can lead better lives. Vertex scientists and our collaborators are working on new medicines to cure or significantly advance the treatment of hepatitis C, cystic fibrosis, epilepsy and other life-threatening diseases. Founded more than 20 years ago in Cambridge, Mass., we now have ongoing worldwide research programs and sites in the United States, United Kingdom and Canada. Vertex has consistently been recognised as one of the industry's top workplaces by leading publications such as Science magazine, The Boston Globe, Boston Business Journal, San Diego Business Journal and The Scientist and most recently was named the top employer in Science magazine's 2011 annual survey. For more information and to view Vertex's press releases, please visit www.vrtx.com As the UK-based subsidiary, Vertex Pharmaceuticals Europe Ltd brings together scientists of multiple disciplines and various backgrounds to form a highly creative and productive team. Our scientists work in an environment where chemists, biologists, structural biologist and computational chemists focus together on cancer and inflammatory diseases. Our research facility in Oxfordshire is equipped with the latest technology and together through collaboration of the wider organisation our world class teams are tackling the most ambitious projects in the industry. VERTEX is an Equal Employment Opportunity/Affirmative Action employer. All employment decisions are made without regard to race, sex, national origin, colour, religion, age, disability, veteran status, genetic information or any other status protected by federal, state or local law. Vertex Pharmaceuticals (Europe) Limited Registered in England and Wales, company no. 2907620 Registered Office: 88 Milton Park, Abingdon, Oxfordshire OX14 4RY, UK This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.
[ccp4bb] Renumbering and retaining state information pdb file
Hi, I am trying to tidy up an old NMR structure (not mine) and I want to renumber the residues in all the states. When I use pdbset starting at X, the numbers are changed but the state information is lost. How can I retain the state in my modified pdb file? Thanks, Amar - Amar Joshi Ph.D Bayliss Lab Department of Biochemistry Henry Wellcome Building University of Leicester Lancaster Road, Leicester LE1 9HN Tel: 0116 229 7082 Email: aj...@leicester.ac.uk --
Re: [ccp4bb] GeForce Graphics cards
On the subject of nVidia graphics cards, linux and stereo, I feel I ought to mention the Asus VG278H. This is a 120Hz 27 1920x1080 monitor with a built-in nVidia 3D vision emitter, which comes bundled with a pair of 3D vision glasses. The great thing about the built-in emitter is that it takes stereo synch from the DVI cable even under Linux. This removes the need for a Quadro card with a 3-pin mini-DIN connector or 3-pin adapter. Here in the UK our cheapest supplier was selling it for £380 ex. VAT. There is little information about using it with Linux on the web, but as I understand it you still need a Quadro card. I got it running with little trouble using a Quadro 2000, Ubuntu 12.04 LTS and the latest nVidia drivers. It may be possible to use cheaper Quadro cards. The picture and stereo quality is excellent when compared to our existing stereo systems. Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.ukhttp://icr.ac.uk/ The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] GeForce Graphics cards
Yes, we have this monitor running fine on a Quadro FX 380. Stereo is perfect using coot, pymol and many other SW. [2262774.741] (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) [2262774.741] (**) NVIDIA(0): Option Stereo 10 [2262774.741] (**) NVIDIA(0): Option MetaModeOrientation clone [2262774.741] (**) NVIDIA(0): USB IR emitter stereo requested [2262774.741] (**) NVIDIA(0): Enabling 2D acceleration [2262775.874] (II) NVIDIA(GPU-0): Display (Ancor Communications Inc ASUS VG278HR (DFP-0)) [2262775.875] (II) NVIDIA(GPU-0): supports NVIDIA 3D Vision stereo. [2262775.997] (II) NVIDIA(0): NVIDIA GPU Quadro FX 380 (G96GL) at PCI:1:0:0 (GPU-0) Am 14.02.13 10:55, schrieb Chris Richardson: On the subject of nVidia graphics cards, linux and stereo, I feel I ought to mention the Asus VG278H. This is a 120Hz 27 1920x1080 monitor with a built-in nVidia 3D vision emitter, which comes bundled with a pair of 3D vision glasses. The great thing about the built-in emitter is that it takes stereo synch from the DVI cable even under Linux. This removes the need for a Quadro card with a 3-pin mini-DIN connector or 3-pin adapter. Here in the UK our cheapest supplier was selling it for £380 ex. VAT. There is little information about using it with Linux on the web, but as I understand it you still need a Quadro card. I got it running with little trouble using a Quadro 2000, Ubuntu 12.04 LTS and the latest nVidia drivers. It may be possible to use cheaper Quadro cards. The picture and stereo quality is excellent when compared to our existing stereo systems. Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.ukhttp://icr.ac.uk/ The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- Joachim Reichelt Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: Rüdiger Eichel, Abteilungsleiter Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Ulf Richter, MBA Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477
Re: [ccp4bb] observed reflections
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Careina, the number of observed reflections is the number of reflections your integration software found on the images. If you compare this to the theoretically possible number of reflections (calculated from the cell and resolution limits), you come to the completeness of the dataset and the multiplicity of reflections, both of which are quality measures of the data set(s). Hence you should include the number in the outer resolution shell, too. Best, Tim On 02/14/2013 06:27 AM, Careina Edgooms wrote: Dear ccp4 I apologise for the straightforward question. I'm just a bit confused about the observed reflections quoted in tables. What exactly is this and should it include outer shell separately? Best Careina - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRHLkVUxlJ7aRr7hoRAhRvAKCHlihfMzDNGKCZYnOJROkaKOgY7QCgvxvs 0BuJ+WyLTYQtLKJ0TeB0TeI= =ClBx -END PGP SIGNATURE-
Re: [ccp4bb] S-nitrosylation protein
Dear Uma, A very complehensive survey of the state-of-the-art in this topic can be found in the following literature resources: (1) Garman EF. Radiation damage in macromolecular crystallography: what is it and why should we care? Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):339-51. (2) The January 2013 issue of the Journal of Synchrotron Radiation featuring a special section with papers presented at last year's Intl workshop on X-ray damage of biological crystalline samples. The annotated editorial by Garman and Weik in that issue is also very helpful. Best regards Savvas On 13 Feb 2013, at 23:38, Uma Ratu wrote: Dear All: I plan to use X-ray crystallography method to study the S-nitrosylated protein structure. The native protein crystals diffracted to 2A with synchrontron. I now have the crystals of S-ntrosylated protein. Since S-NO moiety appears to be unstable to synchrotron radiation, could you advice / comments on the stratage on the data collection of S-nitrosylated protein crystals? The protein crystals did not diffract well with in house X-ray. Thank you for your comments. Uma
Re: [ccp4bb] Renumbering and retaining state information pdb file
There should be many ways to do this. You can split the file, renumber with pdbset, and then reassemble it. This may be useful http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Useful_scripts_(aka_smart_piece_of_code) Cheers, Ed Original message From: Amar Joshi aj...@leicester.ac.uk Date: To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Renumbering and retaining state information pdb file Hi, I am trying to tidy up an old NMR structure (not mine) and I want to renumber the residues in all the states. When I use pdbset starting at X, the numbers are changed but the state information is lost. How can I retain the state in my modified pdb file? Thanks, Amar - Amar Joshi Ph.D Bayliss Lab Department of Biochemistry Henry Wellcome Building University of Leicester Lancaster Road, Leicester LE1 9HN Tel: 0116 229 7082 Email: aj...@leicester.ac.uk --
Re: [ccp4bb] S-nitrosylation protein
Collect small slices of data (instead of a complete data set) on several crystals then merge the data together to get a full data set. The slices of must be small enough so that the damage to the S-NO group is still very limited on each slice. You may have to play with beam attenuation a bit, depending on how fast the degradation occurs. Good luck Thierry From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Uma Ratu Sent: Wednesday, February 13, 2013 5:38 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] S-nitrosylation protein Dear All: I plan to use X-ray crystallography method to study the S-nitrosylated protein structure. The native protein crystals diffracted to 2A with synchrontron. I now have the crystals of S-ntrosylated protein. Since S-NO moiety appears to be unstable to synchrotron radiation, could you advice / comments on the stratage on the data collection of S-nitrosylated protein crystals? The protein crystals did not diffract well with in house X-ray. Thank you for your comments. Uma 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] S-nitrosylation protein
Dear All: Many thanks for your commoents and advice. I will keep them in mind. Uma On Thu, Feb 14, 2013 at 7:54 AM, Fischmann, Thierry thierry.fischm...@merck.com wrote: Collect small slices of data (instead of a complete data set) on several crystals then merge the data together to get a full data set. The slices of must be small enough so that the damage to the S-NO group is still very limited on each slice. You may have to play with beam attenuation a bit, depending on how fast the degradation occurs. ** ** Good luck ** ** Thierry ** ** *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Uma Ratu *Sent:* Wednesday, February 13, 2013 5:38 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] S-nitrosylation protein ** ** Dear All: I plan to use X-ray crystallography method to study the S-nitrosylated protein structure. The native protein crystals diffracted to 2A with synchrontron. I now have the crystals of S-ntrosylated protein. Since S-NO moiety appears to be unstable to synchrotron radiation, could you advice / comments on the stratage on the data collection of S-nitrosylated protein crystals? The protein crystals did not diffract well with in house X-ray. Thank you for your comments. Uma 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] UWM is seeking testers for a new protein expression kit
Hello everyone, Thanks for the great interest in the kit, I have at least 30 requests already. For those of you asking about next steps, it will be for me to send a material transfer agreement for you and your office to sign. I will need the contact information, email, phone, University name and address. Once this is complete, I can send the kit. Due to the overwhelming response, it will be most appreciated if people are willing to pay for the shipping on dry ice. We generally use Fed Ex, but have used UPS as well. Thanks again, Jessica Jessica Silvaggi, Ph.D. Licensing Manager UWM Research Foundation Phone: 414-906-4654 Mobile: 508-769-5171 jsilva...@uwmfdn.orgmailto:jsilva...@uwmfdn.org 1440 East North Ave. Milwaukee, WI 53202 From: Jessica Silvaggi Sent: Wednesday, February 13, 2013 3:41 PM To: 'CCP4BB@JISCMAIL.AC.UK' Subject: UWM is seeking testers for a new protein expression kit Hi everyone, Dr. M.L.P. Collins at the University of Wisconsin-Milwaukee has developed a new method for making large quantities of active, viable proteins using Rhodospirillum rubrum as a host. R. Rubrum is a bacterium that has traditionally been studied for its simple photosynthetic system, has demonstrated recent success in expressing high-yield protein. To provide a brief overview, R. rubrum possesses the unique characteristic of forming an intracytoplasmic membrane (ICM) in response to membrane protein synthesis. The ICM is non-essential for growth and can incorporate foreign and over-expressed membrane proteins without disrupting normal cellular function. This characteristic has stimulated the expression of active and correctly folded membrane protein where other systems have failed. In an attempt to gather additional testing data, the UWM Research Foundation would like to provide FREE protein expression kits to laboratories or universities that are having difficulties with their current method of producing large-scale proteins. Having limited resources, our researchers have only had the ability to test a number of proteins but thus far have seen exceptional promise. We currently have 8 other universities or companies using the new kit and are now ready to distribute to other participants. The link listed below provides a more detailed explanation of the testing process including the specific proteins currently being tested. You may also view Dr. Collin's publication on her findings of using R. rubrum as a host. If you are interested in learning more about this new system or have any additional comments, you may email me at jsilva...@uwmfdn.orgmailto:jsilva...@uwmfdn.org. Testing Kit Link Slides http://www.uwmresearchfoundation.org/getdoc/2a36a544-e47c-442e-baaf-9fb3442694f0/Slides-for-Kit-Testing-2013.aspx Dr. Collin's Publication Butzin, N.C; Owen, H.A.; and M.L.P. Collins. 2010. A new system for heterologous expression of membrane proteins: Rhodospirillum rubrum. Protein Expression and Purification, 70: 88-94. http://www4.uwm.edu/letsci/biologicalsciences/facultystaff/collins/upload/Butzin_et_al_2010.pdf
[ccp4bb] how to add atoms in refmac library
Dear all My protein has Zinc atom but the refmac does not identifies it during refinement..Can anybody please tell me how to add Zinc atom into the refmac library for the successful refinement of the coordinates. -- Regards Faisal School of Life Sciences JNU
[ccp4bb] Thanks for the new graphical CCP4 installer
It is easy to use and even nice looking. Regards, F.
