[ccp4bb] SHELEX .pdb and .res output and MLPHARE HA file
Hiya, I used shelex C/D/E on a SAD data, and wanted to refile the positions in MLPHARE before going for AddSOLVE. Confused with the output of two shelex files. shelx1.pdb file says CRYST1 50.050 65.520 105.180 90.00 90.00 90.00 SCALE1 0.019980 0.00 0.000.0 SCALE2 0.00 0.015263 0.000.0 SCALE3 0.00 0.00 0.0095080.0 HETATM1 S HAT 1 13.301 15.247 9.244 1.000 20.00 HETATM2 S HAT 2 11.528 28.067 11.167 0.803 20.00 HETATM3 S HAT 3 15.167 5.763 19.810 0.613 20.00 HETATM4 S HAT 4 13.307 30.233 13.293 0.599 20.00 HETATM5 S HAT 5 12.792 19.519 4.781 0.572 20.00 HETATM6 S HAT 6 13.273 15.312 20.083 0.373 20.00 END shelxd_fa.res file says: REM TRY 37 CC 37.28 CC(weak) 19.64 TIME 56 SECS REM TITL eba28_4_shelxc_fa.ins SAD in C2221 CELL 0.98000 50.05 65.52 105.18 90.00 90.00 90.00 LATT -7 SYMM -X, -Y, 1/2+Z SYMM -X, Y, 1/2-Z SYMM X, -Y, -Z SFAC SE UNIT 128 SE01 1 0.265762 0.232712 0.087886 1. 0.2 SE02 1 0.230339 0.428368 0.106166 0.8032 0.2 SE03 1 0.303047 0.087959 0.188342 0.6130 0.2 SE04 1 0.265884 0.461433 0.126384 0.5992 0.2 SE05 1 0.255577 0.297905 0.045451 0.5723 0.2 SE06 1 0.265198 0.233696 0.190944 0.3728 0.2 HKLF 3 END I have only 4 Se atoms, as judged from cell content analysis, so I guess I do see some Sulphurs. What should I do with atom identifiers in MLPHARE? Cheers, Partha
Re: [ccp4bb] SHELEX .pdb and .res output and MLPHARE HA file
You probably dont need to refine the positions but i guess there is no harm in it.. You do need to refine the ano occupancy which reflects the f values. Your sites 2 and 4 are quite close so the MSE might be disordered? It doesnt really matter what you call the atom type since nothing is on the absolute scale.. The shelx.ha needed for MLPHARE would read something like this: Atom_type x yz Real_occup Anom_occup BFAC ATOM SE0.265762 0.232712 0.087886 0 1 BFAC 20 and so on Eleanor Partha Chakrabarti wrote: Hiya, I used shelex C/D/E on a SAD data, and wanted to refile the positions in MLPHARE before going for AddSOLVE. Confused with the output of two shelex files. shelx1.pdb file says CRYST1 50.050 65.520 105.180 90.00 90.00 90.00 SCALE1 0.019980 0.00 0.000.0 SCALE2 0.00 0.015263 0.000.0 SCALE3 0.00 0.00 0.0095080.0 HETATM1 S HAT 1 13.301 15.247 9.244 1.000 20.00 HETATM2 S HAT 2 11.528 28.067 11.167 0.803 20.00 HETATM3 S HAT 3 15.167 5.763 19.810 0.613 20.00 HETATM4 S HAT 4 13.307 30.233 13.293 0.599 20.00 HETATM5 S HAT 5 12.792 19.519 4.781 0.572 20.00 HETATM6 S HAT 6 13.273 15.312 20.083 0.373 20.00 END shelxd_fa.res file says: REM TRY 37 CC 37.28 CC(weak) 19.64 TIME 56 SECS REM TITL eba28_4_shelxc_fa.ins SAD in C2221 CELL 0.98000 50.05 65.52 105.18 90.00 90.00 90.00 LATT -7 SYMM -X, -Y, 1/2+Z SYMM -X, Y, 1/2-Z SYMM X, -Y, -Z SFAC SE UNIT 128 SE01 1 0.265762 0.232712 0.087886 1. 0.2 SE02 1 0.230339 0.428368 0.106166 0.8032 0.2 SE03 1 0.303047 0.087959 0.188342 0.6130 0.2 SE04 1 0.265884 0.461433 0.126384 0.5992 0.2 SE05 1 0.255577 0.297905 0.045451 0.5723 0.2 SE06 1 0.265198 0.233696 0.190944 0.3728 0.2 HKLF 3 END I have only 4 Se atoms, as judged from cell content analysis, so I guess I do see some Sulphurs. What should I do with atom identifiers in MLPHARE? Cheers, Partha
[ccp4bb] Postdoctoral Research position, University of Cambridge
Dear All This current vacancy may be of interest to final year PhD or recently postdoctoral researchers. Best wishes Peter Leadlay Professor Peter Leadlay, University of Cambridge, Department of Biochemistry, Cambridge CB2 1GA, UK. HERCHEL SMITH POSTDOCTORAL RESEARCH FELLOWSHIP IN BIOCHEMISTRY(Structural Biology /Biosynthesis), UNIVERSITY OF CAMBRIDGE This post is one of nine research fellowships being advertised in the 20th December 2007 issue of Nature, as well as on jobs.ac.uk. The closing date has been set for applications as 17th January. For this particular post, the Herchel Smith Fellow will be expected to carry out his/her independent laboratory-based research programme within the Department of Biochemistry and accommodated within the laboratory space of the Herchel Smith Professor of Biochemistry, Professor Peter Leadlay FRS. The successful applicant will be expected to work on some aspect of the biosynthesis and biochemistry of antibiotic natural products, especially polyketides, i.e. within the general field of Antibiotic Biosynthesis. Applications are particularly encouraged from candidates wishing to study structure-activity relationships of key biosynthetic enzymes including use of X-ray crystallography and other biophysical approaches for structural analysis. However, the area of research within which the appointment will be made also includes the molecular microbiology and genetics of actinomycetes; the elucidation of novel biosynthetic pathways and their regulation; the engineering of pathways for overproduction of specific metabolites and for production of novel, potentially clinically useful metabolites, using either knowledge-based approaches or directed evolution; and studies to determine novel cellular targets and mechanisms of action of natural products. Those interested in applying are encouraged to visit the Department's website at http//www.gen.cam.ac.uk as well as that of the School of the Biological Sciences at http//www.bio.cam.ac.uk, and the Leadlay website at http://www.bio.cam.ac.uk/~pflgroup/index.html. Informal enquiries may be addressed to Professor Leadlay at [EMAIL PROTECTED], or, on practical aspects of the Scheme, to Jürgen Wastl ,Administrative Officer (RAE) Academic Division, University of Cambridge, The Old Schools, Trinity Lane, Cambridge CB2 1TT Juergen Wastl [EMAIL PROTECTED]
[ccp4bb] Coot 0.4 on Mac OS X 10.4
Y'all - I was wondering if anyone had a precompiled, stand-alone binary (Universal or Intel) of coot 0.4 for Mac OS X 10.4 that is not dependent on Fink (or anything else, for that matter)? Thanks so much. Best - MM Mischa Machius, PhD Associate Professor UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353
Re: [ccp4bb] Coot 0.4 on Mac OS X 10.4
Wrong board, here's what Bill posted to the cootbb yesterday: Hope that solves your problem, Juergen forwarded email: Hi Folks: In response to the numerous death threats, I've tried to make a stand- alone coot for OS X 10.5 intel. http://tinyurl.com/24mchk It might work on 10.4 intel as well. I have not tried it. Everything you need is sequestered in /usr/local/coot Peace and Joy, Bill Mischa Machius wrote: Y'all - I was wondering if anyone had a precompiled, stand-alone binary (Universal or Intel) of coot 0.4 for Mac OS X 10.4 that is not dependent on Fink (or anything else, for that matter)? Thanks so much. Best - MM Mischa Machius, PhD Associate Professor UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353 -- Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002 Web: http://faculty.washington.edu/jbosch
Re: [ccp4bb] Coot 0.4 on Mac OS X 10.4
On Dec 20, 2007, at 10:26 AM, Juergen Bosch wrote: Wrong board, I see it as one unified world of structural biology. I have stopped distinguishing between the boards and preceding messages with Off topic... Pretty much anyone who is subscribed to cootbb is also subscribed ccp4bb. Anyway, the 10.5 version doesn't work on 10.4 (at least on my machine). Cheers - MM here's what Bill posted to the cootbb yesterday: Hope that solves your problem, Juergen forwarded email: Hi Folks: In response to the numerous death threats, I've tried to make a stand- alone coot for OS X 10.5 intel. http://tinyurl.com/24mchk It might work on 10.4 intel as well. I have not tried it. Everything you need is sequestered in /usr/local/coot Peace and Joy, Bill Mischa Machius wrote: Y'all - I was wondering if anyone had a precompiled, stand-alone binary (Universal or Intel) of coot 0.4 for Mac OS X 10.4 that is not dependent on Fink (or anything else, for that matter)? Thanks so much. Best - MM - --- Mischa Machius, PhD Associate Professor UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353 -- Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002 Web: http://faculty.washington.edu/jbosch Mischa Machius, PhD Associate Professor UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353
[ccp4bb] Senior Scientist/Scientific Software Developer, PDB at UCSD
The following position is available at the RCSB Protein Data Bank at UCSD: Function as a senior scientist and scientific software developer for the RCSB Protein Data Bank (PDB; http://www.pdb.org http://www.pdb.org) at the University of California San Diego (UCSD). Work closely and collaboratively with the PDB software architects, programmers, and scientists, at San Diego Supercomputer Center (SDSC) and the PDB partner sites, to expand the PDB's functionality and reliability as a premier biological data and information resource. Work with the PDB staff to define the scientific objectives for the PDB website. Identify functional requirements and develop or enhance the current analysis tools offered by the PDB to the scientific community. Develop innovative approaches that will satisfy users' current needs and anticipate their future needs based on progress in the science of structural biology and structural bioinformatics. Act as a domain expert in structural and computational biology to solve scientific problems and answer user requests. Work will be focused on three areas: 1. Develop new scientific query and analysis capabilities for the PDB, 2. expose this functionality on the PDB website, 3. develop 3D graphical analysis tools for visualizing structural features and interactions. For more information about UCSD, please visit http://www.ucsd.edu/ http://www.ucsd.edu/ Qualifications: Ph.D. level degree in Computational Biology or Chemistry, Bioinformatics, Structural Biology or comparable combination of education and experience. Demonstrated advanced experience in scientific programming in the life sciences using the Java programming language. Track record of productivity and delivering well-designed scientific software in an industrial or academic environment. Demonstrated experience developing the presentation layer of a dynamic, database-driven web application using HTML, CSS, JavaScript, and JSP in a Java EE environment and experience with database design, Structured Query Language, and RDBMS's such as MySQL. Strong interpersonal and oral and written communication skills. Demonstrated ability to communicate to the appropriate level of the user's technical understanding. Ability to interact and communicate clearly, professionally, and effectively with members of a diverse population in person. Degree in Computer Science or comparable combination of education and experience with considerable focus in Java and Java Enterprise software development. Demonstrated experience in developing molecular graphics applications. Experience with Open GL, JOGL, or Java 3D. Preferred. Please apply online at: http://joblink.ucsd.edu/bulletin/job.html?cat=executive http://joblink.ucsd.edu/bulletin/job.html?cat=executivejob_id=44882 job_id=44882 Peter Rose, Ph.D. Scientific Lead RCSB/Protein Data Bank (www.pdb.org) San Diego Supercomputer Center (SDSC) and Skaggs School of Pharmacy and Pharmaceutical Sciences Pharmaceutical Sciences Building University of California San Diego 9500 Gilman Drive, Mailcode 0743 La Jolla, CA 92093-0743 Email: [EMAIL PROTECTED] Voice: (858) 822-5497 Fax: (858) 822-0873
[ccp4bb] Lead Web Architect, PDB at UCSD
The following position is available at the RCSB Protein Data Bank at UCSD: The RCSB PDB at the University of California, San Diego has a position open for a Lead Web Architect. The incumbent will function as a lead architect and Enterprise Java web developer of the RCSB Protein Data Bank (PDB) database and website in an agile working environment. The Protein Data Bank (www.pdb.org) is the single worldwide archive of structural data of biological macromolecules. Provide senior-level expertise and leadership in enhancing the PDB website's presentation layer to match new functional requirements by working with a team of scientists and software developers. Develop best project management and software engineering practices. Ensure cutting-edge web-development techniques, tools, and architectures are employed. Translate new and emergent requirements for the website into strategic plans to select the best web technologies and architectures for the PDB site. Author functional requirements, technical design documents, and project plans. Drive the ongoing design and develop the presentation layer for the 3-tier Enterprise Java based implementation of the PDB web application. Incorporate advanced scientific query and analysis tools, and novel representation of results in the web application. Provide technical leadership, guidance, and training on new web technologies to RCSB team and provide high level and implementation level suggestions for improving design, coding, and testing methodologies. Requirements: Masters level degree in Computer Science or comparable combination of education and experience with considerable focus in Java EE software development; Established demonstrated work experience in the role of an architect and developer on medium to large size database-driven web applications using Java EE technology; Demonstrated advanced experience with three tier architecture design using UML,object-oriented analysis and design, and application of design patterns; Advanced experience developing the presentation layer of a dynamic, database-driven web application using HTML, CSS, JavaScript, JavaScript Toolkits, Ajax, JSP, XML, Java, and Struts2; Demonstrated experience with object-relational mapping such as Hibernate or EJB3; Advanced experience with Structured Query Language and RDBMS's such as MySQL; Experience in an agile software development environment and test-driven design; Degree in bioinformatics, computational biology or chemistry, or related scientific field or comparable combination of education and experience with extensive knowledge and research experience with biological and chemical application software and data analyses preferred. Please apply online at: http://joblink.ucsd.edu/bulletin/job.html?cat=new http://joblink.ucsd.edu/bulletin/job.html?cat=newjob_id=44789 job_id=44789
Re: [ccp4bb] SHELEX .pdb and .res output and MLPHARE HA file
In this case I would recommend searching for more Se atoms, e.g. FIND 6 or 8 for SHELXD. If you then input the results into SHELXE (or are using these programs via hkl2map) you do not need use MLPHARE as well. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Thu, 20 Dec 2007, Partha Chakrabarti wrote: Hiya, I used shelex C/D/E on a SAD data, and wanted to refile the positions in MLPHARE before going for AddSOLVE. Confused with the output of two shelex files. shelx1.pdb file says CRYST1 50.050 65.520 105.180 90.00 90.00 90.00 SCALE1 0.019980 0.00 0.000.0 SCALE2 0.00 0.015263 0.000.0 SCALE3 0.00 0.00 0.0095080.0 HETATM1 S HAT 1 13.301 15.247 9.244 1.000 20.00 HETATM2 S HAT 2 11.528 28.067 11.167 0.803 20.00 HETATM3 S HAT 3 15.167 5.763 19.810 0.613 20.00 HETATM4 S HAT 4 13.307 30.233 13.293 0.599 20.00 HETATM5 S HAT 5 12.792 19.519 4.781 0.572 20.00 HETATM6 S HAT 6 13.273 15.312 20.083 0.373 20.00 END shelxd_fa.res file says: REM TRY 37 CC 37.28 CC(weak) 19.64 TIME 56 SECS REM TITL eba28_4_shelxc_fa.ins SAD in C2221 CELL 0.98000 50.05 65.52 105.18 90.00 90.00 90.00 LATT -7 SYMM -X, -Y, 1/2+Z SYMM -X, Y, 1/2-Z SYMM X, -Y, -Z SFAC SE UNIT 128 SE01 1 0.265762 0.232712 0.087886 1. 0.2 SE02 1 0.230339 0.428368 0.106166 0.8032 0.2 SE03 1 0.303047 0.087959 0.188342 0.6130 0.2 SE04 1 0.265884 0.461433 0.126384 0.5992 0.2 SE05 1 0.255577 0.297905 0.045451 0.5723 0.2 SE06 1 0.265198 0.233696 0.190944 0.3728 0.2 HKLF 3 END I have only 4 Se atoms, as judged from cell content analysis, so I guess I do see some Sulphurs. What should I do with atom identifiers in MLPHARE? Cheers, Partha
[ccp4bb] Question about protein expression (not CCP4 related)
Hello, Sorry about the non CCP4 related question. I have few questions regarding protein expression: 1. I was wondering if anyone used the Multisystem Expression vectors from Novagen and if so whats your opinion about these vectors? These are the pTriEx series of vectors that can be used for protein expression in E.coli, baculovirus and mammalian cells using the same construct. Since most of the proteins in our lab is expressed in many different systems the pTriEx series of vectors appear particulary useful! 2. We are currently using the Bac to Bac system from Invitrogen for generating baculovirus which requires purification of the bacmid DNA from DH10Bac cells before transfection. Looks like the newer systems, such as BaculoGold (BD biosciences) or BacVector (Novagen) systems skip this step altogether and saves time. Does anyone have experience with both systems and if so which one would you prefer? 3. Is anyone purifying their protein using the Strep-tag II/Strepactin affinity system and if so how does it compare to His-tag? I am looking forward to reading your opinions and suggestions. Thanks a lot, Anirban Anirban Adhikari, Ph. D. Postdoctoral Research Scholar Department of Molecular Biology UT Southwestern Medical Center 5323 Harry Hines Blvd, Dallas, TX 75390-9063
[ccp4bb] Post Dr. Position in Taipei
Post Doctoral Fellow Academia Sinica, Taiwan Department: Institute of Molecular Biology Location: Taipei, Taiwan Start Date: ASAP Duration: 2 year initially Description: A postdoctoral position is available in the Institute of Molecular Biology at Academia Sinica, Taipei, Taiwan, ROC. We are interested in cell-defending nucleases, specific projects including the structural and functional studies of apoptotic nucleases participating in chromosome fragmentation in apoptosis, and a number of RNases involved in mRNA degradation and miRNA biogenesis. For further information on the principle investigator and research lab, visit the website: http://hyuan.imb.sinica.edu.tw. The Institute offers an exciting, well-equipped, multi-disciplinary working environment. Applicants should have experience in protein chemistry and preferably protein crystallography. Salary will be commensurate with qualifications and experience year after Ph.D. degree, starting at US$ 23,000-30,000/year in the first year. The position is available immediately with an initial appointment of 2 years. Please send CV and two references to: Hanna S. Yuan, Professor Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, 11529. E-mail: [EMAIL PROTECTED] Fax: 886-2-27826085 Tel: 886-2-27884151 * Hanna S. Yuan Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan Fax: 886-2-27826085 Tel: 886-2-27884151 WWW: http://hyuan.imb.sinica.edu.tw *
