[ccp4bb] CONE built-in in pymol
Hello, according to the pymol wiki http://www.pymolwiki.org/index.php/Arrows, pymol 1.1 has a CONE built-in. While the code of the API is quite nicely readable and I can guess the meanings of most of the parameters, I was wondering whether anyone could point me to documentation of that command - I couldn't find it on the wiki. Thanks a lot, Tim P.S.: I am aware that there is a pymol mailing list. -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] Method to calculate the axis of an alpha helix
Pete Artymiuk wrote: --- I have an old badly-written Fortran program (I wrote it for a Vax, but it still compiles and runs in g95 - isn't Fortran wonderful?) that takes Arnott Dover's polar coordinates and converts them to a helix of any required length* in PDB (or Diamond!) format. --- Wow, that is an old program! For everyone under the ago of 60 reading this list, Diamond format was the very first PDB format, used for the first 100 or so entries that we had. It was based on the output format of the Diamond real-space refinement program and each line was 132 characters long. Long lines were awkward, in some ways, to handle on computers of that time so we designed what is now known as PDB format. If you want to know more, you can look at page 9 of the September 1974 PDB Newsletter (available on the RCSB web site if you start at http://www.rcsb.org/pdb/static.do?p=general_information/news_publications/newsletters/newsletter.html#pre1999) for the format of coordinate records in the original format. The reason that I know that there were about 100 entries released in the original format is that I was the one who had to convert them all into the new PDB format in 1976. Frances Bernstein = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 =
[ccp4bb] open job Proteros Biostructures
Dear All, on behalf of our Human Resources Department I would like to forward a posting for an open job in our Structural Biology team at Proteros. Please reply to the contact given below. Best regards, Stephan Krapp PROTEROS is a leading service provider for the solution of complex three-dimensional structures of proteins and in complex with ligands for structure-guided drug discovery. Our work significantly contributes to fast and rational development of new therapeutic compounds for our global clients. Since its foundation in 1998, PROTEROS has been a continuously growing renowned enterprise collaborating with a large variety of international Pharma, Biotech and Crop Science companies. To support our existing crystallography team we look for a Research Scientist - Protein Crystallography (m/f) Job description You will be responsible for -planning and accomplishment of protein crystallization experiments within the scope of drug discovery projects -protein-ligand complexation: co-crystallization and soaking procedures -analysis and evaluation of protein crystallization experiments and protein X-ray diffraction patterns -X-ray diffraction data collection at in-house generators and synchrotron beamlines -evaluation of protein X-ray diffraction data -protein structure solution (experimental phasing or MR), model building and refinement -development and optimization of methods and work-flows in protein crystallization and protein crystal structure determination The successful candidate will meet the following requirements You have a degree in Chemistry or within a proximal area of life science and a Ph.D. in X-ray protein crystallography with excellent track record providing you with a profound knowledge and experience in protein crystallization, protein-ligand complex formation in crystals and protein structure determination. A good knowledge of LINUX systems and acquaintance with current software packages employed in protein crystallography are mandatory. Experience in crystallization and structure determination of integral membrane proteins would be a significant benefit. You are proactive and able to work effectively under strict time lines. Additionally, you have excellent communication skills and like to work in a multi-disciplinary team. Work experience in the life science industry is an asset. Please apply by sending your full application documents to: bewerb...@proteros.demailto:bewerb...@proteros.de or to: Rebekka Neuhauser | Am Klopferspitz 19 | 82152 Martinsried | Germany Dr. Stephan Krapp Proteros Biostructures GmbH Am Klopferspitz 19 D-82152 Planegg-Martinsried Germany Tel.: +49 (0) 89 700761 -0 Fax: +49 (0) 89 700761 -15 E-mail: kr...@proteros.demailto:kr...@proteros.de www.proteros.de Die in dieser e-mail beinhaltete Information unterliegt der Geheimhaltung. Sie ist ausschließlich für den genannten Empfänger bestimmt. Falls Sie nicht der genannte Empfänger sind, bitten wir Sie, uns darüber in Kenntnis zu setzen und alle bestehenden Kopien zu vernichten. This message and any attached files contain privileged and/or confidential information intended only for the use of the addressee. If you are not the addressee, or the person responsible for delivering it to the person addressed, you may not read, use, copy or deliver this to anyone else. If you received this message by mistake, please immediately notify us and delete it from your system. All care has to be taken to ensure this message and any attachments are virus free. No responsibility is accepted for any virus infections caused by the receipt of this message. Geschäftsführer: Dr. Torsten Neuefeind, Prof. Dr. Christian Hilz, Dr. Dirk Ullmann Amtsgericht München HRB-Nr. 121 476 - VAT-ID: DE 195 857 418 - Steuernummer 143/173/20265
[ccp4bb] Postdoc position at Hauptman-Woodward Medical Research Institute, Buffalo, New York
Applications are invited for a post-doctoral position in the Snell/Luft laboratory at the Hauptman-Woodward Medical Research Institute (HWI), Buffalo, NY. The position, funded by the Defense Threat Reduction Agency (DTRA), targets the oxidative stress pathway in the brain and lungs and involves a close collaboration with the Phizicky and Grayhack laboratories at the University of Rochester, NY. A significant number of protein targets are available. The research will focus on the structural biology of these targets and their complexes making use of both X-ray crystallography and Small Angle X-ray Scattering. A full program of synchrotron beamtime for both single crystal and SAXS studies is available. The HWI laboratory is well equipped with state-of-the art molecular biology, crystallization, computing and X-ray equipment. It is a highly collaborative environment with the building housing HWI being designed around this philosophy to promote research and interaction. The ideal candidate should have experience in crystallization and structural crystallography and a willingness to become involved in new structural techniques. Expertise in molecular biology and/or SAXS is a plus but not required. Opportunities to develop stand-alone independent research projects exist. Candidates should have excellent technical, interpersonal and communication skills and would be expected to become a key component of the team involved in this research. Salary and benefits are competitive and funding is initially available for 2 years with the possibility of extension. HWI is a private, not-for-profit organization, founded in 1956, studying the structures and functions of macromolecules of biomedical interest. HWI houses the Department of Structural Biology of the State University of New York at Buffalo's School of Medicine and Biomedical Sciences. HWI is part of the Buffalo-Niagara Medical Campus, a consortium of research, clinical, and educational institutions founded to cultivate a world-class medical campus in state-of-the art facilities in downtown Buffalo, NY, USA. Informal enquiries are welcome to either Eddie Snell (esn...@hwi.buffalo.edu) or Joseph Luft (l...@hwi.buiffalo.edu). To apply please send a current resume and the names of two references to Anne Kent, Human Resources Coordinator (k...@hwi.buffalo.edu). Thanks, Eddie. Edward Snell Ph.D. Assistant Prof. Department of Structural Biology, SUNY Buffalo, Senior Scientist, Hauptman-Woodward Medical Research Institute 700 Ellicott Street, Buffalo, NY 14203-1102 Phone: (716) 898 8631 Fax: (716) 898 8660 Skype: eddie.snell Email: esn...@hwi.buffalo.edu Telepathy: 42.2 GHz Heisenberg was probably here!
Re: [ccp4bb] database-assisted data archive
Hi everyone Thanks for your emails. Apparently, there is a wide range of suggestions and ideas about what (and how) can be stored in a database with X-ray crystallography data. We would all like to be able to store all our research data in a database, with as little an effort as possible, in a very simple way, and we should also be able to easily upload it to our laptops. How many of you think this is possible? As I mentioned in an earlier email, the new CCP4i will include a small database. The primary function of the database will be to store data on projects, jobs, files and users. One of the objectives is to allow other programs (such as Coot, CCP4mg and iMosflm) to be more integrated with the main CCP4 suite interface, allowing data from those programs to be accessible from CCP4i and vice-versa. The database will be tested thoroughly before it is released as part of the new CCP4i. We welcome user feedback. George Pelios CCP4
[ccp4bb] atomic B factors
Can anybody shed some light on why my atomic B factors all end up as 2.00 after restrained refinement with REFMAC5? Is there a fix? Thanks. Ray email ray-br...@att.net
Re: [ccp4bb] CONE built-in in pymol
Hi Tim, CGO objects are sparsely documented in PyMOL. Aside from the old PyMOL Manual and the content on the wiki, there's not much else. The parameters for a CGO cone object in PyMOL are: (1) CONE the keyword (2-4) x, y, z position of the base of the cone (3-5) x, y, z position of the tip of the cone (6) radius of the base (7) radius of the tip (doesn't have to be 0) (8-10) r, g, b color specification for the base of the cone (11-13) r, g, b color specification for the tip of the cone (14) if 1 the base of the cone is filled in and colored; if 0 the base of the cone is open (15) if 1 the tip of the cone is filled in and colored; if 0 the tip of the cone is open Last, you can find more info here (http://pymol.sourceforge.net/newman/user/S0500cgo.html#14) on CGOs in PyMOL. Hope this helps, -- Jason On Thu, Aug 19, 2010 at 6:59 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Hello, according to the pymol wiki http://www.pymolwiki.org/index.php/Arrows, pymol 1.1 has a CONE built-in. While the code of the API is quite nicely readable and I can guess the meanings of most of the parameters, I was wondering whether anyone could point me to documentation of that command - I couldn't find it on the wiki. Thanks a lot, Tim P.S.: I am aware that there is a pymol mailing list. -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.9 (GNU/Linux) iD8DBQFMbQ6ZUxlJ7aRr7hoRAoxnAKC900VnP+FAVmL89jWtNB6xosFD5ACeJx4C XioMtnyCI2F6D7VOsQI07V8= =GFYk -END PGP SIGNATURE- -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] database-assisted data archive
TARDIS and MyTARDIS (for public and private data respectively) is currently in production at the Australian Synchrotron and has just received funding to expand to working with all data being produced from all beamlines (not just macromolecular) - and also to all instruments at the Australian nuclear facility ANSTO. One of the major drawcards of this system is that for users of the Australian Synchrotron there is zero barrier to entry as far as data cataloguing and access. Once the frames come off the beamline, their headers are extracted and catalogued in a database. This is all accessible for download anywhere today via the web portal http://tardis.synchrotron.org.au under one's synchrotron user account. Information is gathered from the proposal and scheduling systems at the facility and fed to this MyTARDIS node, so there is literally nothing a user *has* to enter to have their data described and accounted for in the system. Furthermore, an instance of MyTARDIS can be set up at the lab or institution to receive a local copy of the data and metadata. For instance, if a crystallographer from Melbourne university has a MyTARDIS set up in their lab, the MyTARDIS node at the Australian Synchrotron detects if new data off a beamline is owned by this crystallographer and sends a copy of all data and its associated metadata for download through a local web portal - under their regular university login system. A sharing interface allows crystallographers to grant access to fellow researchers so that they can also download data and browse/search through metadata. Later on, a user will be able to add datasets with results and log files to these catalogued raw diffraction datasets and publish them. Published data appears in the central index TARDIS.edu.au and contains a persistent handle for citation. No data is actually stored at this central index: TARDIS.edu.au simply provides rich metadata and download links to federated MyTARDIS nodes and their stored data. There are plans to have (at least) the first diffraction image converted to JPG or PNG and stored/displayed by the web portal (as Andreas mentioned), as well as crystal quality ranking and other (eg. XDS) processing. As a final note, while the preferred method of data storage in TARDIS is the zero-effort one via synchrotrons, there's a method of manually depositing diffraction datasets, irrespective of date or origin. See: http://tardis.edu.au/deposit for more details. A mailing list (Google Group) has just been set up for discussion of TARDIS/MyTARDIS. Feel free to join in to keep abreast of changes and discuss finer points of the solution: http://groups.google.com/group/tardis-users
[ccp4bb] Heavy atom sites?
Hi all, I recently solved a structure using SAD or SIRAS successfully (refinement using native data). But I came across some questions about the heave atom (Hg) sites. SG : P212121. Cell: 61.000 137.700 142.170 90.00 90.00 90.00 (native and derivative are very similar). 1. I used shelxD finding the Hg sites, but got different results from SAD and SIRAS. Here paste the first 3 sites: X Y Z X Y Z (fractional) (orthogonal) SAD: Hg10.598389 0.567345 0.09804136.759 78.146 13.983 Hg20.901955 0.570168 -0.09888155.407 78.535 -14.102 Hg30.727585 0.594368 -0.24033044.696 81.868 -34.276 SIRAS: Hg10.598717 0.432159 0.09836336.522 59.508 13.984 Hg20.901527 0.430199 -0.09843754.993 59.238 -13.995 Hg30.727432 0.406845 -0.24025344.373 56.023 -34.157 It seems there is a symmetry plane m(x,1/2,z) between SAD sites and SIRAS sites. The above HA coordinates were in real space not the partterson space, right? So could someone tell me why there is a m? PS: the Harker section plots (FFT for patterson in CCP4) of difference patterson and ano-difference patterson are very similar. 2. I put the Hg sites caculated by shelxD (say, the SAD sites) to SHARP and got the density map (looks very good). RESOLVE was used to autobuild the model. The Fo-Fc map (Fo from Hg-data, Fc from the model after refinement) at sig5 obviously showed the Hg sites (around Cys). But the heave atom coordinates (from shelxD or sharp) didn't match the Fo-Fc density. I don't know why is that? Dose it bucause the coordinate system mismatch? Any help would be much appreciated. Thanks, Pu
