Re: [ccp4bb] [COOT] CCP4 - Coot in Applications
Thanks Scott. Using your stand-alone Coot package - 0.7 (revision 4459) [with guile 1.8.8 embedded] [with python 2.7.3 embedded], everything works perfectly. The previous issue of invalid window errors no longer occurs, and all scripts that use coot now work correctly (as the path /usr/local/bin/coot is defined and understood) I would tentatively suggest therefore that there are some build issues with the Coot provided as a package from CCP4 - but *weirdly* only when you invoke it from the command line using /Applications/coot.app/Contents/Resources/script - which frequently crashes X11… As a reminder - this was causing me quite a few issues, as other software packages don't expect Coot to live in /Applications - and symbolic linking / path defining wasn't working consistently. NB: Running OS X 10.7.5 (Lion). With regards Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 On Dec 6, 2012, at 6:05 AM, William G. Scott wrote: Dear Tony: Any chance you might be willing to try installing from here? http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot That might give us a positive control (if it works) or help to track down the problem (if it doesn't). It should work the way you want it to. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA Ok - annoying thing…. 1) using /Applications/coot.app/Contents/Resources/script to launch Coot from the command line (terminal window) works IF you don't have X11 open already. 2) if you DO have X11 open, coot pretty much always crashes with the aforementioned invalid window errors. Nov 23 12:17:02 coot-real[80005] Error: kCGErrorIllegalArgument: CGSGetSurfaceBounds Nov 23 12:17:02 coot-real[80005] Error: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged. Nov 23 12:17:02 coot-real[80005] Error: kCGErrorIllegalArgument: CGSBindSurface: Invalid window 0x8da Nov 23 12:17:02 coot-real[80005] Error: kCGErrorIllegalArgument: CGSBindSurface: Invalid window 0x8da Nov 23 12:17:02 coot-real[80005] Error: kCGErrorIllegalArgument: CGSBindSurface: Invalid window 0x8da Ideas and suggestions welcome. I guess I could make sure that X11 is not running each time I invoke a script or run coot from the command line - but it's not exactly ideal. -- NB: Running Mac OS X, 10.7.5 - Lion.
Re: [ccp4bb] Perfluoropolyether as cryoprotectant for membrane proteins ?
Thank you all for sharing your experience with Perfluoropolyether and freezing membrane proteins ! Now I myself heard about one membrane protein where Perfluoropolyether was the solution for the freezing problem. And it seems it worked in my case as well :-) Ulrike
[ccp4bb] Macromolecular Crystallography School announcement : 2013 in Uruguay
Dear Colleagues, We are pleased to announce the *second Macromolecular Crystallography School 2013 *at the Institut Pasteur de Montevideo (Uruguay). All details can be found at www.pasteur.edu.uy/mx2013 http://www.pasteur.edu.uy/mx2013 *Title:* Macromolecular Crystallography School 2013: From data processing to structure refinement and beyond *Dates:*April 9th-17th, 2013. *Site:*Institut Pasteur de Montevideo (Montevideo), Uruguay *The workshop content:* Conceived to provide theoretical background and hands-on abilities in the use of computational tools to exploit X ray diffraction data. Through lectures, tutorials and hands-on trouble-shooting, the students will be trained in state-of-the-art macromolecular crystallography. Particular emphasis will be given to data processing, phasing/structure determination and model refinement/validation. The workshop will feature authors and experts of many modern crystallographic software packages. This workshop represents the continuation within the series started in 2010 (http://www.pasteur.edu.uy/mxcourse) on Macromolecular Crystallography. In this opportunity it is being co-organized by the Center for Structural Biology of the Mercosur CeBEM (www.cebem.org.ar http://www.cebem.org.ar), jointly with the Collaborative Computational Project Number 4 (CCP4 -- UK www.ccp4.ac.uk http://www.ccp4.ac.uk). Support from the Institut Pasteur International Network, the International Union of Crystallography and Institut Pasteur de Montevideo is also greatly acknowledged. *Applicants:* Graduate students, postdoctoral researchers and young scientists are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets so they can be used during the workshop's hands-on sessions. There is no registration fee. Support for accommodation, per diem and local transportation will be provided to all participants from abroad. Support to cover travel expenses will be considered on a case-by-case basis. Specific requests should be well-grounded as we will only be able to select a limited number. *Application:* Application *deadline is February 10, 2013*. Application form, the program, contact info and other details can be found at www.pasteur.edu.uy/mx2013 http://www.pasteur.edu.uy/mx2013 Please address further inquiries to mx2...@pasteur.edu.uy mailto:mx2...@pasteur.edu.uy Ronan Keegan and Alejandro Buschiazzo -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf
[ccp4bb] refining against weak data and Table I stats
Hello all, I've followed with interest the discussions here about how we should be refining against weak data, e.g. data with I/sigI 2 (perhaps using all bins that have a significant CC1/2 per Karplus and Diederichs 2012). This all makes statistical sense to me, but now I am wondering how I should report data and model stats in Table I. Here's what I've come up with: report two Table I's. For comparability to legacy structure stats, report a classic Table I, where I call the resolution whatever bin I/sigI=2. Use that as my high res bin, with high res bin stats reported in parentheses after global stats. Then have another Table (maybe Table I* in supplementary material?) where I report stats for the whole dataset, including the weak data I used in refinement. In both tables report CC1/2 and Rmeas. This way, I don't redefine the (mostly) conventional usage of resolution, my Table I can be compared to precedent, I report stats for all the data and for the model against all data, and I take advantage of the information in the weak data during refinement. Thoughts? Douglas ^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^` Douglas L. Theobald Assistant Professor Department of Biochemistry Brandeis University Waltham, MA 02454-9110 dtheob...@brandeis.edu http://theobald.brandeis.edu/ ^\ /` /^. / /\ / / /`/ / . /` / / ' ' '
Re: [ccp4bb] refining against weak data and Table I stats
Another consideration here is your PDB deposition. If the reason for using weak data is to get a better structure, presumably you are going to deposit the structure using all the data. Then the statistics in the PDB file must reflect the high resolution refinement. There are I think three places in the PDB file where the resolution is stated, but i believe they are all required to be the same and to be equal to the highest resolution data used (even if there were only two reflections in that shell). Rmerge or Rsymm must be reported, and until recently I think they were not allowed to exceed 1.00 (100% error?). What are your reviewers going to think if the title of your paper is structure of protein A at 2.1 A resolution but they check the PDB file and the resolution was really 1.9 A? And Rsymm in the PDB is 0.99 but in your table 1* says 1.3? Douglas Theobald wrote: Hello all, I've followed with interest the discussions here about how we should be refining against weak data, e.g. data with I/sigI 2 (perhaps using all bins that have a significant CC1/2 per Karplus and Diederichs 2012). This all makes statistical sense to me, but now I am wondering how I should report data and model stats in Table I. Here's what I've come up with: report two Table I's. For comparability to legacy structure stats, report a classic Table I, where I call the resolution whatever bin I/sigI=2. Use that as my high res bin, with high res bin stats reported in parentheses after global stats. Then have another Table (maybe Table I* in supplementary material?) where I report stats for the whole dataset, including the weak data I used in refinement. In both tables report CC1/2 and Rmeas. This way, I don't redefine the (mostly) conventional usage of resolution, my Table I can be compared to precedent, I report stats for all the data and for the model against all data, and I take advantage of the information in the weak data during refinement. Thoughts? Douglas ^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^` Douglas L. Theobald Assistant Professor Department of Biochemistry Brandeis University Waltham, MA 02454-9110 dtheob...@brandeis.edu http://theobald.brandeis.edu/ ^\ /` /^. / /\ / / /`/ / . /` / / ' ' '
[ccp4bb] Postdoctoral Position on Membrane Protein Structural Biology
The Cherezov laboratory at The Scripps Research Institute (http://cherezov.scripps.edu) is looking for an exceptional and highly motivated candidate to work on the development of new technologies for membrane protein crystallization in lipidic environment as well as carry out crystallographic data collection and processing at synchrotron and free-electron laser sources. Prior experience with handling membrane proteins and demonstrated success are desired. Please apply by sending a cover letter describing your intent and experience, a CV with a full list of publications, and 3 references to Vadim Cherezov (vcher...@scripps.edu).
[ccp4bb] pdbset: filtering out ANISOU lines
Hello, Would it be possible to have pdbset take care of only the ATOM lines in a given PDB? I managed to make it do what I want but in case there are ANISOU lines, I want to ignore them. Currently, I'm using grep before pdbset, but I would prefer to avoid it as I am doing some computational experiment which is quite data intensive. If there is a way to filter out ANISOU lines or to work only on ATOM lines with pdbset, then I would be very happy. Thanks a lot, Francois.
