Re: [ccp4bb] pointless question
OK you're right, this is a bug in reindexing merged MTZ files relative to a reference file (unmerged files are OK) I've fixed this in version 1.3.8 available from our ftp site ftp.mrc-lmb.cam.ac.uk/pub/pre/ pointless-1.3.8.tar.gzsource pointless-1.3.8.linux Linux executable pointless-1.3.8.osxi86 OSX executable My apologies for this - I should have spotted the problem a long time ago Phil On 6 May 2009, at 23:17, Robert Nolte wrote: Phil, I tried the version with 6.11, as well as the latest prebuilt version I could find on your site, 1.3.2. Both of them have the same behavior. The mtz file has F's in it. I get the same error when I try the I's from Truncate, and the original scalepack2mtz I's. However, if instead of using hklin with a MTZ file, I use scain with the scalepack file, the program functions as I think should. Thanks for looking into the problem. Bob Nolte -Original Message- From: Phil Evans p...@mrc-lmb.cam.ac.uk Sent: May 6, 2009 5:28 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] pointless question I think Pointless 1.2.23 was a broken version which escaped to the wild in CCP4 release 6.1.0. The more recent release 6.1.1 has a fixed version, and some more recent versions are also available from our ftp site eg ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless-1.3.2... sorry about this Phil On 6 May 2009, at 19:21, Robert Nolte wrote: I'm hoping someone can help me with a pointless problem. I am trying to reindex data into an orientation that I used to solve the structure initially. While I can get pointless to give me the reindexing needed to make the new data match the old data for the project, when I ask it to write the data to HKLOUT it does not carry out the reindexing. I was under the impression from the documentation it would write out the reindexed solution. Am I doing something wrong or have I found a bug in my particular space group. I seem to recall getting this to work on a different project in the past. I have also tried a number of different versions of pointless, and all give me the same results. The output file is shown below. Thanks in advance for any help. Regards, Bob Nolte - pointless hklin input.mtz hklref reference.mtz hklout reindex.mtz pointless.log contents of pointless.log ### ### CCP4 6.1: POINTLESS version 1.2.23 : 26/09/08## ### User: unknown Run date: 28/ 4/2009 Run time: 13:48:05 Please reference: Collaborative Computational Project, Number 4. 1994. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. OS type: linux Release Date: 26th September 2008 ** ** * POINTLESS * * 1.2.23 * ** * Determine Laue group from unmerged intensities * * Phil Evans MRC LMB, Cambridge * * Uses cctbx routines by Ralf Grosse-Kunstleve et al.* ** ** --- Reading reference data set from file reference.mtz Maximum resolution in file reference.mtz:1.810 Columns for F, sigF (squared to I): F_881 SIGF_881 Number of valid observations read:18733 Highest resolution: 1.81 Unit cell: 72.6672.6665.9890.0090.00 120.00 Space group: P 3 2 1 Spacegroup information obtained from library file: Logical Name: SYMINFO Filename: /apps/ccp4/ccp4-6.1.0/lib/data/ syminfo.lib Maximum resolution in file input.mtz:1.870 Columns for F, sigF (squared to I): F_880 SIGF_880 Number of valid observations read:17028 Highest resolution: 1.87 Unit cell: 72.5872.5866.2090.0090.00 120.00 Space group: P 3 2 1 Possible alternative indexing schemes Operators labelled exact are exact by symmetry For inexact options, deviations are from original cell (root mean square deviation between base vectors) Maximum accepted RMS deviation between test and reference cells (TOLERANCE) = 2.0 [h,k,l]exact [-h,-k,l]exact Normalising reference dataset Log(I) fit for intensity normalisation: B (slope) -18.82 Normalising test dataset Log(I) fit for intensity normalisation: B (slope) -18.21 Alternative indexing relative to reference file reference.mtz $TEXT:Result:$$ $$ Alternative reindexing CC R(E^2)Number Cell_deviation [-h,-k,l] 0.9670.092
Re: [ccp4bb] pointless question
It also has the same/analogous bug in space group P3 with Pointless v1.2.10 - I wasn't sure if I was missing something obvious and went back to using my default combination of REINDEX/SCALEIT for the tests and reindexing. Phil Jeffrey Princeton Robert Nolte wrote: An output file is created on hklout with or without the -copy flag. The problem is why is it picking the unity matrix (solution #2) for the reindexing operator rather than the first matrix (-h -k l) that it identifies under reindexing (which is clearly the correct answer). -Original Message- From: Jan Abendroth Sent: May 6, 2009 2:45 PM To: Robert Nolte Subject: Re: [ccp4bb] pointless question Hi Bob, including a -copy flag might not be totally pointless: pointless -copy hklin ... Jan 2009/5/6 Robert Nolte rtno...@earthlink.net mailto:rtno...@earthlink.net I'm hoping someone can help me with a pointless problem. I am trying to reindex data into an orientation that I used to solve the structure initially. While I can get pointless to give me the reindexing needed to make the new data match the old data for the project, when I ask it to write the data to HKLOUT it does not carry out the reindexing. I was under the impression from the documentation it would write out the reindexed solution. Am I doing something wrong or have I found a bug in my particular space group. I seem to recall getting this to work on a different project in the past. I have also tried a number of different versions of pointless, and all give me the same results. The output file is shown below. Thanks in advance for any help. Regards, Bob Nolte - pointless hklin input.mtz hklref reference.mtz hklout reindex.mtz pointless.log contents of pointless.log ### ### CCP4 6.1: POINTLESS version 1.2.23 : 26/09/08## ### User: unknown Run date: 28/ 4/2009 Run time: 13:48:05 Please reference: Collaborative Computational Project, Number 4. 1994. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. OS type: linux Release Date: 26th September 2008 ** ** * POINTLESS * * 1.2.23 * ** * Determine Laue group from unmerged intensities * * Phil Evans MRC LMB, Cambridge * * Uses cctbx routines by Ralf Grosse-Kunstleve et al.* ** ** --- Reading reference data set from file reference.mtz Maximum resolution in file reference.mtz:1.810 Columns for F, sigF (squared to I): F_881 SIGF_881 Number of valid observations read:18733 Highest resolution: 1.81 Unit cell: 72.6672.6665.9890.0090.00 120.00 Space group: P 3 2 1 Spacegroup information obtained from library file: Logical Name: SYMINFO Filename: /apps/ccp4/ccp4-6.1.0/lib/data/syminfo.lib Maximum resolution in file input.mtz:1.870 Columns for F, sigF (squared to I): F_880 SIGF_880 Number of valid observations read:17028 Highest resolution: 1.87 Unit cell: 72.5872.5866.2090.0090.00 120.00 Space group: P 3 2 1 Possible alternative indexing schemes Operators labelled exact are exact by symmetry For inexact options, deviations are from original cell (root mean square deviation between base vectors) Maximum accepted RMS deviation between test and reference cells (TOLERANCE) = 2.0 [h,k,l]exact [-h,-k,l]exact Normalising reference dataset Log(I) fit for intensity normalisation: B (slope) -18.82 Normalising test dataset Log(I) fit for intensity normalisation: B (slope) -18.21 Alternative indexing relative to reference file reference.mtz $TEXT:Result:$$ $$
[ccp4bb] anode lifetime?
Does anyone have a reasonable estimate for the expected working lifetime of a copper anode on a MicroMax007? (Yes, I'm thinking about stimulus funding...). Thanks, Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu
[ccp4bb] negative difference density in protein interiors
Specifically, hemoglobin, in original PHASER (unrefined) solution DELFWT an continuing to show up in refined DELFWT coefficients. But I have seen it in other cases too. What does it mean? Thanks Laurie Betts University of Pittsburgh X-ray Crystallography Facility Manager Department of Structural Biology 3501 Fifth Avenue, Pittsburgh, PA 15260 412-383-5839 lab...@pitt.edu
[ccp4bb] positions for single molecule diffraction
Dear All, On behalf of my colleague Prof. Abbas Ourmazd, I'd like to post the following opportunities for post-docs and graduate students. Please respond not to me but to Abbas Ourmazd directly. Best Marius Schmidt === Determining the Structure of Individual Biological Molecules Nanoparticles A limited number of postdoctoral and doctoral positions are immediately available to determine the structure of single biological molecules and nanoparticles. The project involves developing new theoretical concepts and algorithms for reconstructing the structure of faint objects at extremely low signal levels. The implications range from single-molecule tomography to online search algorithms. The work will be conducted at the University of Wisconsin-Milwaukee and state-of-the-art US and European facilities, including the X-ray Free Electron Laser at the Stanford Accelerator Laboratory. This is an outstanding opportunity to work at the intersection of mathematics, physics, informatics, and biology. Candidates with background in any of the relevant areas are encouraged to send applications to Prof. Abbas Ourmazd (ourm...@uwm.edu), from whom further information can also be obtained. Applications should include a summary of experience and interests, a resume, and names and contact details for three referees. = Dr.habil. Marius Schmidt Asst. Professor University of Wisconsin-Milwaukee Department of Physics Room 454 1900 E. Kenwood Blvd. Milwaukee, WI 53211 phone: +1-414-229-4338 email: m-schm...@uwm.edu http://users.physik.tu-muenchen.de/marius/
[ccp4bb] The X6A workbench: Advanced Structural Biology Tools, is back!
Yes! The X6A workbench: Advanced Structural Biology Tools, is back. The next session is scheduled for: June 9 through 12, 2009 http://protein.nsls.bnl.gov We would like to invite you to participate in this four day hands-on course at the NIGMS Research Facility at the National Synchrotron Light Source. This course is intended for beginners who would like to obtain an overview on macromolecular structure determination. The course includes lectures on synchrotron and beam line hardware, crystal growth and handling, data collection and processing, phasing and the first steps in model building and refinement. The main sessions of the workshop will consist of hands-on experience at the beam line actually handling crystals and screening for cryoprotectants, collecting and processing data. Significant amount of time is spent phasing and obtaining the first electron density map. Registration; http://protein.nsls.bnl.gov; you must have an active guest appointment at Brookhaven National Laboratory at the time of the course. An updated schedule will be posted on the website of the course by the end of May, 2009. For further information contact: Vivian Stojanoff Phone: +1 631 344 8375 or Jean Jakoncic Phone: +1 631 344 3930
[ccp4bb] Postdoc Position in Structural Biology of Membrane Proteins
A postdoc position is immediately available in Da-Neng Wang's lab at the Skirball Institute, New York University School of Medicine, New York, to understand the mechanisms of membrane transporters using X-ray crystallography in combination with various biochemical techniques (http://saturn.med.nyu.edu/research/sb/wanglab/). A strong background in structural biology, membrane protein biochemistry, or eukaryotic protein expression is required. Send a CV, statement of research interests and names of references to Da-Neng Wang at w...@saturn.med.nyu.edu. Da-Neng Wang, Ph.D. Skirball Institute of Biomolecular Medicine New York University School of Medicine 540 First Avenue New York, NY 10016 USA Phone:(212) 263-8634, -8635 Fax:(212) 263-8951 E-mail:w...@saturn.med.nyu.edu WWW:http://saturn.med.nyu.edu/research/sb/wanglab/ 2009 Skirball Symposium: http://saturn.med.nyu.edu/research/symposium/2009/
