[ccp4bb] ccp4i unable to read mtz files, resolved
BSD Dear All, (From 10 days ago; I forgot to post the solution). Thanks to Nicholas Moir, we tracked the problem down to a missing library related to LDAP authentication: libnss_ldap.so.2 We only got the error using ccp4i, however. MTZDUMP from the command line worked. Thanks to everyone else who offered suggestions. Harry - Harry M. Greenblatt Staff Scientist Dept of Structural Biology [EMAIL PROTECTED] Weizmann Institute of SciencePhone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel
[ccp4bb] number of MTZ files input to scaleit
Hi folks silly question, I know, and I'm sure this must have been answered before, but I want to put 10+ datasets into the same file and get scaling statistics between them. I find that SCALEIT is happy to do the scaling once all the datasetsa re together (according to the man page it's okay with 20) but CAD will only let me put 9 datasets in an MTZ file. Do I have to run CAD twice (or more...) to get all my datasets together? Or is there some other way that I've missed? Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 2QH
Re: [ccp4bb] number of MTZ files input to scaleit
Hi Harry, The only way I have ever found to do this is to do lots of cad runs. Especially if you want them all to share the same unit cell, project name and crystal name... Cheers, Graeme -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Harry Powell Sent: 26 June 2007 14:06 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] number of MTZ files input to scaleit Hi folks silly question, I know, and I'm sure this must have been answered before, but I want to put 10+ datasets into the same file and get scaling statistics between them. I find that SCALEIT is happy to do the scaling once all the datasetsa re together (according to the man page it's okay with 20) but CAD will only let me put 9 datasets in an MTZ file. Do I have to run CAD twice (or more...) to get all my datasets together? Or is there some other way that I've missed? Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 2QH
Re: [ccp4bb] Free travel money: Rigaku announces post-doc travel bursaries
I just wanted to re-post this in case you know someone who wants some travel money. Jim Rigaku Americas Corporation is pleased to announce the availability of five (5) awards of $500 each to post-doctoral research fellows to help with the costs of travel to upcoming summer meetings such as the ACA meeting in Salt Lake City, Utah (July 21-26), the ECM meeting in Marrakech, Morocco (August 22-27), and/or another upcoming meeting. One can apply for the award through a simple web form on the Rigaku web site: http://www.rigaku.com/protein/postdoc.html , but you must do so before the July 8th, 2007 deadline. The 5 awards will go to the post-doctoral fellows who provide the most compelling explanation as to how they intend to pursue a career in structural biology.
[ccp4bb] Protein Crystallographer (R5-R7) - St. Louis, MO
Pfizer Global Research in St. Louis currently has an opening for a highly motivated and talented protein crystallographer to join our Structural Computational Chemistry Department. The successful candidate will become a member of a productive and innovative structure based drug design group, working within cross-functional structural biology teams to solve structures of new drug targets and generate protein-ligand co-crystal structures. As a member of several drug discovery project teams, you will have an opportunity to partner with a wide variety of researchers, including medicinal chemists, biologists, and computational chemists to leverage structural information to direct the optimization of lead chemical matter into potential drug candidates. The successful candidate will be expected to design protein constructs for crystallization, partner with biochemists involved in protein purification, guide crystallization experiments, collect X-ray diffraction data on home and synchrotron sources, determine and interpret crystal structures, and leverage these structure results in structure based design efforts. Additionally, there will be a significant role in identifying new targets for structural studies and new technologies or approaches to enhance the efficiencies of X-ray crystallography methods within the group. Qualifications: •Ph.D. in Biochemistry, Chemistry, or equivalent with 3-5 years post-PhD experience in protein crystallography •Ability to independently guide reagent and crystallization efforts for protein crystallography projects. •Experience in protein purification, biophysical analysis of proteins, crystallization, novel phasing methods or high throughput crystallography. •Ability to successfully partner with colleagues of various disciplines. •Excellent written and verbal communication skills. Job Requisition #: 71197 To learn more about our people, our products, and our plans for the future, visit www.pfizer.com/careers Protein Crystallographer.doc- Req# 71197.doc Description: application/applefile Protein Crystallographer.doc- Req# 71197.doc Description: Binary data
[ccp4bb] anisotropic atoms, refmac, ccp4, coot the pdb
Hello Everyone This isn't really a question, just a warning to check your anisotropic temperature factors both after refinement and after deposition at the pdb. We've been having a lot of trouble with anisotropic temperature factors lately. Here's what's been going on. We have three different proteins, each diffracting better than 1.2 A - the best resolution is ~ 0.8 A. All have been refined with refmac (yes I know shelxl is great for such problems, but that's not the issue here). For structures refined with some versions of refmac (including the ccp4-6.0.2 linux distribution from early this year), the anisotropic components output on the ANISOU card are ridiculous. When we run anisoanl, ALL atoms are flagged as non-positive definite. When I ask coot to show anisotropic ellipsoids, they have only two dimensions (coot doesn't crash, Paul has the negative numbers trapped). Refinement of the same data set/coordinates with shelxl produces anisotropic temperature factors which are reasonable as judged by these two methods. I can fix the refmac problem by installing the latest version of refmac from Garib's web page (not the version in ccp4-6.0.2). The anisotropic ellipsoids are now good (as judged by anisoanl and coot). (Repeating myself, these are all very high resolution structures). So, I thought the problem was solved. We reviewed structures we'd deposited with the pdb but were as yet unreleased and found one with unrealistic thermal ellipsoids, which confused us since the depositor had done the sanity checks before depositing the coordinates. When we compared the file we submitted to the pdb and the file which was returned to us, the numbers on ALL the ANISOU cards had been rotated in this fashion: ANISOU1 N MET A 1 1612 1818 1492 2 -160 -14 AN has become ANISOU1 N MET A 1 1612 2-14 1818 1492 -160 N In other words the aniso card, (u11,u22,u33,u12,u13,u23) has been rearranged to be (u11,u12,u23,u22,u33,u13) (this doesn't make any sense to me) I can speculate that the refmac/pdb issues are interlinked and one arises from an attempt to fix the other, but I don't know that that's true. I did a quick check of structures released by the pdb in the last year with resolution 1.1 A and found at least one with the same problems (I stopped looking after I'd found one). Sue Sue Roberts Biochemistry Biopphysics University of Arizona [EMAIL PROTECTED]
Re: [ccp4bb] anisotropic atoms, refmac, ccp4, coot the pdb
On Tuesday 26 June 2007 10:43, Sue Roberts wrote: Hello Everyone This isn't really a question, just a warning to check your anisotropic temperature factors both after refinement and after deposition at the pdb. I encourage everyone who is refining, depositing, or inspecting structures with anisotropic ADPs to validate them using the Parvati web server: http://skuld.bmsc.washington.edu/parvati/parvati.html (If it mis-handles these apparently totally messed-up files that Sue refers to, please let me know) Ethan We've been having a lot of trouble with anisotropic temperature factors lately. Here's what's been going on. We have three different proteins, each diffracting better than 1.2 A - the best resolution is ~ 0.8 A. All have been refined with refmac (yes I know shelxl is great for such problems, but that's not the issue here). For structures refined with some versions of refmac (including the ccp4-6.0.2 linux distribution from early this year), the anisotropic components output on the ANISOU card are ridiculous. When we run anisoanl, ALL atoms are flagged as non-positive definite. When I ask coot to show anisotropic ellipsoids, they have only two dimensions (coot doesn't crash, Paul has the negative numbers trapped). Refinement of the same data set/coordinates with shelxl produces anisotropic temperature factors which are reasonable as judged by these two methods. I can fix the refmac problem by installing the latest version of refmac from Garib's web page (not the version in ccp4-6.0.2). The anisotropic ellipsoids are now good (as judged by anisoanl and coot). (Repeating myself, these are all very high resolution structures). So, I thought the problem was solved. We reviewed structures we'd deposited with the pdb but were as yet unreleased and found one with unrealistic thermal ellipsoids, which confused us since the depositor had done the sanity checks before depositing the coordinates. When we compared the file we submitted to the pdb and the file which was returned to us, the numbers on ALL the ANISOU cards had been rotated in this fashion: ANISOU1 N MET A 1 1612 1818 1492 2 -160 -14 AN has become ANISOU1 N MET A 1 1612 2-14 1818 1492 -160 N In other words the aniso card, (u11,u22,u33,u12,u13,u23) has been rearranged to be (u11,u12,u23,u22,u33,u13) (this doesn't make any sense to me) I can speculate that the refmac/pdb issues are interlinked and one arises from an attempt to fix the other, but I don't know that that's true. I did a quick check of structures released by the pdb in the last year with resolution 1.1 A and found at least one with the same problems (I stopped looking after I'd found one). Sue Sue Roberts Biochemistry Biopphysics University of Arizona [EMAIL PROTECTED] -- Ethan A MerrittCourier Deliveries: 1959 NE Pacific Dept of Biochemistry Health Sciences Building University of Washington - Seattle WA 98195-7742
[ccp4bb] Opportunity for beamline technician
Please see our web site for a position open for a senior research associate to work at our beamline at the APS in Chicago. If you are interested, please apply online. I'm not officially involved in the hiring. http://sgxpharma.com/careers/Sr.ResearchAssociateSGXChicago.php SGX has an opportunity for a Senior Research Associate to join our X-ray synchrotron beamline team, SGX-CAT. The staff at SGX-CAT are responsible for the operation and maintenance of the beamline, including the collection of crystallographic data from protein crystals. This group is located at the Advanced Photon Source of Argonne National Laboratory near Chicago and interacts closely with SGX headquarters in San Diego. The qualified individual will have a B.S./M.S. in a physical or biological science. The ability to reason quantitatively and learn new concepts quickly is critical for this position. The candidate will become familiar will all aspects of the facility through interactions with the existing staff. A working knowledge of Unix computer systems is desirable and the ability to develop new Unix-based beamline control and analysis software is a plus. Excellent communication skills are necessary, which will be used for interactions inside and outside the company. A commitment to providing data of the highest quality is essential. Availability on nights and weekends will occasionally be required. Shane Atwell SGX Pharmaceuticals
