Re: [ccp4bb] Refmac and links between ligands
Problem solved. One must also switch to the "make sugar NO" keyword. Otherwise Refmac tries to use the discovered sugar and ion as if it was sugar-peptide bond. Jan Dohnalek On Mon, Feb 1, 2010 at 2:52 PM, Jan Dohnalek wrote: > Dear all > I understand that when I use the Refmac keyword > make link no > Refmac should not apply found links. > It keeps finding links between ligands (Na+ and ligand OH) and (I think) > refines them as it issues a warning (not INFO), does not say "(not be used)" > for these and the output .pdb file contains the LINK records newly created > for these atoms. > > The actual distances look pretty much as if they were restrained ... > > Is there a way to make Refmac ignore these links? > > Jan Dohnalek > > -- > Jan Dohnalek, Ph.D > Institute of Macromolecular Chemistry > Academy of Sciences of the Czech Republic > Heyrovskeho nam. 2 > 16206 Praha 6 > Czech Republic > > Tel: +420 296 809 390 > Fax: +420 296 809 410 > -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
Re: [ccp4bb] how to supply the following twin operator to detwin?
The determinant of the matrix is zero, so it can't be a twin operator
Re: [ccp4bb] how to supply the following twin operator to detwin?
Francis, I think the only format that detwin will accept is: -h/2+k/2-l, h/2-k/2-l, -h/2-k/2 i.e. '*'s are definitely not allowed. However the matrix that is generated contains only integer elements, so in fact it won't accept the '/'s either. Is this supposed to be a merohedral (or pseudo-merohedral) twin operator? If not then it won't work. Personally I wouldn't use detwin anyway, I think it's likely to cause more problems than it solves! Cheers -- Ian > -Original Message- > From: owner-ccp...@jiscmail.ac.uk > [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Francis E Reyes > Sent: 01 February 2010 23:33 > To: CCP4 bulletin board > Subject: how to supply the following twin operator to detwin? > > Hi All > > I'm having trouble with the following ... > > > title [No title given] > operator -1/2*h+1/2*k-l, 1/2*h-1/2*k-l, -1/2*h-1/2*k > labin I(+)=I_Unspecified(+) SIGI(+)=SIGI_Unspecified(+) > I(-)=I_Unspecified(-) SIGI(-)=SIGI_Unspecified(-) > end > > > I keep getting symmetry operator error. > > Thanks > FR > > - > Francis Reyes M.Sc. > 215 UCB > University of Colorado at Boulder > > gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D > > 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing i.tic...@astex-therapeutics.com and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
[ccp4bb] how to supply the following twin operator to detwin?
Hi All I'm having trouble with the following ... title [No title given] operator -1/2*h+1/2*k-l, 1/2*h-1/2*k-l, -1/2*h-1/2*k labin I(+)=I_Unspecified(+) SIGI(+)=SIGI_Unspecified(+) I(-)=I_Unspecified(-) SIGI(-)=SIGI_Unspecified(-) end I keep getting symmetry operator error. Thanks FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
[ccp4bb] Post-Doc position
Hauptman-Woodward Medical Research Institute Post-doctoral Positions Virus-Host Interactions and Structures The laboratories of Drs. L. Wayne Schultz and Tim Umland are seeking a highly motivated individual to participate in a joint interdisciplinary research project investigating Influenza A and SARS-CoV virus-host protein-protein interactions and structures. A position at the Post-Doctoral level is available, to be fill as soon as possible. Competitive applicants should have demonstrated scientific productivity and innovation at the graduate level, and possess a Ph.D., M.D., or similar degree. The successful applicant will have previous experience in all aspects of macromolecular crystallography, as well as molecular biology, protein expression and purification. They will interact with our groups to determine the crystal structures of virus-host protein complexes important in dictating host tropism. Salary and benefits are competitive, and funding is available be for up to 2 years. The Hauptman-Woodward Medical Research Institute (HWI) is a private, not-for-profit organization 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. To apply for a post-doctoral position, please send your CV and the names of three references to Drs. Schultz (schu...@hwi.buffalo.edu) and Umland (uml...@hwi.buffalo.edu). Please visit the web site for the Laboratory for the Study of Infectious Diseases (LSID) for additional information: http://labs.hwi.buffalo.edu/lsid The Hauptman-Woodward Institute is an Equal Opportunity Employer
Re: [ccp4bb] Refining against images instead of only reflections
I have re-visited these calculations over the weekend. As far as I can tell, there is just no way to change background-subtracted spot intensities with "diffuse" scattering unless the motions are somehow "synchronized" across different unit cells. Call it "optical" or "acoustic" or whatever you like. I have now repeated the previously-posted nearBragg simulations with 10x more atoms, but still 10% of the scattering matter involved in a two-headed displacement. I have also done a "disordered solvent" simulation where more than half of the unit cell volume is filled with completely random atoms. In both cases the result was the same as before: subtracting the "average-electron-density" diffraction image from the "average diffraction over many configurations" image is a smooth and "locally uniform" image with no signs of spot intensities. This implies that subtracting a smooth "local background" from each spot will yield the Fourier coefficients of the average electron density (as long as the crystal has no "synchronized disorder"). Examples of "synchronized disorder" would be something like a sound wave moving through the crystal. This would cause the motion of atoms in one unit cell to be related in some way to those in another. Another way to do this is if the lattice is distorted by defects. As this is a pet model of mine, I have now added an example of it on my little web page: http://bl831.als.lbl.gov/~jamesh/diffuse_scatter/index.html#dilatation This effect does produce little "bumps" under Bragg peaks that can become quite significant. Perhaps this is the "acoustic DS" that Ian is talking about? Or perhaps it should be called "defect DS"? The really interesting bit I think is that no matter what the lattice-distortion model, the fractional changes in spot intensities are the same. If this is true in general, then such a "synchronized disorder correction" would be fairly easy to incorporate into a refinement program (very few new parameters). The shape of the DS between spots could guide this correction, but might be unnecessary if the disorder is apparent in the average electron density. So, I can still claim to be relevant to the original post! -James Holton MAD Scientist Ian Tickle wrote: James, I think the problem is that your simulation just doesn't contain enough atoms in the unit cell with correlated displacements to exhibit significant optic DS, i.e. with only 1 or 2 atoms it will be dominated by Einstein-model DS which as I explained before is locally uniform and therefore can be fitted by a planar background function. Cheers -- Ian -Original Message- From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of James Holton Sent: 29 January 2010 09:43 To: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] Refining against images instead of only reflections All I'm saying is that when I calculate the average general scattering from 8192 random configurations of one disordered atom per unit cell: http://bl831.als.lbl.gov/~jamesh/diffuse_scatter/xtal_diffuse.gif and then subtract from that the general scattering from an "occupancy-weighted model" with the two possible atom positions are at half occupancy: http://bl831.als.lbl.gov/~jamesh/diffuse_scatter/xtalAB_Fsum.gif I get an difference image that shows only the smooth diffuse-scatter background, with no spots to speak of: http://bl831.als.lbl.gov/~jamesh/diffuse_scatter/xtals_diffuse_minus_Fsu m. gif But, if I calculate the average general scattering from an "all A" and an "all B" crystal: http://bl831.als.lbl.gov/~jamesh/diffuse_scatter/xtalAB_Isum.gif and subtract from it the same partial-occupancy model image as above: http://bl831.als.lbl.gov/~jamesh/diffuse_scatter/xtalAB_Fsum.gif I get an image where some of the spots have been subtracted out, but others are still quite pronounced: http://bl831.als.lbl.gov/~jamesh/diffuse_scatter/xtals_Isum_minus_Fsum.g if So, in the first case, the partial-occupancy model produced exactly the same background-subtracted spot intensities as the "unsynchronized disorder" case, but this was not so when the disorder was synchronized. What did I do wrong? As far as my "operational" definition of a "Bragg peak" (a term which already has two definitions), I am merely suggesting that the nearly-universal practice of subtracting the "local background" is a very pragmatic definition of a "spot intensity". Nearly all available data were collected in this way, and it actually is a reasonable thing to do if the disorder from cell to cell is uncorrelated (as evidenced above). However, I totally agree with you that the disorder in protein crystals may well be correlated across large patches of unit cells. If that is the case, then the "average occupancy model" that is all but universally implemented by refinement programs will never be able to explai
[ccp4bb] Phenix version 1.6 released
The Phenix developers are pleased to announce that version 1.6 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Just some of the new features in this version (1.6) are: - New Graphical User Interfaces for AutoMR, and Phaser (in MR and SAD modes) - Improved reflection file editor GUI and command line tool - Updated map calculation GUI - C++ version of Resolve - Refinement of residues spanning symmetry axes in phenix.refine - New RNA sugar pucker geometry restraints in phenix.refine - Torsion angle dynamics refinement updates - Optional real space refinement of ligands in LigandFit wizard For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that there is a new publication that should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Acting Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Patty Jimenez [ pajime...@lbl.gov ] [ 1-510-486-7963 ] --
[ccp4bb] Postdoctoral position in Structural Biology at the CNIO, Madrid, Spain
*An opening for a post-doctoral position is available immediately at the Structural Biology and Biocomputing Programme of the Spanish National Cancer Research Centre (CNIO) in Madrid, Spain.* We are seeking a motivated scientist to join our group to study molecular mechanisms of cell signaling and adhesion. The project focuses on the structural and biochemical characterization of mechanisms that regulate and integrate growth factor receptor and integrin signaling. Candidates should have experience with protein expression, purification, crystallization, structure determination and refinement. Experience with baculovirus and/or mammalian expression systems is an advantage. The candidate will work with a team of highly motivated structural biologists and biochemists with collaborations both, within the CNIO with cell biology and computational groups, as well as externally with leading international research groups. For more information on the group see: http://www.cnio.es/ing/grupos/plantillas/presentacion.asp?grupo=50007726 The CNIO offers: •Access to state-of-the-art facilities for robotic crystallization setup, crystal visualization and X-ray diffraction data collection. •A vibrant, multi-disciplinary and international working environment. •The opportunity to be part of a European Cancer Research Centre of excellence that successfully combines basic and applied research. •A competitive salary and an attractive benefits package. •Situated in one of Europe’s cultural capitals Applications with CV and inquiries should be sent by email to the group leader, Dr. Daniel Lietha (dlie...@cnio.es). All enquiries and applications will be treated confidentially.
[ccp4bb] 15th Annual Structural Biology Symposium
Dear Colleague, You and your colleagues are cordially invited to join us for the 15th Annual Structural Biology Symposium to be held at the Hotel Galvez on beautiful Galveston Island on Friday, March 19th, 2010. The meeting is organized by the Sealy Center for Structural Biology & Molecular Biophysics and co-sponsored by the Keck Center for Computational & Structural Biology. In previous years, over 300 scientists from the U.S. and abroad, have participated in the annual event. The goal of the symposia is to bring together leaders in all areas of structural biology to present current topics. The program of the symposium 2010 includes the following prominent speakers: Keynote Speaker: Jack E. Johnson, Ph.D. Professor, Dept. of Molecular Biology Scripps Research Institute, La Jolla, CA Philip N. Bryan, Ph.D, University of Maryland Biotechnology Institute, Bethesda, MD Kay Choi, Ph.D., The University of Texas Medical Branch, Galveston, TX John D. Ladbury, Ph.D., University of Texas M.D. Anderson Cancer Center Eva Nogales, Ph.D., University of California, Berkeley, Berkeley, CA Christopher Putnam, Ph.D., Scripps Research Institute, La Jolla, CA Gregory D. Van Duyne, University of Pennsylvania School of Medicine, Philadelphia, PA Poster sessions and social events, included in the program, provide ample opportunity for formal and informal discussions with the speakers. Awards will be given to graduate students and post-docs for best poster presentations. To insure maximum participation, the costs of attending the symposium have been kept to a minimum. Reasonably priced rooms have been reserved at the historic beachfront Hotel Galvez on Galveston Island at the site of the meeting, for symposium participants and meals are provided on-site during the Symposium. Please visit our symposium web-site at http://www.scsb.utmb.edu/symposium/ for on-line registration and abstract submission or contact Angelina Johnson, Phone: (409) 772-8083, Fax: (409) 772-6334 or email at: ajohn...@utmb.edu,. Registration for the Symposium is open now and we encourage you and your colleagues to go on-line and register. We are looking forward to seeing you on March 19th, 2010. On behalf of the Organizing Committee: Sincerely yours, Robert O. Fox, Ph.D. Vince Hilser, Ph.D. Symposium Chair Symposium Co-Chair Deputy Director Director Sealy Center for Structural Biology and Sealy Center for Structural Biology and Molecular Biophysics Molecular Biophysics Professor Professor Department of Biochemistry and Molecular Biology Department of Biochemistry and Molecular Biology
Re: [ccp4bb] Refmac and links between ligands
Can you check your input file. It may contain contain link record already regards Garib On 1 Feb 2010, at 13:52, Jan Dohnalek wrote: Dear all I understand that when I use the Refmac keyword make link no Refmac should not apply found links. It keeps finding links between ligands (Na+ and ligand OH) and (I think) refines them as it issues a warning (not INFO), does not say "(not be used)" for these and the output .pdb file contains the LINK records newly created for these atoms. The actual distances look pretty much as if they were restrained ... Is there a way to make Refmac ignore these links? Jan Dohnalek -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
Re: [ccp4bb] Coot- Find water
james09 pruza wrote: The find water option in coot is not picking up more that 10 water molecules but density is there. How can it be sorted out?? By changing the "Find peaks above", "Minimum distance" and "Maximum distance" values in the dialog? Paul.
[ccp4bb] Refmac and links between ligands
Dear all I understand that when I use the Refmac keyword make link no Refmac should not apply found links. It keeps finding links between ligands (Na+ and ligand OH) and (I think) refines them as it issues a warning (not INFO), does not say "(not be used)" for these and the output .pdb file contains the LINK records newly created for these atoms. The actual distances look pretty much as if they were restrained ... Is there a way to make Refmac ignore these links? Jan Dohnalek -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
