Re: [ccp4bb] Anisotropic diffraction
Hi, My first thought was same with David: the truncation won't change the crystal's space group. The symmetry of the crystal is reflected by the symmetry of the amplitudes of many many reflections across all resolutions. Ellipsoidal truncation itself only removes some very weak reflections from the outer shells. The remaining reflections will still have a good number of reflections carrying the symmetry of the crystal. However a second thought on the anisotropic scaling and B-factor correction led me to this scenario: suppose we have a crystal that's really P6, but we have cowardly indexed it to a lower space group P2, with the 2-fold axis, b, coinciding the real 6-fold axis. By losing the a=c restrain, the anisotropic scaling along H and L now may not be strictly equal (for example, could be caused by outliers that would have been identified and filtered out if indexed correctly as P6), resulting in the loss of the 6-fold symmetry in the scaled dataset. Apparently this is an artifact due to an improper SG assignment before the anisotropic scaling and B-factor correction. Just some crazy thoughts. Please correct me if I am wrong. BTW, to Theresa: an very informative introduction on ellipsoidal truncation and anisotropic scaling can be found here: http://services.mbi.ucla.edu/anisoscale/ -- From: "Theresa Hsu" Sent: Friday, April 27, 2012 3:18 PM To: Subject: [ccp4bb] Anisotropic diffraction Dear crystallographers A very basic question, for anisotropic diffraction, does data truncation with ellipsoidal method change the symmetry? For example, if untruncated data is space group P6, will truncated data index as P622 or P2? Thank you. Theresa
[ccp4bb] A topical one...Re: [ccp4bb] Publication ethics Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Dear Mark, And of course this one is topical:- http://publicationethics.org/case/lost-raw-data Best wishes, John Prof John R Helliwell DSc FInstP CPhys FRSC CChem F Soc Biol. Chair School of Chemistry, University of Manchester, Athena Swan Team. http://www.chemistry.manchester.ac.uk/aboutus/athena/index.html On 27 Apr 2012, at 11:40, Mark J van Raaij wrote: > have a look at this case, no danger of your coordinates going to anyone but > yourself if you do it this way: > http://publicationethics.org/case/author-creates-bogus-email-accounts-proposed-reviewers > > > On 26 Apr 2012, at 12:02, Jrh wrote: > >> Dear Colleagues, >> I have followed this thread with great interest. It reminds me of the Open >> Commission Meeting of the Biological Macromolecules Commission in Geneva in >> 2002 at the IUCr Congress. Ie at which it was concluded that protein >> coordinates and diffraction data would not be provided to referees. >> >> The ethics and rights of readers, authors and referees is a balancing act, >> as Jeremy and others have emphasised these different constituency's views. >> >> The aim of this email though is to draw your attention to the Committee on >> Publication Ethics (COPE) work and case studies, which are extensive. Ie >> see:- >> >> http://publicationethics.org/ >> >> The COPE Forum will also provide advice on case submissions that are made of >> alleged publication malpractice, various of which are quite subtle. The >> processes as well though following on from obvious malpractice eg how a >> university research malpractice committee can be convened are also detailed. >> >> Greetings, >> John >> >> Prof John R Helliwell DSc >> >> >> >> On 26 Apr 2012, at 06:10, Jeremy Tame >> wrote: >> >>> The problem is it is not the PI who is jumping, it may be a postdoc he/she >>> is throwing. >>> >>> Priority makes careers (look back at the Lavoisier/Priestly, >>> Adams/LeVerrier or >>> Cope/Marsh controversies), and the history of scientific reviewing is not >>> all edifying. >>> >>> Too many checks, not enough balances. Science is probably better served if >>> the >>> author can publish without passing on the pdb model to a potentially >>> unscrupulous >>> reviewer, and if there are minor errors in the published paper then a >>> competing >>> group also has reason to publish its own view. The errors already have to >>> evade the >>> excellent validation tools we now have thanks to so many talented >>> programmers, >>> and proper figures and tables (plus validation report) should be enough for >>> a review. >>> The picture we have of haemoglobin is now much more accurate than the ones >>> which came out decades ago, but those structures were very useful in the >>> mean >>> time. A requirement of resolution better than 2 Angstroms would probably >>> stop poor >>> models entering PDB, but I don't think it would serve science as a whole. >>> Science >>> is generally a self-correcting process, rather than a demand for perfection >>> in every >>> paper. Computer software follows a similar pattern - bug reports don't >>> always invalidate the >>> program. >>> >>> I have happily released data and coordinates via PDB before publication, >>> even back in the >>> 1990s when this was unfashionable, but would not do so if I felt it risked >>> a postdoc >>> failing to publish a key paper before competitors. It might be helpful if >>> journals were >>> more amenable to new structures of "solved" proteins as the biology often >>> emerges >>> from several models of different conformations or ligation states. But in a >>> "publish or >>> perish" world, authors need rights too. Reviewers do a necessary job, but >>> there is a >>> need for balance. >>> >>> The attached figure shows a French view of Le Verrier discovering Uranus, >>> while >>> Adams uses his telescope for a quite different purpose. >>> >>> >>> >>> >>> On Apr 26, 2012, at 2:01 AM, Ethan Merritt wrote: >>> On Wednesday, April 25, 2012 09:40:01 am James Holton wrote: > If you want to make a big splash, then don't complain about > being asked to leap from a great height. This gets my vote as the best science-related quote of the year. Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742 >>>
[ccp4bb] CSX2012 Spectroscopy & X-ray Workshop, 4.-6. July, ETHZ
3rd Workshop on the Simultaneous Combination of Spectroscopies with X-ray Absorption, Scattering and Diffraction Techniques - CSX2012 http://www.psi.ch/csx2012 Abstract submission reminder Abstract submission deadline: 1 May 2012 Dear Colleagues, Please find at the links below the brochure and the poster for the "3rd Workshop on the Simultaneous Combination of Spectroscopies with X-ray Absorption, Scattering and Diffraction Techniques" CSX2012, to be held from 4 - 6 July in Zurich, Switzerland. http://indico.psi.ch/getFile.py/access?resId=0&materialId=poster&confId=1118 http://indico.psi.ch/getFile.py/access?resId=0&materialId=0&confId=1118 This is a gentle reminder that the abstract submission deadline is approaching. We will be accepting abstract submissions until May 2nd, 09:00 am. The objective of the workshop is to provide an international platform for an in-depth discussion of both the application and instrumentation aspects of the combination of in-situ optical spectroscopy and X-ray methods. It is the 3rd in a series of workshops previously held at the ESRF in 2008 and at SOLEIL in 2010. It is being organized by the Swiss Light Source as a satellite workshop of the 11th International Conference on Synchrotron Radiation Instrumentation (SRI 2012). We would be delighted if you were interested in joining us at ETH Zurich in July. Further details and announcements are available at the conference website at http://www.psi.ch/csx2012 . We would appreciate very much if you could distribute this information to interested colleagues at your institution. With best wishes, Martin Fuchs on behalf of the scientific organization committee --- Martin Fuchs - martin.fu...@psi.ch -- Swiss Light Source at Paul Scherrer Institut CH-5232 Villigen PSI, Switzerland WWW: http://sls.web.psi.ch Phone: +41 56 310 5455 Fax: -5292
[ccp4bb] Ligand geometry
Dear All: I use Refmac5 to refine my model. After the run, I check the model quality by Coot. Here is the problem: In Coot, the ligand - NAD, has bad geometry as indicated by a big red bar. While the geometry of NAD fit nicely with the electron density. If I use refine tools (i.e. regularize Zone or real space refine zone), the geometry of NAD turns to perfec with bond, angle and so on. But the ligand slightly turn away from the electron density map. If I run Refmac5 again with this modified model, the NAD turns back, fit nice to electron density, but gives red bar in coot geometry. The Refinment Parameters in Refmac5 is set @ "use automatic weight" and "use experinmental sigmals to weight X-ray terms". Thank you for advice and comments Ros
Re: [ccp4bb] Ligand geometry
Hi Uma, How different are your NADs optimised in Refmac and Coot? Are you sure you are using the same geometric restraints? Coot has to know where Refmac's restraint files are. This info is passed through an environment setting on your computer (I don't know the name by hart. Anyone?). Are you using Windows, Linux or OSX or something else? You can try to find more details about geometric outliers by checking Refmac's log file. That way you may find which specific bond/angle is the problem. Cheers, Robbie Date: Sat, 28 Apr 2012 11:47:58 -0400 From: rosiso2...@gmail.com Subject: [ccp4bb] Ligand geometry To: CCP4BB@JISCMAIL.AC.UK Dear All: I use Refmac5 to refine my model. After the run, I check the model quality by Coot. Here is the problem: In Coot, the ligand - NAD, has bad geometry as indicated by a big red bar. While the geometry of NAD fit nicely with the electron density. If I use refine tools (i.e. regularize Zone or real space refine zone), the geometry of NAD turns to perfec with bond, angle and so on. But the ligand slightly turn away from the electron density map. If I run Refmac5 again with this modified model, the NAD turns back, fit nice to electron density, but gives red bar in coot geometry. The Refinment Parameters in Refmac5 is set @ "use automatic weight" and "use experinmental sigmals to weight X-ray terms". Thank you for advice and comments Ros
