Re: [ccp4bb] NCS axis detrmination
Old fashioned and basic, but why not just use the dot product cos (Diff) = l1 l2 +m1 m2 +n1 n2 where l m n are the direction cosines of the two rotation axes. The output of GESANT or LSQKAB give you the direction cosines. Any calculator will do the sum! Eleanor On 30 June 2017 at 03:06, Genevieve Evans wrote: > Hi Vandra, > > For changes in a dimer when comparing two crystal forms, in addition to > looking at the change in the NCS axis, > you may want to consider the following software: > > DynDom > S. Hayward, A. Kitao, H. J. C. Berendsen, "Model-Free Methods of Analyzing > Domain Motions in Proteins from Simulation: A Comparison of Normal Mode > Analysis and Molecular Dynamics Simulation of Lysozyme" Proteins, > Structure, Function and Genetics, 27:3, 425-437, 1997. > http://fizz.cmp.uea.ac.uk/dyndom/ > > HingeFinder > Willy Wriggers and Klaus Schulman, "Protein Domain Movements: Detection of > Rigid Domains and Visualization of Effective Rotations in Comparisons of > Atomic Coordinates." Proteins: Structure, Function, and Genetics, 29:1, > 1-14, 1997. > http://biomachina.org/disseminate/hingefind/hingefind.html > > I’ve personally found the above software to be very helpful. > > Cheers, > Genevieve > > Dr Genevieve Evans > > School of Chemistry and Biochemistry > The University of Western Australia (M310) > 35 Stirling Highway > CRAWLEY WA 6009 > Australia > > > On 30 Jun 2017, at 8:12 AM, Zhijie Li > wrote: > > Hi Vandna, > > Assuming you have two copies, chain A and B. > > In UCSF chimera: > > 1) open two copies of the pdb (model #0 and #1) > 2) in command line, type: > > match #1:.B@CA #0:.A@CA showMatrix true > > Besides moving model #1 chain B to model #0 chain A, the match command > also outputs the rotation and translation matrices and angles, axes in > Favorite-> Reply Log. > Note that you might need to specify residue number range for the two > chains if the number of CAs in them are not equal - just to make the match > working. The match command does not guess the range of residues to align as > the MatchMaker does. Alt confs involving CAs also count. You may run: > > del @CA.B > > to delete all alt conf B CA atoms before the match command to make it > working > > > If you wish to draw the rotation axis in Chimera, you need to make a bild > file that draws an arrow from the "Axis point" with direction specified by > the Axis vector. Assuming the "Axis" is "Ax Ay Az" and the "Axis point" is > "x y z", you need to calculate X1=x+Ax*20, Y1=y+Ay*20, Z1=z+Az*20, then > put this in the arrow.bld file: > > .arrow x y z X1 Y1 Z1 > > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html > > > > COOT also outputs the matrices in the terminal window. But COOT does not > seem to directly show the more human friendly "rotation angle" and "shift > along axis". > > Zhijie > > > > On 29/06/2017 3:16 PM, Vands wrote: > > Hi every one , > I am looking for a tool to perfectly determine the > NCS axis. I have two forms of crystals where diamer is with NCS but on a > comparison of both forms, it looks like NCS axis is little off when > i superpose two forms, i would like to measure rotation or translation > between axes . > > > -- > Vandna Kukshal > Senior Scientist > Dept. Biochemistry and Molecular Biophysics > Washington University School of Medicine > 660 S. Euclid, Campus Box 8231 > St. Louis, MO 63110 > > > > > >
Re: [ccp4bb] [phenixbb] crystal imaging system
Hi Sebastiano I always feel uneasy when these conversations come up on the bb because smaller companies tend to be overlooked in the discussion. Being a member of a smaller company myself I know how frustrating this is, because you feel that you can't speak up yourself because it looks like an advertisement. I know very little about imaging systems, but I think you should at least consider the systems made by Jansci, XtalQuest and XtalConcepts There may be others. Best wishes, Patrick On 30 June 2017 at 15:55, Chris Waddling wrote: > We had the Tritek CrystalPro and now have two Formulatrix RI-1000s. We're > very happy with what we have now, and though I don't know what improvements > Tritek has made since the version we owned, at the time we found their > software clunky, imaging not the best or most consistent, and automation > challenging. It took a great deal of time to make it work marginally. > > The formulatrix systems on the other hand have been robust and their > support excellent (we pay for annual software support but let the hardware > support go). They're easy to run and maintain. > > Chris > > Dr Christopher A Waddling > > Crystallography Facility Manager > > Department of Biochemistry and Biophysics > > University of California, San Francisco > > Genentech Hall, Box 2140 > > 600 16th St., S126C > > San Francisco, CA > > 94143 > > 415-476-8288 > > > > On Jun 30, 2017, at 5:36 AM, Sebastiano Pasqualato < > sebastiano.pasqual...@gmail.com> wrote: > > > Dear all, > we are in the process of considering the purchase of a new Crystal Imager. > > So far, we have been considering the Formulatrix Rock Imager 182 and the > TriTek Crystal Pro HT. > I would be extremely grateful to anyone who could provide me: > > - feedback and user experience (positive/negative) on those instruments; > - information on other instruments you would suggest. > > Thank you very much in advance, > wishing you a pleasant weekend, > best regards, > ciao, > S > > > > -- > *Sebastiano Pasqualato, PhD* > Crystallography Unit > Department of Experimental Oncology > European Institute of Oncology > IFOM-IEO Campus > via Adamello, 16 > 20139 - Milano > Italy > > tel +39 02 9437 5167 <+39%2002%209437%205167> > fax +39 02 9437 5990 <+39%2002%209437%205990> > web http://is.gd/IEOXtalUnit > > ___ > phenixbb mailing list > pheni...@phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-le...@phenix-online.org > > -- patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
[ccp4bb] LIVESTREAMING: Cryo-EM Symposium, 6-7 July 2017, Grenoble, France
Dear colleagues, onJuly6th and 7th, the European Photon & Neutron Campus in Grenoblewill host a unique CRYO-EM Symposium in the framework of the newly established cryo-EM platform. The new facility will be open to the user community based on peer-review of scientific merit and technical feasibility. Scientists from ESRF, IBS and EMBL will support user operation. Registration for the event is now closed, but you can follow the talks, presented by worldwide experts in the field, through YouTube live streaming: https://www.youtube.com/user/LightforScience We will be live from 1.30pm on 6 July 2017. Check out the programme here: http://www.esrf.eu/cryo-em.fr On behalf of the Organising committee: Stephen Cusack (EMBL), Trevor Forsyth (ILL/Keele), Wojciech Galej (EMBL), Gordon Leonard (ESRF), Marco Marcia (EMBL), Christoph Mueller-Dieckmann (ESRF), Hugues Nury (IBS), Guy Schoehn (IBS), Montserrat Soler-Lopez (ESRF), Jean Susini (ESRF) and Winfried Weissenhorn (IBS).
[ccp4bb] Landscape report on open research data
Dear Colleagues, I draw your attention to this report published today:- http://www.universitiesuk.ac.uk/policy-and-analysis/research-policy/open-science/Documents/ORDTF%20report%20nr%201%20final%2030%2006%202017.pdf It has been produced under the auspices of the UK's Open Research Data Task Force set up by the UK's Minister of Science, Jo Johnson:- http://www.universitiesuk.ac.uk/policy-and-analysis/research-policy/open-science/Pages/open-research-data-task-force.aspx Admittedly the report has a UK focus but includes extensive surveys of country by country activities. Crystallography features various times in the document, as does genomics and astronomy. As well as being an excellent survey I think the report brings out numerous issues within this very important topic. All best wishes, John Emeritus Professor John R Helliwell DSc
Re: [ccp4bb] [phenixbb] crystal imaging system
We had the Tritek CrystalPro and now have two Formulatrix RI-1000s. We're very happy with what we have now, and though I don't know what improvements Tritek has made since the version we owned, at the time we found their software clunky, imaging not the best or most consistent, and automation challenging. It took a great deal of time to make it work marginally. The formulatrix systems on the other hand have been robust and their support excellent (we pay for annual software support but let the hardware support go). They're easy to run and maintain. Chris Dr Christopher A Waddling Crystallography Facility Manager Department of Biochemistry and Biophysics University of California, San Francisco Genentech Hall, Box 2140 600 16th St., S126C San Francisco, CA 94143 415-476-8288 > On Jun 30, 2017, at 5:36 AM, Sebastiano Pasqualato > wrote: > > > Dear all, > we are in the process of considering the purchase of a new Crystal Imager. > > So far, we have been considering the Formulatrix Rock Imager 182 and the > TriTek Crystal Pro HT. > I would be extremely grateful to anyone who could provide me: > > - feedback and user experience (positive/negative) on those instruments; > - information on other instruments you would suggest. > > Thank you very much in advance, > wishing you a pleasant weekend, > best regards, > ciao, > S > > > > -- > Sebastiano Pasqualato, PhD > Crystallography Unit > Department of Experimental Oncology > European Institute of Oncology > IFOM-IEO Campus > via Adamello, 16 > 20139 - Milano > Italy > > tel +39 02 9437 5167 > fax +39 02 9437 5990 > web http://is.gd/IEOXtalUnit > > ___ > phenixbb mailing list > pheni...@phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-le...@phenix-online.org
Re: [ccp4bb] dictionary conversion
Hi Paul, On Fri, Jun 30, 2017 at 02:00:14PM +0100, Paul Emsley wrote: > Hi, > > What is the best (or easiest) way to convert restraint information > (and in particular torsion restraint information) from the mmcif > output of privateer or acedrg to a dic file suitable for refinement > with Buster/TNT? the easiest is to not do it ;-) BUSTER can use dictionaries from eg. $CCP4/lib/data/monomers/?/???.cif directly ie. similar format to what Grade[1] produces. You are welcome to write to buster-deve...@globalphasing.com if you encounter problems in doing so. Regards, ClAuS & Andrew (for buster-develop) [1]: http://grade.globalphasing.org/cgi-bin/grade/server.cgi
[ccp4bb] dictionary conversion
Hi, What is the best (or easiest) way to convert restraint information (and in particular torsion restraint information) from the mmcif output of privateer or acedrg to a dic file suitable for refinement with Buster/TNT? Thanks, Paul
[ccp4bb] crystal imaging system
Dear all, we are in the process of considering the purchase of a new Crystal Imager. So far, we have been considering the Formulatrix Rock Imager 182 and the TriTek Crystal Pro HT. I would be extremely grateful to anyone who could provide me: - feedback and user experience (positive/negative) on those instruments; - information on other instruments you would suggest. Thank you very much in advance, wishing you a pleasant weekend, best regards, ciao, S -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEOXtalUnit
[ccp4bb] PSI / CCP4 Workshop "3D Electron Crystallography for Macromolecular Compounds"
Dear all, we would like to announce the PSI / CCP4 Workshop "3D Electron Crystallography for Macromolecular Compounds" The workshop will take place at PSI between 18th and 22nd September 2017. Please see the full program, list of speakers, and registration instructions at https://indico.psi.ch/conferenceDisplay.py?confId=5525 This workshop addresses crystallographers in the field of structural biology who want to expand their field of possibilities to electron crystallography. The list of speakers encompasses experts in sample preparation, electron microscopy hardware, electron detectors, and methods from data processing via structure solution to model building. They will present recent results from the field of electron crystallography. Participants will have the possibility of vivid discussions and get answers for their open questions in a very young field. Tutorials include data processing with DIALS and XDS, as well as Molecular Replacement and Refinement at the characteristics of electron diffraction data. Please register before 1st September 2017. On behalf of the organisers, Tim Gruene -- -- Paul Scherrer Institut Dr. Tim Gruene - persoenlich - Principal Investigator Biology and Chemistry OFLC/104 CH-5232 Villigen PSI Phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A signature.asc Description: This is a digitally signed message part.
