[ccp4bb] Beamtime @ SLS
=== SYNCHROTRON BEAM TIME FOR MACROMOLECULAR CRYSTALLOGRAPHY AT SLS === Proposal application deadline: Monday, October 15, 2012 Periods: January 1, 2013 - April 30, 2013 (Normal / Test proposals) January 1, 2013 - December 31, 2014 (Long-term proposals) Proposal submission: http://www.psi.ch/sls/px-beamlines-call-for-proposals Travel support: http://www.psi.ch/useroffice/sls-elisa-biostruct PSI DUO application for iphone: http://itunes.apple.com/ch/app/psi-duo/id375328818?mt=8 What's New? - PILATUS detectors at three PX beamlines - X06DA Multi-axis goniometer (PRIGO) - X06DA In-situ X-ray diffraction screening for any SBS format plate - X10SA Micro-beam with apertures (10 x 10, 30 x 30 micrometer) - Faster Sample changer (CATS) operation X06SA Beamline features (http://www.psi.ch/sls/pxi/pxi) - Undulator beamline with flux of 2x10^12 photons/sec at 12.4 keV (1Å) and fully tunable from 6.0 to 17.5 keV (2.07 - 0.71 Å) - Focused beam size and divergency: HRD - 85x10 microns and 0.35x0.06 mrad; MD2 - 25x5 microns and 0.5x0.4 mrad - PILATUS 6M pixel detector at the High Resolution Diffractometer, allowing continuous, fine phi-sliced data acquisition (25 frames per second) with 20 bit dynamic range (see http://pilatus.web.psi.ch/ or www.dectris.com for further information) - MAR225 CCD at Micro-Diffractometer MD2, allowing data collection with a focussed beam size of 25 x 5 micrometers, and smaller beam size with triple-aperture assembly ( 5 x 5, 10 x 10, 20 x 20 micrometer). X06DA Beamline features (http://www.psi.ch/sls/pxiii/pxiii) - Super-bending magnet beamline with flux of 5x10¹¹ photons/sec at 12.4 keV (1Å) and fully tunable from 6.0 to 17.5 keV (2.07 - 0.71 Å) - Focused beam size and divergency: 80x45 microns and 2x0.5 mrad (with possibility to reduce horizontal divergency to 0.4 mrad) - Mini-hutch design for fast manual mounting - PILATUS 2M (60 Hz, 450 um Si sensor) - Multi-axis goniometer (PRIGO) for crystal re-orentation - In-situ X-ray diffraction screening (with any SBS format plate) available during users shifts (R. Bingel-Erlenmeyer, et al., Crystal Growth Design 2011, 11, 916) X10SA Beamline features (http://www.psi.ch/sls/pxii/pxii) - Undulator beamline with flux of 2x10^12 photons/sec at 12.4 keV (1Å) and fully tunable from 6.0 to 20 keV (2.07 - 0.62 Å) - Focused beam size and divergency: 50x10 microns and 0.6x0.1 mrad - Micro-beam with apertures (10 x 10, 30 x 30 micrometer) - PILATUS 6M pixel detector Best regards, The MX group at SLS __ Meitian Wang Swiss Light Source at Paul Scherrer Institut CH-5232 Villigen PSI - http://www.psi.ch/sls/ Phone: +41 56 310 4175 Fax: +41 56 310 5292
[ccp4bb] Home lab Pilatus?
All - is anyone out there thinking of purchasing or has ordered a Pilatus 300K or 1M for home lab MX use and who would be willing to share info? Obviously I know all about the bigger Pilatus detectors at the synchrotrons, I'm interested specifically in the models indicated above that are designed for home lab use. Replies to me, preferably off-list. Cheers -- Ian Ian J. Tickle, DPhil. Senior Director of X-ray Technology Astex Pharmaceuticals 436 Science Park Milton Road Cambridge CB4 0QA, UK WWW: astx.com
[ccp4bb] CCP4 update 6.3.0 006
Dear CCP4 Users, A CCP4 update has just been released, consisting of the following changes: * MrBUMP: model building options added * PISA: new QT interface * AMPLE: bug fixes and expanded interface (Linux and MAC only) * tlsextract: correction of output format which broke parsing of output * DiffractionImage: corrections to reading of pilatus mini-cbf * ccp4i: New AMPLE (Linux and Mac) and MrBUMP interfaces, QT-PISA launcher and bug fixes * crank: bug fix (Windows only) The easiest way to obtain the update is to install the CCP4 update client, if you have not done so already. Note that auto-updates will work correctly only with CCP4 release 6.3.0, therefore upgrade if necessary. Report bugs to c...@stfc.ac.uk. Many thanks for using CCP4, -- Ronan Keegan -- Scanned by iCritical.
[ccp4bb] Indexing with XDS
Dear all I took some images from test crystal and tried to index them to get cell parameters, not enough for structure solution. I can see spots at 3.5 A with ADXV but when I indexed, XDS reports up to 3.0 A in INCLUDE_RESOLUTION_RANGE in XDS_ASCII.HKL. Questions: 1. How do I know that the spot at 3.0 is not background noise? 2. What is the function of FRAME.cbf file? Thank you. Theresa
Re: [ccp4bb] calculating dialectric properties of enzyme active site
On 10/07/2012 12:02 AM, Boaz Shaanan wrote: Hi If you want to calculate the electrostatic properties of your protein/mutants you can use Delphi or APBS. Calculation of the dielectric constants is most challenging. I think that these two programs use some approximations to estimate the variation of dielectric constants between the outside (water with epsilon = 80 and inside with epsilon = 4 or whatever values you use as input) but I'm not sure they output those values. For, APBS, the epsilon values used can be found in the .in file generated by pdb2pqr if you use it to generate the file driving APBS. However, the variation is taken into account when reporting the electrostatic potential which you can display using PyMol or UCSF-chimera. As for the hydrophobicity - there are hydrophobicity scales around (whether you believe them or not is a different matter) which you can use to display on the surface, again by Pymol or Chimera (and probably many other programs). My 2p/2c thoughts. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Yarrow Madrona [amadr...@uci.edu] Sent: Saturday, October 06, 2012 4:48 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] calculating dialectric properties of enzyme active site Hello CCP4 list readers, Does anyone know how to calculate the dielectric properties of an enzyme active site? I would like to compare the polarity/hydrophobicity of similar proteins and different mutants. Thank you. -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697
