Re: [ccp4bb] Mg2+ or water
On Dec 21, 2010, at 2:08 AM, Vellieux Frederic wrote: Programs that check viruses in incoming emails remove all files that carry double extensions because this is a way to hide the real nature of the file. This doesn't sound correct, at least not for any antivirus package that is worth the money. Only a subset of file extensions will be executed by Windows automatically. No Microsoft program will yet open an .odp file, so it certainly isn't known as an executable to the OS a priori. If your antivirus program, by default, has the behavior you describe, then you might want to zap it and get something else because it most certainly will be touching junk that it shouldn't and missing other legitimate threats. James
[ccp4bb] synchrotron beam time at EMBL Hamburg 2011
Call for access to Synchrotron Beamline Facilities 2011 EMBL Hamburg, Germany We announce a call for synchrotron beam time applications in biological small-angle scattering (SAXS) and X-ray crystallography (PX). Up to 32 weeks of beam time will be available at the DORIS storage ring at the synchrotron DESY from March 2011 to February 2012. On the DORIS storage ring, EMBL Hamburg will operate the beamlines in SAXS (responsible scientist Dmitri Svergun) and PX (responsible scientist Victor Lamzin). Electronic beam proposal forms and a detailed description of the DORIS beamlines will be available from January, 15th, 2011 at www.embl-hamburg.de (click on 'Access to Infrastructures'). The deadline for submission of proposals is January, 31st, 2011. An external Priorities Committee will assess the proposals. EMBL is constructing three new beamlines for applications in PX and SAXS at the Petra-III synchrotron storage ring, which are expected to become available in 2011-2012 (responsible scientist Thomas Schneider). For further information and for potential participation in the commissioning as test users see www.embl-hamburg.de/services/petra A high-throughput crystallisation facility at the EMBL-Hamburg (responsible scientist Jochen Mueller-Dieckmann) is available to external users, see www.embl-hamburg.de/facilities/access_infrastructures/htpx). For further information tel. 40-89902-110, s...@embl-hamburg.de (SAXS) b...@embl-hamburg.de (PX) Access to the EMBL Hamburg facilities will in part be supported by the European Commission, Research Infrastructure Action under the FP7 projects ELISA and PCUBE.
[ccp4bb] Fourth annual CCP4 summer school in USA, at APS, June 7-15
Dear Colleagues, Building on the success of the past 3 years, we are pleased to announce the fourth annual CCP4 summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2011/index.php Title: CCP4 school: From data collection to structure refinement and beyond Dates: June 7 to 15. Site: Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA The school content: Data collection workshop the first two days: beamline training and data collection on GM/CA-CAT beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three Sections - lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection workshop and/or hands-on sessions. Application: Application deadline is April 8. Application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2011/index.php Fees: There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers will arrange economical lodging at the Argonne Guest House. The workshop will also cover the expenses for all meals and refreshments. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov
[ccp4bb] Release of Mosflm 7.0.7 iMosflm 1.0.5
Hi folks We are pleased to announce the release of the latest versions of Mosflm and iMosflm. They are available from our website at http://www.mrc-lmb.cam.ac.uk/harry/mosflm While we have concentrated on making the programs more robust and easier to use, there are also a number of new features, particularly in iMosflm - see http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver707/mosflm_user_guide.html#major_changes for full details, but here's a brief list: iMosflm New features and improvements: Open several or a range of images with CTRL-click or SHIFT-click, respectively. Display of the active mask for images from Rigaku detectors can now be toggled. Plots of the number of overloads, spatial overlaps and 'bad spots' for each image can now be displayed . Warning messages have been enhanced with feedback from Mosflm Automatic spot finding can be disabled when entering Autoindexing. QuickScale can now be run either treating data as anomalous or ignoring anomalous data in Scala. Symmetry known to iMosflm can now be passed to Pointless when running QuickScale. The program Ctruncate is now run automatically following Scala when using the QuickScale button. Site specific parameters can be read from a saved Mosflm file (.mos) on startup using the ~init command line argument. The 'View' menu has been renamed 'Settings' in the main iMosflm interface window. The small cross in the Warnings pop-up box has been replaced by a green, tick icon. A new entry field, 'Size of smaller fraction of summed partials', has been added to Processing options ~ Advanced refinement. With its default, initial value of 0.25 this will set the proportions that partials are divided into for post-refinement so that 0.25 of the intensity is in part one and 0.75 in part two. Values from 0.2 to 0.5 are permitted. Previous default value was 0.5. Mosflm New features and improvements: Better support for Pilatus (including ESRF-ID29) Rigaku detectors. Improved stability in postrefinement, so Mosflm refines mosaic spread to negative values less often; also add user control over partitioning of partials for postrefinement, and for re-scaling the normal matrix. Improved detection of blank images. Change number of segments generated automatically for postrefinement by iMosflm - now four segments for triclinic, three for monoclinic and orthorhombic, two for higher symmetry. Increase allowed length of filenames to 400 characters for images, directories, temporary files. Can now index some samples containing multiple lattices. Image names can now start with digits and have no alphabetic characters, and no extension either. Many, many bug fixes and better communications with iMosflm. Harry, Andrew Owen -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
[ccp4bb] Reduced PDBe services between 23 December and 10 January
Hi all, This is to inform PDB/EMDB depositors (at PDBe only) and users of PDBe services (http://pdbe.org/) that we will be operating with a reduced level of service in the next few weeks: - on 23 and 24 December we are operating with a skeleton crew, especially in the depositon and annotation department. We will do our best to process entries that are deposited during these days but cannot guarantee that we will succeed in all cases. - from 25 December to 3 January (inclusive), the EBI will be closed. You may still deposit structures and data into the PDB and EMDB, but there will be no annotation and processing taking place. We will monitor our web services in this period and will endeavour to fix any serious problems. Please note that e-mail sent to PDBe in this period is unlikely to receive a reply until the beginning of January. - from 4-6 January, we will resume normal service and catch up with the annotation and e-mail backlogs. - from 7-10 January, the entire campus data centre will be shut down for urgent repairs and service. This means that it will not be possible to deposit any PDB or EMDB data at PDBe in this period and that most of the PDBe web site and services will not be operational. (However, ftp services should not be affected by this as they don't reside on campus.) - from 11 January, we hope to be fully operational again (like the Death Star in Return of the Jedi). We apologise for any inconvenience these service interruptions/reductions may cause. On behalf of all PDBe staff: best wishes for the coming holiday season! --Gerard Kleywegt --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
Re: [ccp4bb] AKTA Prime dead/delay volume...and a transmembrane protein...
It depends on how your system is configured - primary considerations being tubing length and tubing inner diameter (AKTA can come with at least three different PEEK tube diameters, depending on what you purchased it for). New systems often arrive with at least one tube-change kit (i.e. pre-cut tubes of lengths suitable for direct replacement) - again, depending on the options you purchased. From the bottom of the column to the fraction collector It's not at all hard to figure out the dead volume experimentally by setting your column to a bypass and injecting a bolus of colored solution at the same time as fraction collection begins (set your fractions to low volume for added accuracy). As an added bonus by examining the absorption profile of fractions on the edge of the peak you will also find out how much dilution and mixing is introduced at the 'bottom end' of the system (it should be rather small, if your system is correctly configured). Notably, as Christian pointed out there should be a value set in Unicorn. Depending on who did the installation and how long ago etc. that value may or may not represent reality :) The following method (from AKTA manual online) is a good, simple test (accurate to around 100ul in my experience): http://www.gelifesciences.com/aptrix/upp01399.nsf/Content/laboratory_support~laboratory_faq~faq~delay_volume?OpenDocumenthometitle=chromatography_support *Method III - Determining the delay volume by balancing eluted water* Manually set the flow path to the direction of the fraction collector. Unscrew the tubing that is connected to inlet of the UV flow cell and insert a luer adaptor instead. Fill a syringe with water and inject water into flow cell unless it drops at the outlet of the fraction collector (in which case you have likely exceeded the pressure in the tubing which might be more than 4 bar, depending on configuration and flow restrictor used). Now fill the syringe with air (at least 20 ml because of compression) and displace the water. Collect eluting water in a small cup. Determine the system delay volume by balancing the cup before and after elution. Repeat two times for calculation of a mean value. Enter the mean value in system settings in UNICORN. Artem On Tue, Dec 21, 2010 at 9:17 AM, James Pauff pauf...@yahoo.com wrote: Hello all, Does anyone have a rough estimate (or has anyone actually determined) an average dead/delay volume between buffers run on an AKTA Prime FPLC? We are attempting to overexpress/isolate a smaller His-tagged transmembrane protein, and require running several detergent buffers in succession over the column. This obviously creates fractions that are just dead volume/ddH2O between buffers, and we would like to narrow in on where to look for the protein prior to analyzing the fractions (i.e. how many fractions can we discard?). Should we run ddH2O and then the first mL into 'waste' before running each buffer over the column (and collecting fractions)? Just not used to this system yet! Thank you! Jim
