Dear Consortium Members and Affiliates,
This Is Just To Say
I have updated
the scientific software
that is on
you are hopefully
to solve structures
New versions of Coot, REFMAC,
MOSFLM and iMosflm,
Scwrl4, EMAN2, PHENIX,
LigPlot+, UltrascanII, EPMR,
Desmond, CONCOORD and Rcrane
(With apologies to William Carlos Williams.)
We are pleased to be hosting a WebEx seminar run by Jason Vertrees, the lead PyMOL developer at Schrodinger, on August 16th at 1 PM. The title of the talk is "Hints, Tips and New Features for PyMOL v1.4". We will send out an email with more details as the 16th approaches, so save the date!
The following software updates should be available later today.
Linux and Mac OS X Intel
Coot has been updated to version 0.6.2. Requested by everybody.
PHENIX has a new nightly version dev-835. The PHENIX website has a changelog for a list of the new features and bug fixes since the latest release.
REFMAC has been updated to version 5.6.0119, and the new monomers library can be found /programs/share/refmac/dictionary/5.30. This version has jelly body refinement, and all the new bells and whistles, but the CCP4 interface has not been updated it for it. There will be an update to CCP4 6.2.0 in the near future. The REFMAC website has tutorials and presentations on some of the new features. Requested by the Pascal Lab at Thomas Jefferson University.
MOSFLM and iMosflm have been updated to versions 7.0.8 and 1.0.6 respectively. The new MOSFLM has better support for Pilatus detectors including "very finely phi-sliced datasets, very short exposures with lots of zero-count pixels, small spots are profile fitted better and increased number of images allowed in integration blocks." The new iMosflm fixes slowness problems with very large datasets. Harry Powell's website has a user guide, tips and tricks, an FAQ and more. Requested by the Garcia Lab at Stanford (among others).
EMAN2 and SPARX have been updated to version 2.03. The EMAN2 wiki has documentation, tutorials and more. Requested by the Leschziner Lab at Harvard.
SCWRL4 is an update for the SCWRL3 program. The SCWRL4 website has usage notes and a complete description of the software. Requested by the Wagner Lab at HMS.
LigPlot+ has been updated to version 1.3.3. This is primarily a bug fix update. Requested by the Fremont Lab at Washington University.
UltrascanII has been updated to the latest 9.9 development release. The license format has changed for this release, so you'll need to register for a new license. Requested by the Harrison Lab at HMS.
Rcrane, the Coot plugin for semi-automated building of RNA structures, has been updated to version 0.6. The Pyle Lab website has a change log. A hat tip to the developer, Kevin Keating, for the update.
CONCOORD version 2.1 is a new package for the software tree that can "generate protein conformations around a known structure based on geometric restrictions." The CONCOORD website has a full description of the software as well as usage documentation. Requested by the Berkeley Center for Structural Biology at LBL.
Desmond version 3.0 has been added to the Schrodinger Molecular Modeling Suite. There are tutorials and a user guide on the Desmond website. Requested by one of our Vanderbilt Labs.
Gnuplot wasn't able to output PNG, JPEG, etc. All the versions in the tree, for both OS X and Linux, were rebuilt with GD support for output to additional image formats. Reported by Jianghai Zhu, Spring Lab.
The Autodock Vina plugin for PyMOL had some errors in the required MGLTools utility scripts. The scripts are fixed and the plugin should now work properly. Reported by Tirumala Chowdary, Heldwein Lab.
The 64-bit linux version of CCP4mg was linked against a very new version of glibc that prevented it from running on older linux releases. The application was rebuilt for our currently supported platforms. Reported by multiple people.