Dear Consortium Members and Affiliates,
By now most of you have heard the sad news of the passing of Warren Delano, the developer of the well-known molecular visualization software PyMOL. His friends and family have started a fund with the intent of endowing an annual award for excellence in computational biosciences. To find out more or make a donation, please visit the Warren L. Delano Memorial Fund page.
It has been a solid month since our last update, and we have quite a few new and updated packages including updates to Coot, PHENIX nightly, Jalview, GROMACS, EMAN2 and em2em. The new applications include ALINE, WASP, PSIPRED and MMULT.
Have a safe and happy Thanksgiving.
The following software updates will be available today:
Linux and Mac OS X (PPC and Intel)
Coot has been updated to a more recent development version, 0.6-pre-1-revision-2486 on linux and revision-2450 on OS X.
PHENIX nightly build version dev-235 has been installed. It is not set as the default version. You can enable it by using a ~/.sbgrid file. I'll quote Nat Echols, a PHENIX developer, so you know what you're getting into if you choose to use this version: "the main caveat about the nightly builds is that they may break backwards compatibility with older configurations (especially phenix.refine); this is why we temporarily discarded the version numbering. We try not to do this too often, and we'll try to let everyone know when we do, but we may experiment more between major releases." There is new documentation for the development version of PHENIX. Requested by the Brunger Lab at Stanford.
Jalview, a multiple alignment editor, has been updated to version 2.40b2. This beta version includes the latest bugfixes as well as a few new features. Documentation and details are at the Jalview website.
ALINE is a new software package that will read common sequence alignment formats which the user can then alter, embellish, mark up, colorize and more to produce the kind of sequence figure commonly found in biochemical articles. The ALINE documentation is scant, but the software seems pretty straightforward. Requested by the Garcia Lab at Stanford.
WASP is a new addition to the software tree. WASP searches PDB files for misidentified water molecules which instead should be modeled as cations. There's no documentation; just run it! Requested by the Mayer Lab at NIH.
PSIPRED uses a simple and accurate secondary structure prediction method incorporating two feed-forward neural networks which perform an analysis on output obtained from BLAST. This software was added for use by the Rosetta fragment generation utilities, which should be available soon. More information is available on the PSIPRED website.
MMULT is a new package that does multiple aligntment of protein structures, providing a common 3D superimposition, a corresponding structure-based sequence alignment and a dendrogram for the set of structures aligned. Requested by the Jeruzalmi Lab at Harvard University.
Mac OS X (PPC and Intel)
pipe2xeasy has been compiled for OS X. It was previously only available in the linux branch.
Linux and Mac OS X Intel
EMAN2 has been updated to a recent nghtly version from 20091102. This version works better on linux and worse on OS X. The reverse was true of the last version. In the latest EMAN2 builds, the developers now store information about your project in a Berkeley Database that is not well-suited for use on a network file system. This may cause problems if you are using a network home directory. If you're using EMAN2, please send me an email, so I can keep you informed as I try to figure out a good workaround for this issue.
em2em has been updated to version 090720. This update includes a 64-bit version for linux. You can find the em2em documentation on Image Science's website.
bfactor.exe for linux was linked against the latest version of glibc and wasn't running on CentOS 4 machines. I rebuilt 32 and 64-bit versions of bfactor as static binaries. Reported by Steve Reichow in the Gonen Lab.
PHENIX had various bugs in the AutoSol, Refinement, MainWindow and Dialog interfaces. Tickets were opened by several people with patches supplied by Nat Echols, a PHENIX developer. Hat tip to Yunsun Nam (Harrison Lab), John Pascal (Pascal Lab) and Jorge Zuniga (Brunger Lab) for reporting the PHENIX bugs.
Coot on linux doesn't support the Rotate-Translate Zone function being a button on the toolbar. This is because we create a build that is compatible with older linux distributions like CentOS/Red Hat 4. As a workaround, you can create a shortcut to this function by adding this line to your ~/.coot file:
(add-key-binding "Rotate-Translate Zone" "r" (lambda () (do-rot-trans-setup 1)))
Change the "r" bit to your favoritie mnemonic shortcut. Reported by Tim Springer of Springer Lab.
PHENIX on OS X was not finding the SBGrid installed Coot properly, so it wasn't able to load a project into Coot. The fix was to add the Coot 'bin' directory to the PATH instead of using an alias. Reported by Engin Ozkan of Garcia Lab.
ARIA, a software package for NMR, was missing the custom CNS binary it requires for calculations. I tracked down the CNS 1.1 source, patched it and built the required binary. Reported by Joel Butterwick from the Mackinnon Lab.
CARA was missing the required xeasy.lib definitions file. The file was put in place for all the various CARA versions in the linux and OS X branches. Reported by Matthew Call from the Chou Lab.
LIGPLOT and hbplus on OS X Intel were built on OS X 10.3 and were failing on new Intel Macs. I rebuilt the binaries to support OS X 10.4 and up. Reported by Matt Bick from the Darst Lab.
BEST had its detector information file installed in the wrong directory. Reported by Jon Schuermann at the NECAT.