All listed applications will be available on Linux and OSX computers (both Intel and PPC) after the Friday evening update.
Pymol will be updated to Release Candidate 6 (RC6) and the APBS plugin installation will be corrected to properly locate electrostatics modules. You can use the APBS plugin to calculate and display electrostatics. Fedora Core Linux installations might require installation of compat-readline43.i386 for compatibility. We have also noticed that structures with B-factors higher than 99 the APBS plugin will not work. To solve this issue, use lx_moleman, LIMIT option (osx_molman on Mac) to limit your high B-factors.
New version of O! We will upgrade to release 11.0. You will now be able to build a structure from a map automatically using the AutoO_build command; the Lsq_proper command will help you to improve NCS operators. For the full list of updates and changes please visit O website.
COOT will be upgraded to version 0.2, code name "Arashiyama Park". This release provides many fixes, and some extra features. In particular, the secondary structure restraints in regularize and refine zone should facilitate low-resolution refinement.
CHIMERA will be upgraded to version 1.2304. Tools added in this release include â€Morph Conformations†– to create trajectories between known conformations, Model Loops, and Minimize Structure. For the full list of changes please visit the CHIMERA web site.
EMBOSS (The European Molecular Biology Open Software Suite) will be updated to version 4.0.0. The application provides an Open Source molecular biology toolkit. For the list of all EMBOSS applications please visit the web site.
As always we remind our readers that they are welcomed and encouraged to report any software bugs utilizing the SBGrid Bug Tracker (www.sbgrid.org/bugs). We can always correct software bugs in between scheduled software updates.
Please note that immediately after software updates you will be using the newest installed versions. If you find problems you can always switch to an older version of application while we seek a solution. Please use ‘sbgrid –n’ for more info.