MMB 2.19 – Model the Structure and Dynamics of Macromolecules

MMB 2.19


MMB (a contraction of MacroMolecule Builder) was previously known as RNABuilder. The latter is available up to revision 2.2. We renamed the software since even some longtime users were unaware that the package now handles protein as well as RNA. Aside from the renaming, MMB 2.3 differs from RNABuilder 2.2 in two important ways. Release 2.3 has fully overhauled guts. It uses the BiopolymerClassContainer, a much cleaner programming construct which will make future upgrades and extensions more efficient. As of release 2.3.4, we link against new Molmodel binaries which have more efficient tracking of atoms in rigid regions. This yields a two-fold speed improvement and four-fold lower memory requirement for many problems. Also in this release, some rarely used features have been removed, but these were never in the tutorial literature so their absence should go largely unnoticed. The default input file name is now commands.dat rather than contacts.dat. A couple of somewhat obscure bugs were fixed. The error messages are more informative, and more aggressively prevent the user from risky or incorrect construction of the input file.



MMB Team




  • Windows/ Linux / Mac OsX
  • VMD





Samuel Coulbourn Flores, Russ B. Altman.
Structural insights into Pre-Translocation Ribosome Motions.
In Proceedings of Pacific Symposium on Biocomputing’2011. pp.205~216 (2011)

Samuel Flores and Russ Altman,
Turning limited experimental information into 3D models of RNA,
RNA 16(9):1769-78 (2010).

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