MMB (MacroMoleculeBuilder)
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MMB is a multiresolution modeling tool for building 3D structural and dynamical models of macromolecules. It gives you explicit control over the degrees of freedom, forces, constraints, and molecules in your system.

MMB 2.14  Monitor Package
In release 2.14 I improved a few features and added several others. First, Physics where you want it was not including any monoAtoms. Now all atoms created with this command are automatically added to the physics zone. You can read in ion positions from a PDB file also, you just need to be careful about atom and residue names in that file. For example, the atom name for the magnesium ion should be Mg+2, and its residue name should be MG. I have introduced a new residue type, a disulphide bridging cysteine. You can specify it using the single letter code ‘X’. You can also infer it from the input PDB file, if you name the residue in that file CYX, rather than CYS (the latter will be interpreted as a normal, non-bridged cysteine). Thus it is compatible with both the protein and loadSequencesFromPdb commands. To actually bridge the sulphurs, you would use the new addRingClosingBond command. An example of this is supplied, see the new commands.disulphide-bonded-cysteines.dat . There is a new figure to explain this, in the Mobilizers and constraints chapter; the usage is explained in the Forces chapter.There were some silly limitations to how one could mix user defined variables, numbers, and +/- operators, which have now been removed. You can now mix these more or less as you wish, though absolute residue numbers still have to be leftmost in the expression. You can also use a leading ‘- ‘ in a residue number, and this will correctly be interpreted as part of the residue number rather than an operator.Have you ever simply wanted to impose a certain secondary structure in a certain region of your model? Say, make a helix-turn-helix into a single continuous helix? Well, with the new setPhiPsiAngles command you can do just that. It sets the phi, psi, and peptide dihedral angles to the defaults for Alpha, ParallelBeta and AntiParallelBeta secondary structures, overriding whatever values these dihedrals may have taken from the input structure file.The new psiPhiMobility command is used for specifying the bond mobility for the bonds connecting the N to CA, and the CA to C on the protein backbone, for a given stretch of residues. It is equivalent to issuing the singleBondMobility command for the two mentioned bonds, for each residue in the range.Quite importantly, we have brought back the matchGapped macro. When issued, it sets guessCoordinates to True, meaning that if you have missing atoms or even entire residues in your input PDB file, it will guess positions for the missing atoms, and still perfectly match the remaining (non-missing) atoms. Even the default matchFast behavior guesses side chain positions, but with matchGapped you can leave out backbone atoms. You will probably get back bond geometries at the boundary between the known and missing backbone atoms, which you can correct using the singleBondMobility .. Free command. We also have improved the mobilizeInterfaces command, which lets you set the bond mobility for residues at a certain interface. Firstly, it now bases the definition of “interface” on all atoms, not just Cα and C3* atoms. Secondly, it is now much more economical. Lastly, you can define the interface differently .. specifying one or more chains that form a complex, and then asking for all interfaces with other chains.Lastly, we have a new method of adding residues to the physics zone. Just set the new parameter physicsRadius to some value greater than zero. It will look for all “flexible” atoms – defined as atoms in a mobilizedBody of mass 40, and then include all residues within physicsRadius of these, in the physics zone.
MMB 2.14
December 30, 2013

Download Links

Name File Type Platform Updated
Installer.2_14.OSX.tgz (29636 kB) binary Mac Jan 08, 2014
Description: Binaries, examples, and documentation for Mac OSX. Built on Mountain Lion by S Flores. Tested on Snow Leopard by Alex Tek.
Installer.2_14.Linux64.tgz (53480 kB) binary Linux Jan 13, 2014
Description: MMB 2.14 for 64 bit Linux. Compiled on CentOS, tested on Ubuntu by S Flores.
Installer.2_14.Linux32.tgz (28331 kB) binary Linux Jan 14, 2014
Description: MMB 2.14 for 32 bit Linux. Compiled and tested on Debian i386 by A Tek.
Installer.2_14.Windows.zip (17329 kB) binary Windows Jan 21, 2014
Description: MMB 2.14 for Windows. Built on 32-BIT Windows 7 by S Flores. Tested by Alex Tek.

    Please cite these papers
  • Fast fitting to low resolution density maps: elucidating large-scale motions of the ribosome. Flores, SC. Nucleic acids research, 29 Sept. (2013)
  • Fast flexible modeling of RNA structure using internal coordinates, Samuel Flores, Michael Sherman, Chris Bruns, Peter Eastman, Russ Altman; Transactions in Computational Biology and Bioinformatics 8(5): 1247-57 . (2011)
  • Predicting RNA structure by multiple template homology modeling, by Samuel C. Flores, Yaqi Wan, Rick Russell, and Russ B. Altman; Proceedings of the Pacific Symposium on Biocomputing. (2010)
  • Turning limited experimental information into 3D models of RNA, by Samuel Flores and Russ Altman; RNA 16(9): 1769-78. (2010)

MMB 2.8  Monitor Package
In this latest release we enable reading the chain IDs, sequences, residue numbers, and insertion codes directly from the input structure file, for protein and RNA. These molecules can have gaps and insertion codes in the numbering. Other new commands and changes are explained in the reference guide.
MMB 2.8
February 9, 2012

Download Links

Name File Type Platform Updated
Installer.2_8_2.Ubuntu_32Bit.tgz (48482 kB) binary Linux May 08, 2012
Description: MMB 2.8.2 for 32 bit Ubuntu (should work with some other Linux flavors)
MMB.2_8_2.Windows.zip (41180 kB) binary Windows May 08, 2012
Description: Windows 2.8.2 distribution .. fixed a 2.8.1 bug affecting multi-chain DNA or RNA helices
Installer.2_8_3.CentOS64.tgz (43493 kB) binary Linux May 13, 2012
Description: MMB distribution for 64 Bit Linux (typically clusters). Also tested on Scientific Linux and (K)ubuntu. fixes an incompatible library issue.
Installer.2_8_2.OSX.tgz (78961 kB) binary Mac May 16, 2012
Description: MMB 2.8.2 for Leopard, Snow Leopard, and Lion. Tested on the latter two. Fixes a minor bug found with two-polymer nucleic acid duplexes

    Please cite these papers
  • * Turning limited experimental information into 3D models of RNA, by Samuel Flores and Russ Altman (2010) RNA 16(9): 1769-78. * Predicting RNA structure by multiple template homology modeling, by Samuel C. Flores, Yaqi Wan, Rick Russell, and Russ B. Altman (2010) Proceedings of the Pacific Symposium on Biocomputing.Fast flexible modeling of RNA structure using internal coordinates, Samuel Flores, Michael Sherman, Chris Bruns, Peter Eastman, Russ Altman (2011) Transactions in Computational Biology and Bioinformatics 8(5): 1247-57 .Structural insights into pre-translocation ribosome motions, Flores, S. and Altman, R. (2011) Proceedings of the Pacific Symposium on Biocomputing, 16, 205-216. (2011)

(old) MMB 2.10  Monitor Package
In this release, reading in PDB files and generating internal coordinate models based on them, is MUCH faster. matchFast now works even with normal-precision, standard PDB files, and is in fact the only matching method permitted. The accuracy and speed issues associated with coordinate matching in earlier releases are now solidly addressed. Unfortunately MMB no longer guesses missing backbone atom information.
A couple of bugs which may have affected 2.9.2 users have been fixed. The scrubber didn't always behave properly -- I fixed this and also removed the setForceAndStericScrubber parameter .. see the ref guide for details. The applyContactsWithin was also not working properly, and has also been fixed -- also this command now appears in the ref guide, whereas before it was effectively secret. Lastly, there was some code reorganization that doesn't affect the user, just the maintainability.

This is a binary release. Just download the appropriate package and unzip into an appropriate folder. You will find a tutorial guide in the package with instructions for setting your path (needed for Mac and Linux). Run exercise 0 from the same tutorial to make sure everything is working.
MMB 2.10
August 14, 2012

Download Links

Name File Type Platform Updated
Installer.2_10.Ubuntu32.tgz (30636 kB) binary Linux Aug 13, 2012
Description: MMB 2.10 for 32-bit Linux (Ubuntu)
Installer.2_10.CentOS64.tgz (34928 kB) binary Linux Aug 14, 2012
Description: MMB 2.10 release for 64 bit Linux (CentOS)
Installer.2_10.Windows.zip (22588 kB) binary Windows Aug 14, 2012
Description: MMB 2.10 for Windows
Installer.2_10.OSX.tgz (39605 kB) binary Mac Aug 16, 2012
Description: MMB 2.10 for OSX (Leopard, Snow Leopard, Lion, and Mountain Lion)

    Please cite these papers
  • Fast flexible modeling of RNA structure using internal coordinates, Samuel Flores, Michael Sherman, Chris Bruns, Peter Eastman, Russ Altman (2011) Transactions in Computational Biology and Bioinformatics 8(5): 1247-57 . (2011)
  • Structural insights into pre-translocation ribosome motions, Flores, S. and Altman, R. (2011) Proceedings of the Pacific Symposium on Biocomputing, 16, 205-216. (2011)
  • Predicting RNA structure by multiple template homology modeling, by Samuel C. Flores, Yaqi Wan, Rick Russell, and Russ B. Altman (2010) Proceedings of the Pacific Symposium on Biocomputing. (2010)
  • Turning limited experimental information into 3D models of RNA, by Samuel Flores and Russ Altman (2010) RNA 16(9): 1769-78. (2010)

(old) MMB 2.11  Monitor Package
MMB release 2.11.

There is a Cent0S version 5 release compiled by Shaq Liu available upon request (but it's not completely up to date)
MMB 2.11
January 16, 2013

MMB 2.11

Download Links

Name File Type Platform Updated
Installer.2_11.CentOS64.tgz (28697 kB) binary Linux Mar 19, 2013
Description: MMB 2.11 for 64 bit Linux (compiled on CentOS). Tested by Mike Kuiper of VLSCI.
Installer.2_11.OSX.tgz (39460 kB) binary Mac Mar 19, 2013
Description: MMB 2.11 for OSX (Leopard and higher)
Installer.2_11.Ubuntu32.tgz (30139 kB) binary Linux Mar 19, 2013
Description: MMB 2.11 for 32-bit Ubuntu Linux. Should also work on many other 32 bit Linux flavors.
Installer.2_11.Windows.zip (23759 kB) binary Windows Mar 20, 2013
Description: MMB 2.11 for Windows.

    Please cite these papers
  • Fast flexible modeling of RNA structure using internal coordinates, Samuel Flores, Michael Sherman, Chris Bruns, Peter Eastman, Russ Altman (2011) Transactions in Computational Biology and Bioinformatics 8(5): 1247-57 . (2011)
  • Structural insights into pre-translocation ribosome motions, Flores, S. and Altman, R. (2011) Proceedings of the Pacific Symposium on Biocomputing, 16, 205-216. (2011)
  • Predicting RNA structure by multiple template homology modeling, by Samuel C. Flores, Yaqi Wan, Rick Russell, and Russ B. Altman (2010) Proceedings of the Pacific Symposium on Biocomputing. (2010)
  • Turning limited experimental information into 3D models of RNA, by Samuel Flores and Russ Altman (2010) RNA 16(9): 1769-78. (2010)

(old) MMB 2.12  Monitor Package
In this release, we introduce long chain IDs, making memory the only limitation on number of molecules. We also fix a bug with the setHelicalStacking feature, though no one seems to have noticed that existed.
MMB 2.12
April 23, 2013

MMB 2.12

Download Links

Name File Type Platform Updated
Installer.2_12.Windows.zip (33984 kB) binary Windows Apr 24, 2013
Description: MMB 2.12 for Windows
Installer.2_12.OSX.tgz (56866 kB) binary Mac Apr 25, 2013
Description: MMB 2.12 for OSX (Leopard through Lion)
Installer.2_12.CentOS64.tgz (39057 kB) binary Linux May 30, 2013
Description: MMB 2.12 for 64 bit CentOS

(old) MMB 2.13  Monitor Package
This release is mostly about "Physics where you want it," which allows you to turn on the PARM99 force field for specified residues in your system. This is still a little known feature, but features in upcoming papers and will probably become more widely used. There were a couple of bugs in release 2.12 which have been fixed in this release. First, the includeNonBondAtomsInResidues command was including all atoms in the system rather than just those in the specified residues; as a result simulations ran very slowly. In some cases bonded forces were being turned off, which led to odd ring-opening behavior in nucleic acids, proline, etc. There are also some changes that have been made one layer deeper, in MolModel. Whereas the tryptophan aromatic group chain was intended to be rigid, the wrong bond was being treated as a ring closing bond, causing odd out-of-plane motions. All the mentioned problems have been fixed. Even if the above issues didn't cause you a problem before, you will notice "Physics where you want it" runs much faster now. Also I've changed the N-CA bond in proline from rigid to torsion -- though this was more a matter of taste.

There is also a new example, using ICFF to fit Ribose Binding Protein into a density map. A few months from now, we hope to release our MMB GUI -- stay tuned!
MMB 2.13
August 27, 2013

Download Links

Name File Type Platform Updated
Installer.2_13.OSX.tgz (27250 kB) binary Mac Aug 26, 2013
Description: MMB 2.13 for OSX (Leopard to Mountain Lion) (tested: Tosan Omabegho)
Installer.2_13.Windows.zip (28525 kB) binary Windows Sep 02, 2013
Description: MMB 2.13 for Windows (compiled: Alex Tek) (Tested: Keyao Pan)
Installer.2_13.Linux64.tgz (51700 kB) binary Linux Sep 26, 2013
Description: Compiled on RedHat 6.4 linux (compiled: Uppmax, Alex Tek. test: Jiri Cerny, Anel Mahmutovic)

    Please cite these papers
  • Fast flexible modeling of RNA structure using internal coordinates, Samuel Flores, Michael Sherman, Chris Bruns, Peter Eastman, Russ Altman; Transactions in Computational Biology and Bioinformatics 8(5): 1247-57 . (2011)
  • Structural insights into pre-translocation ribosome motions, Flores, S. and Altman, R.; Proceedings of the Pacific Symposium on Biocomputing, 16, 205-216. (2011)
  • Predicting RNA structure by multiple template homology modeling, by Samuel C. Flores, Yaqi Wan, Rick Russell, and Russ B. Altman; Proceedings of the Pacific Symposium on Biocomputing. (2010)
  • Turning limited experimental information into 3D models of RNA, by Samuel Flores and Russ Altman; RNA 16(9): 1769-78. (2010)

(old) MMB 2.3.1 for Windows  Monitor Package
This is a Windows-only release. It is very similar to 2.3. Some error messages have been improved, and some obsolete commands removed (but these were never in the reference guide to begin with).

This is not an installer. It is a compressed archive with a precompiled executable. Please decompress the archive in the location of your choice (we suggest C:usersMMB_Windows_2_3_1). Inside you will find a tutorial with further instructions.
MMB-Windows-2.3.1
May 2, 2011

Download Links

Name File Type Platform Updated
MMB-Windows-2.3.1.zip (24056 kB) binary Windows Jun 10, 2011
Description: Contains executable, parameter file, reference guide, and tutorial guide, command and input structure files

(old) MMB 2.6  Monitor Package
In this release, I've reduced the memory requirement of the density map reader, so it should run as fast on Mac as it does on Linux. The way the continuous derivative of the discrete density is taken, has been improved. Also, this revision supports DNA explicitly. As of 2.6.1, proteinThreading pulls together all corresponding protein atoms, not just backbone atoms.
MMB 2.6 binaries for Mac OSX Leopard and higher
October 20, 2011

This is a dynamically linked compilation.

Download Links

Name File Type Platform Updated
MMB.2_6_2.CentOS64.tgz (51838 kB) binary Linux Nov 10, 2011
Description: MMB 2.6.2 64-bit release for CentOS. This release is intended for clusters.
MMB.2_6_2.Leopard.tgz (50073 kB) binary Mac Nov 10, 2011
Description: MMB 2.6.2 release for Leopard
MMB.2_6_2.Ubuntu.tgz (53069 kB) binary Linux Nov 10, 2011
Description: Ubuntu release of MMB 2.6.2
MMB.2_6_2.Windows.zip (40841 kB) binary Windows Nov 10, 2011
Description: A Windows update, at long last!

    Please cite these papers
  • Fast flexible modeling of RNA structure using internal coordinates, Samuel Flores, Michael Sherman, Chris Bruns, Peter Eastman, Russ Altman (2011) Transactions in Computational Biology and Bioinformatics 8(5): 1247-57 . (2011)
  • Structural insights into pre-translocation ribosome motions, Flores, S. and Altman, R. (2011) Proceedings of the Pacific Symposium on Biocomputing, 16, 205-216. (2011)
  • Flores, S. & Altman, R. (2010). Turning limited experimental information into 3D models of RNA RNA 16, 1769-1778. (2010)
  • * Predicting RNA structure by multiple template homology modeling, by Samuel C. Flores, Yaqi Wan, Rick Russell, and Russ B. Altman (2010) Proceedings of the Pacific Symposium on Biocomputing. (2010)

(old revision) MMB 2.3  Monitor Package
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, M 2.3 differs from RNABuilder 2.2 mostly internally. 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. 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. As you may have gathered, the user experience does not change much in this release.
M.2_3
February 5, 2011

Download Links

Name File Type Platform Updated
M.2_3_04.Leopard-Ubuntu.tgz (37433 kB) binary -- Feb 27, 2011
Description: Includes executables for Leopard (or Snow Leopard) and Linux (compiled on Ubuntu -- but also runs on many other distributions).

    Please cite these papers
  • 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)  [Download]
  • Predicting RNA structure by multiple template homology modeling, by Samuel C. Flores, Yaqi Wan, Rick Russell, and Russ B. Altman (2010) Proceedings of the Pacific Symposium on Biocomputing. (2010)
  • Turning limited experimental information intio 3D models of RNA, by Samuel C Flores and Russ B Altman, RNA 16(9):1769-78 (2010). (2010)

RNABuilder 2.0  Monitor Package
This is the RNABuilder 2.0 binary release
RNABuilder 2.0
July 21, 2010

This contains executable, library, and example files for RNABuilder 2.0.
Notes

Download Links

Name File Type Platform Updated
RNABuilder_2_0.Leopard.tgz (8876 kB) binary Mac Sep 09, 2010
Description: RNABuilder 2.0 for Leopard and Snow Leopard
RNABuilder_2_0_Windows.zip (5192 kB) binary Windows Sep 09, 2010
Description: RNABuilder 2.0 for Windows

Documentation Links

RNABuilderTutorial.2.0.pdf (4436 kB) Sep 09, 2010
Description: RNABuilder 2.0 Tutorial (all platforms)

    Please cite these papers
  • Samuel Flores and Russ Altman, "Turning limited experimental information into 3D models of RNA," RNA (accepted) (2010)

RNABuilder 2.2  Monitor Package
RNABuilder 2.2 supports proteins and introduces the monoAtoms command for instantiating monatomic ions. The updated tutorial has two protein exercises, one for threading and one for morphing.
RNABuilder 2.2
December 23, 2010

Download Links

Name File Type Platform Updated
RNABuilder.2_2.OSX-Ubuntu.tgz (22570 kB) binary -- Dec 22, 2010
Description: This includes Snow Leopard and Linux (Ubuntu) executables, as well as a manual/tutorial.

    Please cite these papers
  • Flores SC and Altman RB, "Turning limited experimental information into 3D models of RNA", RNA (2010) 16:1769-78 (2010)
  • "Predicting RNA structure by multiple template homology modeling", Proceedings of the Pacific Symposium on Biocomputing (2010) 216-227 (2010)
Previous ReleasesHide
RNABuilder 2.1  November 3, 2010

Download Links

Name File Type Platform Updated
RNABuilder_2_1.Ubuntu.tgz (16696 kB) binary Linux Nov 03, 2010
Description: This was compiled on Ubuntu, but is likely to work on most other Linux distributions, though probably not RedHat.

Documentation Links

RNABuilderTutorial.2.1.pdf (4449 kB) Nov 03, 2010
Description: Manual with workshop examples and reference section