Molby

An Interactive Molecular Modeling Software

For Mac OS X and Windows

Molby is a software for building molecular models on the graphic screen. It works on Mac OS X and Windows. It can import and export files for other computational chemistry softwares such as GAMESS and Gaussian. It can also edit molecules by scripts running on the built-in Ruby interpreter.

Molby is a free software, licensed under GPLv2.

News

2014/10/26
Version 1.0b03 is out.
  • Displaying MO surface is implemented.
  • Extra properties are assignable for each frame. On importing Gamess output, the energy values are set as the property.
  • The graphic can be exported as a PNG file.
  • Log files of Natural Bond Orbital can now be imported.
  • The graphic objects are now saved into mbsf files.
2014/05/24
Molby paper is now published! Please check out.
Toshi Nagata, "Molby - Graphical Molecular Modeling Software with Integrated Ruby Interpreter,"
Bull. Chem. Soc. Jpn. 2014, in press. DOI:10.1246/bcsj.20140093
2014/05/06
Molby Gallery is now open.
2014/04/26
Version 1.0b02 is out.
  • Common "Scratch" directory is used for all external programs, namely antechamber, resp, gamess and ortep. Note: the scratch directory cannot contain whitespace characters.
  • In reading MM/MD parameters, check criteria for duplicate parameters are somewhat relaxed (i.e. comparison of floating numbers is allowed for rounding errors)
  • Symmetry Operations dialog was not working for setting new symmetry. Fixed.
  • GAMESS dialog is modified so that manual editing is possible.
  • Mac: 'Window' menu is implemented.
  • Win: crash caused by the 'missing DLL' problems was fixed.
  • Win: document_home is modified to use the Windows API, instead of hard-coded path (which was wrong on Windows Vista and later).
  • Win: "backquote" method was not working well.
  • Win: when the program is started twice, the second invocation was causing crash. Hopefully fixed.
2014/03/28
Version 1.0b01 is out. First beta release!
  • The graphic toolkit is changed from wxWidgets 2.8 to wxWidgets 3.0.
  • Windows: the application no longer uses MDI interface, but uses multi-window interface.
  • Embedded Ruby is now 2.0.0 instead of 1.8.7.
  • C60 fullerene, twist-boat cyclohexane, metal coordination motifs are introduced as the predefined structure.
  • Antechamber can be called for charge and atom types separately.
  • UFF parameters are included.
  • Graphic drawing is implemented in Ruby Dialog (not documented yet).
  • Main menu is rearranged (in particular, there is now a "Xtal" menu)
  • ORTEP3 is included, and graphic user interface for drawing ORTEP is provided.
  • Printing and exporting the main window is now supported.
  • Space-filling view is implemented.
  • Many bug fixes.
2013/06/15
Version 0.6.5 is out.
New Features:
  • Local execution of GAMESS is implemented.
  • For X-ray data (with standard deviations), calculation of bonds and angles with standard deviation is implemented.
  • GAMESS log containing F and G type orbitals can now be imported (cube calculation is not yet implemented).
  • In the 'GAMESS export' dialog, new basis sets can be loaded from external files.
  • Particle mesh Ewald calculation is implemented (experimentally).
  • "Pi-anchor" atoms (i.e. dummy atoms for cyclopentadienyl-metal bonds etc.) are implemented (experimentally).
  • The Ruby console now has history capability.
Bug Fix:
  • CIF files from old TeXsan software cannot be loaded. Fixed.
  • Symmetry expansion in CIF import is improved (may not be complete yet).
  • Deleting bonds was causing bus error. Fixed.
  • Two subsequent dragging of different atoms was causing undo failure. Fixed.
  • Merging/unmerging molecules are revised, so that undo works more consistently.
  • And many others.
2012/10/13
Version 0.6.4 is out.
  • Opening bond/angle/dihedral/improper table now triggers searching MD parameters (but not rebuilding angle/dihedral/improper tables).
  • Property table can now list the unit cell parameters.
  • "Show Graphite" command was using _very_ wrong C-C bond length. Now it uses correct length (1.42 angstrom).
  • Best-fit plane calculations are implemented.
  • The revision number is displayed in the about dialog.
  • Cell parameter minimization is implemented (still experimental).
  • The restriction on the number of bonds (12) is removed.
  • Ruby: Dialog#filter_kit is implemented. The how-to is described in the document (appendix).
  • Ruby: LAMatrix#svd (singular value decomposition) was implemented.
  • Ruby: The methods bond_par, angle_par, dihedral_par, improper_par, vdw_par are moved from Molecule to MDArena.
  • Bug fixes (see the ChangeLog)
2012/06/18
Version 0.6.3 is out.
  • Document for the LAMatrix class was written.
  • Document for the collaboration with other quantum chemistry softwares was written.
  • Mbsf files now retain sigmas for the crystallographic parameters (imported from CIF).
  • New Ruby commands: Molecule#fit_coordinates, Molecule#amend_by_symmetry, Molecule#set(get)_view_center, Molecule#hidden_atoms, Molecule#set_hidden_atoms, Molecule#charge, Kernel#lookup_menu
  • When the MM parameters are edited from the bond/angle table, the force constant can be guessed by Universal Force Field (UFF).
  • The MM parameters can now be specified by explicit atom indices.
  • Other bug fixes (see the change log).
2012/02/03
Version 0.6.2 is out.
  • Graphic objects can be drawn together with the molecule (requires Ruby coding).
  • Modeless operation of Ruby Dialog is implemented.
  • The first comment line of the Ruby script (that is to be imported by "Execute Ruby Script" command) can now contain "coding:shift-jis" or "coding:utf-8" instruction. At present, only these two codings are recognized.
  • LAMatrix (linear algebra matrix) class is implemented in Ruby, which allow matrix arithmetic of arbitrary dimension. No document is provided yet.
  • Empty Console Window command is implemented.
  • Document for MD calculation is written.
  • Rms of crystallographic parameters (from the CIF file) are now kept in the molecule. Copying/saving of such parameters are not yet supported.
2011/11/30
Version 0.6.1 is out.
  • Ring fusion can be performed by copy-paste or "double-click and type-in".
  • Various ring structures (cycloalkanes, aromatics) and solvent boxes are accessible from "Open Predefined" menu.
  • CIF import is improved, so that bonds including the calculated hydrogen atoms are created by guess.
  • Import/export of dcd trajectory files is implemented.
  • Creating AMBER input now allows to select between AMBER8 (also for NAMD) and AMBER11 formats.
2011/10/15
Version 0.6 is out.
  • Mac: a command line version is included in the binary distribution.
  • Some solvent box are included in Scripts/mbsf folder.
  • Setting external forces during MM/MD is implemented.
  • The MO info table is renamed to MO energy, and the alpha and beta orbitals of same indices are shown in the same row.
  • Many other small changes and bug fixes.
2011/08/23
Version 0.5.6.2 is out.
  • Fchk import was broken (enbug in 0.5.6.1); fixed.
  • Final compile date/time is now shown in the 'About' window.
  • Fix mdcrd import to allow coordinates using full 8 digits (like -123.456 or 1234.567).
  • Occasional crash during minimization is fixed.
2011/08/03
Version 0.5.6.1 is out.
  • Crash on running antechamber/parmchk on PPC Mac is (hopefully) fixed.
  • Mac: resp and sqm (semiempirial QM calculation invoked by antechamber) caused crash unless gfortran is installed. To fix this, config.h/Makefiles for AmberTools is modified so that gfortran library is statically linked.
  • Occasionally, termination of the subprocess (like antechamber) was not detected properly, and the subprocess was left as a zombie. Improved, but may not be completely fixed.
  • Loading GAMESS dat file now can be interrupted by ESC.
  • Disable close box of RubyDialogFrame.
  • On importing frcmod, atom type with a single character (like "c") was not recognized properly. Fixed.
  • MO import from GAMESS log/dat files are implemented.
2011/07/30
Version 0.5.6 is out.
  • Gaff and parm99 parameters: the equilibrium bond lengths have now three significant digits after the decimal point.
  • Crash on antechamber/parmchk dialog (and other Ruby-based dialogs as well) is fixed.
  • Ruby: New methods: AtomRef#exclusion, Molecule#resize_to_fit, Molecule#bond_par/angle_par/dihedral_par/improper_par/vdw_par, $stdin.gets, $stdin.readline. Improved: Molecule#each_atom, Molecule#duplicate, Molecule#open, Kernel#message_box, Dialog#item.
  • MM/MD: minimization gets improved stability; the "solvate" command now sets the segment name 'SOLV' for the solvent atoms.
  • New menu commands: "Create New Atom", "Create New Parameter", "Create SANDER Input", "Import AMBER Lib", "Import AMBER Frcmod".
  • New file formats: cif (import), AMBER mdcrd (import).
  • Tables: cut/copy/paste in parameter table is improved. Mac: table did not get focus under certain conditions; fixed.
2011/04/26
Version 0.5.5 is out.
  • Incomplete MM/MD re-initialization after modification of coordinates was fixed.
  • The Ruby command wrap_unit_cell now works correctly.
  • Periodic images can be displayed when a unit cell is defined.
  • Wrong calculation of vdw/elect forces under periodic boundary conditions was fixed.
  • The native format (mbsf) now preserves the display conditions, such as scale, orientation etc.
  • Pasting MD parameters to a molecule with no parameters now works correctly.
  • Importing GaussianW fch(k) files was not working; fixed. The extension ".fch" is now recognized as a Gaussian formatted checkpoint files.
2010/05/07
Version 0.5.4 is out.
  • "Create GAMESS Input" dialog can now specify automatic generation of internal coordinates.
  • Many bugs were fixed.
2010/04/25
Version 0.5.3 is out.
  • Frames can now have variable unit cell parameters.
  • Improved handling of copy/cut/paste in the parameter table.
  • Fix the problem in the Mac version in which the hidden top-level window gets sometimes visible in the Window menu.
  • Bugs in the list control were (hopefully) fixed.
2010/03/20
Version 0.5.2 is out.
  • The reference for built-in Ruby is written. The features of the Ruby commands are cleaned up.
2010/02/06
Version 0.5.1 is out.
  • AmberTools 1.3(partly) is included in the package. The tools make it easy to assign MM atom types and calculate am1-bcc partial atomic charges for organic molecules.
  • Freeze problems after MM/MD is improved (it still happens sometimes).
  • The document "Energy minimization by molecular mechanics" is written.

2010/02/07 Added´╝ÜLinks are given for AmberTools and the online document.

2010/02/01
The English version of the home page (this page) is created.
2010/01/21
First public release.