Subject: CCL: Mol2mol upgrade

From: "Tamas E. Gunda" <tgunda[at]puma.unideb.hu>
Date: Thu, 24 Feb 2005 22:23:14 +0100

Dear CCL Members,

    The new 5.4.0 version of the molecule file conversion,
manipulation and utility program Mol2Mol is now available
> from http://web.interware.hu/frenzy/mol2mol  as trial or
shareware version.
    The current version of Mol2Mol recognizes, and interconverts
about 50 different file formats (including subtypes).
By entering a format string practically every format can be
out/inputted.
 It can slice multiple structural files to single ones (such
as PDB models or MDL SD files to single ones) and vice versa
in several variations. Support for PDB Chime subformat
(with 1-2-3 bonds). Many molecular utilities.

New in Mol2Mol 5.4:

- Input of Gaussian output files (now recognized automatically);
- Input of Gamess output files (now recognized automatically);
    (the structures one by one or in browse mode (with charges added))

-  Support has been added for the Jmol java applet: MDL mol, XMOL xyz and HyperChem hin files can be written as a javascript
variable for using them as inline molecules in html files.

- and a few smaller changes, additions

In the previous version Mol2Mol 5.3:

New utility:
 - Calculation of Gasteiger-Marsili charges, a simple procedure for
  calculating partial charges based on electron negativities.
  Supports organic molecules (C,H,N,O,S,P, halogen atoms).
  Best suited for systems with unconjugated double bonds only)

New geometric utilities:
 - Calculation and dumping of geometrical data defined by named
  selections in HyperChem hin or hcs (Hyperchem conformation
  search) files.
 - Calculation of the dihedral angle of two best fitted mean planes.
  In previous versions only the angle of exact planes (defined
  by three atoms) could by calculated. Now the planes can be
  defined by any number of atoms.

Several small corrections, bug fixes were also made.

In the previous version Mol2Mol 5.2:

 New file format: Hyperchem HCS [conformation search] (read only)

 New utility:
 - Superimposing and rms comparison of two molecules;
   use of all atoms or only selected ones,
   optionally with different weight factors;
   it can be done automatically for all structures in multiple files;
   fitted molecules can be outputted to multiple files.

 New in POV-Ray format:
 - bond types are supported in vector mode too;
 - stereo bond types are supported;
 - support for rendering elemental symbols in vector mode;
 - support for rendering atom aliases in 2D sketch files in vector mode;

and several bug fixes.

   Mol2Mol is a very handy set of tools for everybody dealing with
molecular modelling.
   It is impossible to write here all of the features of Mol2Mol,
but have a look at its home page:

http://web.interware.hu/frenzy/mol2mol

POV-Ray fans may also have a look at:
http://dragon.unideb.hu/~gundat/povraya.htm

The program is available as 30 days unrestricted trial version or
as shareware version.

Dr. T. E. Gunda