XmMol Home Page

What is XmMol?

XmMol is a desktop macromolecular visualization and modeling tool designed to be easy to use, configure and enhance. Its graphics are based on X11, and part of its user interface is based on Motif. Thus it provides a way of displaying structures on any X11 server. Its main features are:

interactive graphics of macromolecules on any X11 display. Drawings are performed as wireframes to preserve interactivity. Space filling static images can be obtained by using an interface to external rendering programs such as MolScript and Raster3D.
strong ability to be interfaced with external programs. A communication protocol allows XmMol to fork external programs called "delegates" and exchange information. This feature allows the easy implementation of new features of XmMol. This offers possibilities for automatic script execution, new file format I/O implementation, file coordinate modification, implementing external renderers, .... Thus, XmMol can also be used as a graphic debugger for numerical methods applied to molecules (minimizers, ...).
Examples of how to implement molecular superimposition, dynamic trajectory animation, as well as calls to external standard programs such as babel or hbplus are provided.
Some modelling tools are supported, such as docking facilities, interactive backbone deformation (part of the Forme package). However, the aim of XmMol is mostly to give each user the opportunity to interface its own methods.

What is XmMol NOT ?

XmMol does not provide interactive sophisticated space filling macromolecular representations. Preference was given to portability and interactivity. Sophisticated space filling representation can however be obtained through XmMol' interface with MolScript or Raster3D, and partly with QTree.
XmMol is not a fully integrated molecular modelling package (see the above section).

Capabilities

Input Formats

PDB and Mac format (XmMol internal format derived from R. Lavery's Flex format) are supported as internal formats. Other formats can however be displayed by using a converter such as Babel.

Molecular Representations

Molecules may be drawn as bonds, trace or ribbons. These types of representations can be assigned to each molecular fragment so that representations merging all the types can be obtained.
Various colorations schemes can be applied such as by file, chain, residue, atom type, secondary structure type, ... The user can also use a panel to define the color associated with each atom.
The interface with MolScript and Rasmol was designed to ensure a good preservation of the view, including representation types as well as colors. Stereo is preserved with MolScript. A WYSIWYG Postscript interface is also supported. A mechanism allows, if all necessary programs are accessible, a direct visualisation of the result.

Display

Any X11 display can be used for visualization (thus works through the net). Stereo is supported as two separated images rotated by a few degrees.

Extensibility

XmMol delegate library provides access to any field of the molecular structures as well as to most of the XmMol internal functionalities relative to display, rendering, colouring, etc. Shared memory usage is supported for some critical fields such as atomic coordinates. External delegates can be inserted as part of XmMol menus and made equivalent to built in methods.

Configurability

Some parameters can be accessed through a configuration file and concern:

Colors used by XmMol, and colors associated with some colouring patterns.
Parameters controlling the stereo
Parameters controlling the spline computation
Parameters controlling Postscript parameters, and the possibilities of displaying the result of queries to Raster3D or MolScript.
Covalent bond hydrogen bond detection.
File automatic uncompression.
Mouse buttons re-assignment.
Default command file (to make XmMol automatically execute series of commands)

Hardware requirements

There are no special requirements for XmMol other than Unix and X windows (X11R4 or upper). For systems (eg. SUN) that do not support non shared libraries, access to Motif libraries should however be ensured. XmMol was compiled and tested for most unix systems including:

HP-UX
SGI IRIX
IBM AIX
SUN Solaris
Dec Alpha
Linux (should run upon mkLinux)

Availability

XmMol is now freely distributed under the terms of the Gnu General Public License. To get a copy of the Gnu General Public License, click here.

You can download the distribution here.

Documentation

XmMol comes with some "online" documentation as well as with the PostScript manuals.

Separately, you can :

download the latest PostScript version of the user manual.
download the latest PostScript version of the delegate task command language manual.

Related Packages

For some features (space filling images, molecular superimposition) XmMol relies on external programs which are not included in the distribution, or which version might have been updated. These include:

None of these libraries/programs are required to run XmMol, but certain features will not be available without them.

Problems, Help, Feedback

If you need additional information, have a suggestion, or need help concerning XmMol, please first read the documentation, including some Frequently Asked Questions. You can also contact the team at RPBS.

Last modified: Mon Jan 27 18:38:11 2008