Mario Valle Web

Tools analysis

Here I collect a disordered list of things about the surveyed tools. The main idea is that this list should provide input material for the design of the "perfect tool".

A checklist

QuestionDescription
Main tool usage and specialization field A quick description of the tool intended usage, its main chemistry field specialization and who this tool is intended to serve (end user, developer)
File formats File formats read
Representations offered Which chemistry representations are offered by this tool
User interaction possibilities Besides viewpoint movement
Other graphical elements and views supported From the graphical point of view which other functionalities are supported
Data model If it is visible
Extensibility Tool extensibility support
Other noteworthy capabilities Something this tool is able to do that is not found in other tools
Other noteworthy limitations Something really annoying
Performance and rendering support Shaders, advanced OpenGL, distribution, etc.

Analyzed tools

DRAWxtl

Main tool usage and specialization field
End user viewer specialized for crystallography
File formats
CIF FDAT GSAS Schakal Shelx Wien2k. Reads also Fourier maps in the following formats: GSAS JANA WIEN VASP FullProf CIF-FoFc
Representations offered
Ball-and-stick plus polyhedron (not only octa and tetra, see fajasit.str) and ellipsoids. Axis labels (Oabc) on the unit cell
Other graphical elements and views supported
Arbitrary arrows, lone pairs
Extensibility
Not extensible at all
Other noteworthy capabilities
Export to POV and VRML
Other noteworthy limitations
Vintage GUI, image export only as PostScript, pollute data directories

Chimera

Main tool usage and specialization field
End user viewer with analysis support for macromolecules
File formats
PDB, Mol2 plus various volumetric formats: NetCDF, DelPhi, XPLOR
Representations offered
Line, ball-and-stick, ribbons surfaces
Other graphical elements and views supported
I do not know
Extensibility
Python
Other noteworthy capabilities
Macromolecular simplified surfaces for identified components
Other noteworthy limitations
Sometimes it is hard to delete generated elements, no conversion for bohr coordinate values