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8. User interface features

8.1 Files

All text files read or written by DomainFinder (e.g. PDB files, VRML files, and textual domain descriptions) can be compressed using the Unix utilities compress or gzip. It is sufficient to use filenames with the appropriate suffixes .Z or .gz; DomainFinder then automatically chooses the right format. Compression is especially useful for VRML files, which can become very large. Most VRML viewers can deal with compressed files directly, just like DomainFinder.

8.2 Protein structure visualization

Many windows in DomainFinder show a three-dimensional protein backbone structure. The representations can be moved, rotated, and scaled with the mouse. Press the left button for translation, the middle button for rotation, and the right button (with vertical movement) for scaling.

The structure visualization in DomainFinder is currently rather slow, which is especially visible during interactive manipulation. Future versions of DomainFinder will probably use a faster structure display technique.


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