The Structure Menu
Viewer
Define the viewer to be used to render structure. Three different viewer are available :
- RasMol (default) The RasMol renderer is distributed with Ordalie, and is assigned as the default viewer. Be aware that RasMol can only display 5 structure at a time.
- VMD (Visual Molecular Display). This program can be downloaded at http://www.ks.uiuc.edu/Research/vmd/. VMD allows more interactions with Ordalie.
- O macro file: All graphical instructions will be written to a file that can then be loaded in O using the "read <filename>" command.
Display
Launch the selected viewer. For the RasMol and VMD viewers, Ordalie will open the Structure Panel window in order to control the structure appearance and feature rendering. See "The Structure Window" for
details.
Superpose
When invoke the Structure Panel will appear in the bottom frame of the Ordalie Main window.The superposition algorithm will try to superpose the Ca atoms of the defined zones. Some predefined zones are accessible through the buttons :
- Select All : superpose structure using the whole sequence
- All strands : select all beta-strands
- All helices : select all alpha-helices
- Clear : clear the current superpose selection
The superposition zones can be also entered by hand using the mouse. The beginning of the zuperposition zone can be set by clicking on the alignment with <Button-1>. The end of the zone is set by clicking of the alignment with <Shift-Button-1>. The selected zone appears in gray. Several zones can be defined. A click on a zone with <Button-2> deselect the zone. A click on any secondary structure element selects this element.
By invoking the "Superpose" button, a window will appear asking for the reference structure, i.e. the structure on which the others will be superpose (the not moving structure).
The superposition zones will be printed in the Log Console window, together with the RMS deviation of the superposed atoms after superposeition.
Color sec. str. by conservation
Je le mets ca ?