>>Q: How would one decide where it would be displayed? >> > The default reference point could be the first coordinate in the pmesh > file. Optionally the number of the reference point coordinates in the > pmesh file could be specified in the pmesh definition line (e.g.: pmesh > example1 "example1.pmesh" 17). The rest would then be similar to atom > labels.
OK ... that is a pretty good idea. >>Q: Could the labels be in one of the corners, in the same color as the >>associated pmesh surface? >> >> > If it would be in the corner in the same color it wouldn't be visible if > the pmesh would be filled. And the label might also be too long to fit > into the pmesh. I meant in the corner of the Jmol display, not in the corner of the mesh. >>I do not understand. >> > Maybe I should tell what we want to do. We want to highlight exon > boundaries in protein structures. In order to be able to highlight for > example PROSITE motifs at the same time the best way would be to show > something between the two amino acids at the border. I don't understand the details of this. But I generally understand that this is some characteristic that you wish to hilite. > With pmesh this would be a filled square, perpendicular > to the trace between the amino acids. While that would certainly work, it does not sound like the kind of application that pmesh was designed for. > With pseudo atoms in the corners of the square and bonds from > each atom to each other atom you would get a square with a cross inside. > Not as good as a filled square but at least it could be labelled and all > squares could be integrated into the PDB file as additional model. OK >>>Q: Is it possible to change the appearance of bonds besides changing >>> their color? >> >>You can adjust color, radius, and translucency. >> >>hbonds are displayed as segmented (dashed) cylinders >> >>Q: What other renderings/formats would be interesting? >> >> >> > When I tested the pseudo atom pmesh replacement I just didn't realized > the possibility to adjust the bond radius by using the wireframe command > (although I used it plenty of times before!). > For their regular use I guess cylinders are sufficient. For their > 'misuse' a flat rectangle would be nice, but then you would have the > orientation problem. So just forget about it. It is not clear to me where you want to take this disussion. Miguel ------------------------------------------------------- This SF.Net email is sponsored by: Power Architecture Resource Center: Free content, downloads, discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
