Hello, We plan to use PyMOL as the alignment/structure viewer in a protein threading package we developed. Mostly there will be some new features/enhancements on the existing viewer. e.g.
- highlight/color by mappings of amino acid porperties (cysteines, charge and hydrophobicity, size, secondary structure) - a sequence alignment pane in sync with the structure window; selecting residues in one selects them in the other - show multiple alignments simultaneously - permit structural superposition of templates (i.e. structures) I'm personally new to PyMOL, and am poking around to explore the features (BTW, excellent graphics!). Right now I'm having difficulty with the syntax of "selection-expressions". I don't see a comprehensive documentation of what counts as selections. Can cysteines already be highlighted? Is any of the mappings already available? On another note, I'm aware of the following way to color by secondary structures: color red, ss h color yellow, ss s color green, ss l+"" which however seems a bit cumbersome. I'd prefer having a "Color by..." with options like "secondary structure", "charge", "size", etc. under the menu item "Display". But then, I figure many prefer command lines. These are just some initial random thoughts. BTW, could someone explain what the different "elems CHNOS*" represent? I'd really appreciate more comprehensive documentation. Thanks, Tina
