Hi Tina, Welcome to PyMOL!
> 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. Great. That is one of the ways I hope people will make use of PyMOL. Do realize however that we're still in "early" days, and so don't expect it to be easy. PyMOL may be inexpensive from a cost standpoint, but you still need to invest substantial resources in order to get the most out of it. > - 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) There are all things PYMOL should be capable of doing in tandem with an external application. > 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: The most comprehensive selection docs can be found at: http://pymol.sourceforge.net/newman/user/S0220commands.html#7 Getting started with commands in another "must read" http://pymol.sourceforge.net/newman/user/S0210start_cmds.html#6 > 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. The idea with PyMOL (from a developer/integrators standpoint) is that you can create the menus which suit the needs of your specific application. > These are just some initial random thoughts. BTW, could someone explain > what > the different "elems CHNOS*" represent? I'd really appreciate more > comprehensive documentation. > That's just the coloring for Carbon, Hydrogen, Nitrogen, Oxygen, Sulfur, in the color pop-up menu. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020