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
