Dan,
I think it's fair to say that PyMOL's currently molecular building
capabilities are at the stage of a technology
demonstration/proof-of-concept, but very little effort has yet been expended
toward making them useful for real work.
Part of that is because we don't yet have a general back-end
modeling engine inside of PyMOL (molecular sculpting is a pure GIGO kind
of thing). That is still an important long-term goal.
But the other reason is that I don't really have a clear idea in my
mind for how such a builder should operate. What I would like to get from
you and all other interested PyMOL users are wish-lists for how PyMOL's
molecular builder should work (better). No hurry though -- feedback over
the next month or two should be fine, and anyone attending MUG or CUP is
welcome to give me an ear-full next week.
Basically, a major goal is to evolve PyMOL into a builder that can
be useful across the board for biology and drug discovery: for proteins,
small molecules, nucleic acids, carbohydrates, solvent, and so on. As a
general tool, it should be capable of supporting crystallography-oriented
building, manual homology modeling, and hypothetical hand modeling of
small molecules, as well as simple illustrative tasks such as the one you're
working on. Of course, specialty tools like O, Quanta, Modeller, and
MacroModel will always be superior in their respective niches, but I hope
PyMOL can become eventually become good enough for simple common molecular
building tasks...
Questions to consider:
What are the best builders out there today that we should learn
from?
What are the key functions PyMOL must absolutely have to be a
builder?
What other extra attractive feature should PyMOL seek to emulate?
How can we make the best use of what is already in PyMOL, unique or
otherwise?
What are the biggest holes in the current versions?
Things that are already on the radar:
Rotamer-libraries.
A 1-D sequence viewer with alignment and editing capabilities.
An integrated builder tutorial.
Finding an existing force-field provider to work with...
Back and forth 2D to 3D for small molecules.
Dan,
It sounds like a feature you would like is that ability to aim the
chain being built towards a certain direction.
In the meantime, to accomplish your task, build the chain first,
then turn on Auto-Sculpting in the Sculpting menu, put the mouse into
editing mode, then control-left-click-and-drag to move the chain where you
want it to go. Ctrl-middle-click to pick one (or more -- in the latests
betas) joints...and then shift-left-or-middle click-and-drag, or
control-left-click-and-drag to move the resulting fragments. If your chain
is small, increase the number of Cycles per Update to accelerate
convergence.
Cheers,
Warren
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Moriarty, Daniel
Sent: Thursday, February 19, 2004 9:47 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] using the build function
Hello everyone,
I'm trying to build some model proteins for a diagram showing
a protein unfolding over several steps. I'm using the build
function in the 0.95beta10 release. The main problem is that
I can't control the angle of the protein chain, so the chain
just goes off in one direction only, unless proline is placed
in the middle of a helix at which point it goes off at a new
angle. This makes me think that it can be specified, but I
just don't know how to do it.
Any help would be appreciated,
Dan
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