The conformational editing features are not fully designed nor well
tested, and the documentation is still incomplete. Until the PyMOL user
interface is a bit more stabilized, documentation seems premature.
I am resistant to the idea of committing to a user interface which hasn't
really been evaluated or optimized for usability. However it is quite
frustrating for all of us knowing that there is considerable power under
the hood which can't yet be accessed by users : ( .
However, you should at least be able to do a few basic things, such as
manually adjusting bond torsions:
1. put the mouse into editing mode (Mouse menu)
2. ctrl-right click on a bond
3. ctrl-left click and drag atoms on either side of the bond.
Other mouse combinations allow you to move fragments in different
ways...just play around with the different combinations on the mouse
Sculpting is a bit less obvious: PyMOL will take a snapshot of
bond lenths, angles, and stereochemistry inside a molecule the first time
sculpting is activated on an object. From then on, no matter what you do,
PyMOL will labor to maintain those constraints while you drag atoms around
or make other conformational changes.
The Sculpting Wizard can help you out in getting started with this
feature. However, the bottom line is that more work needs to be
done on these aspects of PyMOL, and that's why increasing funding for
PyMOL is essential. Until I can afford to start paying people to help me
with development and documentation, progress will cotinue to be slow.
So in closing, I wouldn't look to PyMOL as a workhorse conformational
editing tool just yet -- give it another year or so.
On Thu, 26 Sep 2002, Yu Shao wrote:
> Hello everyone,
> Does anyone know how to use the conformation editing of PyMol, or has it
> been implemented? It's unclear from the menual, which just said that
> "Sorry, no documentation yet -- these features won't be too useful until
> PyMOL is coupled up with an energy minimiation engine." Any infomation
> will be highly appreciated.
> Best wishes,
> Yu Shao
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