Hi Alexander and Bob-
I'm going to go out on a limb here and say that I think Alexander wants
to do something that's not as complex as it seems. While my description
below uses the links on my page, I am really just using Jmol's model kit
mode commands.
I'll use lactose permease (courtesy of RPI) as an example. Go to:
http://chemagic.com/web_molecules/script_page_large.aspx
1) Click to go to the Model Tools
2) From the MM Load menu, select 0000 - so named to bring it to the top
of the menu
The above is lactose permease (two actually because of the crystal
structure data) with a galactospyranoside "dimer" substrate tucked inside.
3) Click the Edit link to go to the edit menu.
4) Click the Model "move" link and the Bonds picking "off" link.
The above selects the move mode that we need below. Additionally, both
clicks together turn off bond and atom editing. For a model this large,
you don't want to see what happens on an accidental edit!
5) In the script command field, enter "set selectHetero on;select
hetero;color pink" and click Run (No Quotes in the Actual Command).
OK, there's your tiny substrate. Substrates really because of the two
proteins.
6) Zoom in until you are sure that you can get a clean click on a pink
substrate atom.
7) Shift-Click-Drag to rotate any way you want with respect to the
protein. OR Click-Drag to move the substrate in the XY plane of the screen.
Alexander, is this analogous to what you want to do?
Note: If that substrate is bound in there, then things get icky. Your
going to end up with the connected bond stretching like a taffy pull. In
this case, however, the substrate is a separate entity.
I hope I'm on the right track here and not wasting your time!
Otis
Otis Rothenberger
chemagic.com
On 11/8/2010 4:12 PM, Robert Hanson wrote:
That's going to rotate the atoms about a specific molecular axis. Do
you want it to rotate about a specific window axis, regardless of how
the model is oriented? Is that the problem? There might be a way of
doing that with quaternions.
On Mon, Nov 8, 2010 at 12:39 PM, Alexander Rose
<alexander.r...@weirdbyte.de <mailto:alexander.r...@weirdbyte.de>> wrote:
Hi,
>From the manual
"set allowRotateSelected FALSE
When set TRUE, this parameter allows user rotation of the molecule
containing the selected atom using the mouse (holding ALT down
while dragging). The coordinates of the rotated molecule will be
sightly degraded in this process."
I would like to rotate an arbitrary set of atoms using the mouse
and currently "set allowRotateSelected TRUE" is the closest thing
I found, but works only for a single complete molecule.
I started to implement something myself using bind and
rotateSelected and in principle it works:
bind "CTRL-ALT-LEFT" "rotateSelected axisangle {1 1 1 _DELTAX}"
but its not quite as "set allowRotateSelected TRUE". I think I
need to make the rotation angle depended on the current view?! Any
suggestions?
Best
Alexander
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Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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