Oh my. I had forgotten about this. If you actually open Bob's Jmol model
kit mode, turn the substrate pink:
set modelKitMode;set selectHetero on;select hetero;color pink
and use the drag (shift to rotate) commands to move the substrate
slightly out of place, then the drag/minimize command will simulate
docking back into place.
I just love this thing!
Otis
Otis Rothenberger
chemagic.com
On 11/9/2010 12:06 AM, Otis Rothenberger wrote:
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
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