Alex,
Yeah, that is the "icky" case. PLM is bonded to the protein chain. You
can break that sulfur bond and then play with PLM independently (using
model kit mode). You can also rotate it about that bond (using model kit
mode). For complete independent movement while attached, Bob obviously
has a plan! Bob, what's that sulfur bond going to do during the movement?
Otis
Otis Rothenberger
chemagic.com
On 11/9/2010 7:23 AM, Robert Hanson wrote:
Alex,
That's what I needed. We will need a new parameter:
set rotateSelectedAtoms
It will be in Jmol 12.1.21, to be released later today.
Bob
On Tue, Nov 9, 2010 at 4:20 AM, Alexander Rose
<alexander.r...@weirdbyte.de <mailto:alexander.r...@weirdbyte.de>> wrote:
Hi,
thanks for your efforts Otis! What I want is not as fancy as Bob
guessed. Let me try to reformulate what I want to achieve: "Use
the mouse to rotate an arbitrary set of atoms around its geometric
center.".
I set up a page with some comments (also attached below) to
clarify things, hopefully:
http://weirdbyte.de/jmol-test/html/move.html
Alex
// comments from the website
load "../data/3cap.pdb"; set selectionHalos ON; select chain=a;
set dragSelected ON; set allowRotateSelected ON;
Rotating (alt-left) and translating (alft-shift-left) of selected
chain a works fine, only selected atoms are moved. This is what I
want in general, a way to move (rotate, translate) only selected
atoms using the mouse, but depending on bonding, I have not found
a way to achive it (for translating I got it, but not for
rotating) as I hope to show below
load "../data/3cap.pdb"; set selectionHalos ON; select chain=a and
plm; set dragSelected ON; set allowRotateSelected ON;
Translating (alt-shift-left) works as expected, moves just the
selected atoms (plm). Rotating (alt-left) moves plm and the bond
protein chain=a, this works as documented "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." However, I am looking for a
way to just rotate the selected plm, regardless of weather it is
bond to the protein chain a.
load "../data/3cap.pdb"; set selectionHalos ON; select chain=a and
plm; set picking dragMolecule;
The picking/drag approach, selection does not matter. Pick/drag
the protein chain a moves just the protein chain a. Pick/drag plm
moves the protein chain a and all bond non protein molecules,
including plm. This is asymmetric, is there a rationale for that?
Actually I do not mind, I just want a way to move (rotate,
translate) only selected atoms using the mouse.
----- Ursprüngliche Mail -----
> Von: "Otis Rothenberger" <osrot...@chemagic.com
<mailto:osrot...@chemagic.com>>
> An: jmol-users@lists.sourceforge.net
<mailto:jmol-users@lists.sourceforge.net>
> Gesendet: Dienstag, 9. November 2010 06:06:00
> Betreff: Re: [Jmol-users] rotate selected atoms using the mouse
> 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 <http://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
------------------------------------------------------------------------------
The Next 800 Companies to Lead America's Growth: New Video Whitepaper
David G. Thomson, author of the best-selling book "Blueprint to a
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business during the next growth cycle. Listen Now!
http://p.sf.net/sfu/SAP-dev2dev
_______________________________________________
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------------------------------------------------------------------------------
The Next 800 Companies to Lead America's Growth: New Video Whitepaper
David G. Thomson, author of the best-selling book "Blueprint to a
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