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>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>
> > An: 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
> > 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 > 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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> David G. Thomson, author of the best-selling book "Blueprint to a
> Billion" shares his insights and actions to help propel your
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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
Billion" shares his insights and actions to help propel your
business during the next growth cycle. Listen Now!
http://p.sf.net/sfu/SAP-dev2dev
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