Make that...
version=12.1.21_dev
# new feature: set allowMoveAtoms
# -- allows rotation/dragging of atoms regardless of bonding
# -- automatically sets/unsets allowRotateSelected and dragSelected
# -- ALT-left --> rotates selected set
# -- ALT-SHIFT-left --> drags selected set
On Tue, Nov 9, 2010 at 6:23 AM, Robert Hanson <hans...@stolaf.edu> 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> 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
>> >
>> >
>> ------------------------------------------------------------------------------
>> > The Next 800 Companies to Lead America's Growth: New Video Whitepaper
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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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>> ------------------------------------------------------------------------------
>> > 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!
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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
>> 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
>> _______________________________________________
>> Jmol-users mailing list
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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
>
--
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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