Hi, I finally got time to test it and it works like a charm. Thank you Bob!
Alex ----- Ursprüngliche Mail ----- > Von: "Robert Hanson" <[email protected]> > An: [email protected] > Gesendet: Dienstag, 9. November 2010 14:24:26 > Betreff: Re: [Jmol-users] rotate selected atoms using the mouse > 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 < [email protected] > > 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 < > [email protected] > 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" < [email protected] > > > An: [email protected] > > 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 < > > [email protected] > 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 > > 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 > > [email protected] > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > > > > -- > > 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 > > _______________________________________________ > > Jmol-users mailing list [email protected] > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > ------------------------------------------------------------------------------ > > 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 > > [email protected] > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > ------------------------------------------------------------------------------ > 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 > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > -- > > > > 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 > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ Increase Visibility of Your 3D Game App & Earn a Chance To Win $500! Tap into the largest installed PC base & get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
