Re: [Jmol-users] Rotate Selected
why isn't it just
bind LEFT _rotateSelected
?
On Wed, Feb 20, 2013 at 9:46 AM, Otis Rothenberger osrot...@chemagic.comwrote:
Bob,
To set up rotation of selected models on an iPad, I have to bind LEFT to
the rotation so that I can eliminate the need for a modifier key. I'm using
the following binding:
bind LEFT rotateSelected Y @{_DELTAX*2};rotateSelected X @{_DELTAY*2}
No matter what I use as a multiplier, I'm getting sluggish/clunky rotation
- some multipliers better than others.
Do you have any suggestions for smoother rotation?
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_feb
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_feb___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Rotate Selected
Bob,
I tried that, and it works with mouse control on my desktop, but the iPad has a
problem.
For the desktop/mouse, I can bind _rotateSelected to LEFT, and pick up the
click/select of a model with a hover call back. Binding LEFT to _rotateSelected
evidently loses the original click select of rotate selected. This is all OK.
One way or another, this all works for the desktop/mouse.
On the iPad, I have no hover. I only have LEFT for binding. Consequently, I
select models sequentially with a link. This is no more clumsy than pressing
the CTRL key while dragging. If I bind _rotateSelected, grabbing the selected
model by an atom on an iPad is really clumsy.
On the other hand, if I bind with the script of my previous note, dragging
anywhere (atom or background) nicely rotates the selected model. A multiplier
of 1.5 is not too bad. I'll go with that for now.
Part of this drives me nuts. I was not the major pusher of iPad compatibility
on the ISU VMK. That was my colleague, Tom. But now that I've done it, people
who have ignored the virtual model kit previously are suddenly excited about it.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Feb 20, 2013, at 4:20 PM, Robert Hanson wrote:
why isn't it just
bind LEFT _rotateSelected
?
On Wed, Feb 20, 2013 at 9:46 AM, Otis Rothenberger osrot...@chemagic.com
wrote:
Bob,
To set up rotation of selected models on an iPad, I have to bind LEFT to
the rotation so that I can eliminate the need for a modifier key. I'm using
the following binding:
bind LEFT rotateSelected Y @{_DELTAX*2};rotateSelected X @{_DELTAY*2}
No matter what I use as a multiplier, I'm getting sluggish/clunky rotation -
some multipliers better than others.
Do you have any suggestions for smoother rotation?
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_feb
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_feb___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_feb___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] rotate selected atoms using the mouse
Hi, I finally got time to test it and it works like a charm. Thank you Bob! Alex - Ursprüngliche Mail - Von: Robert Hanson hans...@stolaf.edu An: jmol-users@lists.sourceforge.net 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 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 - 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
Re: [Jmol-users] rotate selected atoms using the mouse
Curious about the set picking dragmolecule and the compare commands, I have
just made some tests with the latest jmol.jar file from Bob's repository
(12.1.22_dev).
I used a beta globin and an alpha globin pdb files, loaded in 2 different frames
the set picking dragmolecule command works fine. Sometimes (this behavior is
inconsistent) the heme is disconnected from the rest of the model.
After a compare command has been issued, I encountered a bug with rotations :
the model rotated as well as translated, quickly finding its way out of the
window.
I tried the compare command with the following syntax :
compare {2.1} {1.1} subset {spine} rotate translate
It works great, as long as one of the models hadn't been translated by set
picking dragmolecule after having been compared once (eg : first run OK,
then translate). At the next run (sometimes in my trials, the second next), the
2.1 model disappears from the screen and Jmol behaves as if stuck in an
infinite process (the memory allocation keeps changing, no command available).
Anyway, those features look very promising !
-Paul
--
Centralized Desktop Delivery: Dell and VMware Reference Architecture
Simplifying enterprise desktop deployment and management using
Dell EqualLogic storage and VMware View: A highly scalable, end-to-end
client virtualization framework. Read more!
http://p.sf.net/sfu/dell-eql-dev2dev
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] rotate selected atoms using the mouse
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 - 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
Re: [Jmol-users] rotate selected atoms using the mouse
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.dewrote: 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 - 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
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 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 - 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
Re: [Jmol-users] rotate selected atoms using the mouse
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 - 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
Re: [Jmol-users] rotate selected atoms using the mouse
Hi Alexander-
I'm not sure exactly what you want to do, but if you want to
independently translate or rotate non-bonded models, or rotate about a
given bond (i.e. conformation rotation), then there is a really simple
way to do either of these.
1) With one or more models in the same window, the command set picking
dragMolecule will allow you to click/drag the models independently.
Shift/click/drag will allow independent rotation.
2) The command set picking rotateBond will allow you to click select a
bond. After the bond is click selected, shift/click/drag on either side
of the bond will do a conformation rotation.
Alternatively, you can enter Jmol's mode lkit mode and do all of this
via menus - right-click/computaion/model kit.
Otis
Otis Rothenberger
chemagic.com
On 11/8/2010 1:39 PM, Alexander Rose 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
Jmol-users@lists.sourceforge.net
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
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] rotate selected atoms using the mouse
Hi Otis,
Am 08.11.2010 um 20:22 schrieb Otis Rothenberger:
Hi Alexander-
I'm not sure exactly what you want to do, but if you want to
independently translate or rotate non-bonded models, or rotate about a
given bond (i.e. conformation rotation), then there is a really simple
way to do either of these.
1) With one or more models in the same window, the command set picking
dragMolecule will allow you to click/drag the models independently.
Shift/click/drag will allow independent rotation.
(dragMolecule is missing from the documentation)
Anyway it works fine and smooth for _molecules_, not for some atom selection. I
want to use it (and have) to work with proteins. For example to align a dimer
(two molecules) with a lipid bilayer patch.
Whenever there are multiple molecules involved, the majority of existing
functions offer no easy solutions. set dragSelected ON does work for
translating all selected atoms, regardless weather they are from one or more
molecules.
Alex
2) The command set picking rotateBond will allow you to click select a
bond. After the bond is click selected, shift/click/drag on either side
of the bond will do a conformation rotation.
Alternatively, you can enter Jmol's mode lkit mode and do all of this
via menus - right-click/computaion/model kit.
Otis
Otis Rothenberger
chemagic.com
On 11/8/2010 1:39 PM, Alexander Rose 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
Jmol-users@lists.sourceforge.net
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
Jmol-users@lists.sourceforge.net
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
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] rotate selected atoms using the mouse
Alexander, I'm still a little confused about your objective. Try this. Go to: http://chemagic.com/web_molecules/script_page_large.aspx Click the Molecular Editor link. Click duplicate. There are now two models in the window. Click move. After you click move, either model can be click/dragged (translated) to any position in the window. If you hold down the shift key, the model will rotate rather than translate. Is that what you want? I should mention that you can drag individual atoms. The command set picking dragAtom will allow you to do this. The drag link on my page above will do the same thing. After you click the drag link, you can click-drag individual atoms within a model - i.e. sculpt the model one atom at a time. Is that what you would like to do, albeit several atoms rather than just one? Otis Otis Rothenberger chemagic.com On 11/8/2010 3:19 PM, Alexander Rose wrote: Hi Otis, Am 08.11.2010 um 20:22 schrieb Otis Rothenberger: Hi Alexander- I'm not sure exactly what you want to do, but if you want to independently translate or rotate non-bonded models, or rotate about a given bond (i.e. conformation rotation), then there is a really simple way to do either of these. 1) With one or more models in the same window, the command set picking dragMolecule will allow you to click/drag the models independently. Shift/click/drag will allow independent rotation. (dragMolecule is missing from the documentation) Anyway it works fine and smooth for _molecules_, not for some atom selection. I want to use it (and have) to work with proteins. For example to align a dimer (two molecules) with a lipid bilayer patch. Whenever there are multiple molecules involved, the majority of existing functions offer no easy solutions. set dragSelected ON does work for translating all selected atoms, regardless weather they are from one or more molecules. Alex -- 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] rotate selected atoms using the mouse
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
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
Jmol-users@lists.sourceforge.net
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
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
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 - 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 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
--
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
Jmol-users@lists.sourceforge.net
mailto:Jmol-users@lists.sourceforge.net
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
Jmol-users@lists.sourceforge.net
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
Jmol-users@lists.sourceforge.net
Re: [Jmol-users] rotate selected atoms using the mouse
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 - 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 -- 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Rotate selected atoms with the mouse
I really just want to use it as a quick and dirty way of editing molecules without having to script each change -- especially for macromolecules where the general shape can be more important for visualisation than precise bond angles. It's certainly a niche feature and if it's not intended to be a feature in Jmol it's not a problem. I can code what I need into my app quite easily. On the other hand, there was some chat about enabling some editing features. If this goes ahead, this might be quite a nice feature to include, if only to let the user get the general shape right before running an energy minimisation. Cheers, Chris. Robert Hanson wrote: ah, ok. I see. Hard to believe this is going to be useful, considering the degrees of freedom. How do you figure it will be used? On Thu, Apr 30, 2009 at 9:26 AM, Chris Foley christopher.fo...@strath.ac.uk wrote: I'm afraid not. It appeared to work when the water molecule was selected. But all the atoms of HOH were selected. When I tried selecting a methyl group (select c13,h16,h17,h18) the whole caffeine molecule was rotated. In case it helps, I used Windows XP, Sun Java plugin 1.6.0_13 on Internet Explorer. Cheers, Chris. Robert Hanson wrote: Did it work at http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm # 30? On Thu, Apr 30, 2009 at 5:54 AM, Chris Foley christopher.fo...@strath.ac.uk wrote: Thanks for the reply Robert. I downloaded 11.7.33 but unfortunately I can't get the rotation to work. I can translate the atoms as you describe but can't rotate them. Also, is it possible to change the point the atoms rotate around? The kind of thing I want to do is rotate a group around the atom it is attached to. Thanks again, Chris. Robert Hanson wrote: It's in there, at least for Jmol 11.7. See http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm 30. selective atom rotation and translation # Using set dragSelected in Jmol 11.7.25 you can move selected atoms around, translating them with ALT-SHIFT-LEFT mouse and rotating them around their geometric center using ALT-LEFT or CTRL-ALT-RIGHT. Selection halos are automatically turned on during mouse-drag actions. (Still a few bugs there) load caffeine.xyz;load append water.xyz;frame 0;select 2.1;selectionHalos on set dragSelected !dragSelected On Wed, Apr 29, 2009 at 9:16 AM, Chris Foley christopher.fo...@strath.ac.uk wrote: Hi Jmol users, I would like to be rotate the selected atoms with the mouse. The rotateSelected command is almost perfect... but only works via scripting, not mouse interaction. The "allowrotateselected = true" setting is also close but rotates the entire molecule, not just the selected atoms. I was wondering (hoping) if I've missed something that would let me set this up quickly and easily. If not, no worries. I can write a small Java application that will do the job. Cheers, Chris Foley. -- Register Now Save for Velocity, the Web Performance Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- Register Now Save for Velocity, the Web Performance Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave.
Re: [Jmol-users] Rotate selected atoms with the mouse
Thanks for the reply Robert. I downloaded 11.7.33 but unfortunately I can't get the rotation to work. I can translate the atoms as you describe but can't rotate them. Also, is it possible to change the point the atoms rotate around? The kind of thing I want to do is rotate a group around the atom it is attached to. Thanks again, Chris. Robert Hanson wrote: It's in there, at least for Jmol 11.7. See http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm 30. selective atom rotation and translation # Using set dragSelected in Jmol 11.7.25 you can move selected atoms around, translating them with ALT-SHIFT-LEFT mouse and rotating them around their geometric center using ALT-LEFT or CTRL-ALT-RIGHT. Selection halos are automatically turned on during mouse-drag actions. (Still a few bugs there) load caffeine.xyz;load append water.xyz;frame 0;select 2.1;selectionHalos on set dragSelected !dragSelected On Wed, Apr 29, 2009 at 9:16 AM, Chris Foley christopher.fo...@strath.ac.uk wrote: Hi Jmol users, I would like to be rotate the selected atoms with the mouse. The rotateSelected command is almost perfect... but only works via scripting, not mouse interaction. The "allowrotateselected = true" setting is also close but rotates the entire molecule, not just the selected atoms. I was wondering (hoping) if I've missed something that would let me set this up quickly and easily. If not, no worries. I can write a small Java application that will do the job. Cheers, Chris Foley. -- Register Now Save for Velocity, the Web Performance Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- Register Now Save for Velocity, the Web Performance Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Rotate selected atoms with the mouse
Did it work at http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm # 30? On Thu, Apr 30, 2009 at 5:54 AM, Chris Foley christopher.fo...@strath.ac.uk wrote: Thanks for the reply Robert. I downloaded 11.7.33 but unfortunately I can't get the rotation to work. I can translate the atoms as you describe but can't rotate them. Also, is it possible to change the point the atoms rotate around? The kind of thing I want to do is rotate a group around the atom it is attached to. Thanks again, Chris. Robert Hanson wrote: It's in there, at least for Jmol 11.7. See http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm 30. selective atom rotation and translation # Using set dragSelected in Jmol 11.7.25 you can move selected atoms around, translating them with ALT-SHIFT-LEFT mouse and rotating them around their geometric center using ALT-LEFT or CTRL-ALT-RIGHT. Selection halos are automatically turned on during mouse-drag actions. (Still a few bugs there) load caffeine.xyz;load append water.xyz;frame 0;select 2.1;selectionHalos on set dragSelected !dragSelected On Wed, Apr 29, 2009 at 9:16 AM, Chris Foley christopher.fo...@strath.ac.uk wrote: Hi Jmol users, I would like to be rotate the selected atoms with the mouse. The rotateSelected command is almost perfect... but only works via scripting, not mouse interaction. The allowrotateselected = true setting is also close but rotates the entire molecule, not just the selected atoms. I was wondering (hoping) if I've missed something that would let me set this up quickly and easily. If not, no worries. I can write a small Java application that will do the job. Cheers, Chris Foley. -- Register Now Save for Velocity, the Web Performance Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- Register Now Save for Velocity, the Web Performance Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- Register Now Save for Velocity, the Web Performance Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Rotate selected atoms with the mouse
I'm afraid not. It appeared to work when the water molecule was selected. But all the atoms of HOH were selected. When I tried selecting a methyl group (select c13,h16,h17,h18) the whole caffeine molecule was rotated. In case it helps, I used Windows XP, Sun Java plugin 1.6.0_13 on Internet Explorer. Cheers, Chris. Robert Hanson wrote: Did it work at http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm # 30? On Thu, Apr 30, 2009 at 5:54 AM, Chris Foley christopher.fo...@strath.ac.uk wrote: Thanks for the reply Robert. I downloaded 11.7.33 but unfortunately I can't get the rotation to work. I can translate the atoms as you describe but can't rotate them. Also, is it possible to change the point the atoms rotate around? The kind of thing I want to do is rotate a group around the atom it is attached to. Thanks again, Chris. Robert Hanson wrote: It's in there, at least for Jmol 11.7. See http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm 30. selective atom rotation and translation # Using set dragSelected in Jmol 11.7.25 you can move selected atoms around, translating them with ALT-SHIFT-LEFT mouse and rotating them around their geometric center using ALT-LEFT or CTRL-ALT-RIGHT. Selection halos are automatically turned on during mouse-drag actions. (Still a few bugs there) load caffeine.xyz;load append water.xyz;frame 0;select 2.1;selectionHalos on set dragSelected !dragSelected On Wed, Apr 29, 2009 at 9:16 AM, Chris Foley christopher.fo...@strath.ac.uk wrote: Hi Jmol users, I would like to be rotate the selected atoms with the mouse. The rotateSelected command is almost perfect... but only works via scripting, not mouse interaction. The "allowrotateselected = true" setting is also close but rotates the entire molecule, not just the selected atoms. I was wondering (hoping) if I've missed something that would let me set this up quickly and easily. If not, no worries. I can write a small Java application that will do the job. Cheers, Chris Foley. -- Register Now Save for Velocity, the Web Performance Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- Register Now Save for Velocity, the Web Performance Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- Register Now Save for Velocity, the Web Performance Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Rotate selected atoms with the mouse
ah, ok. I see. Hard to believe this is going to be useful, considering the degrees of freedom. How do you figure it will be used? On Thu, Apr 30, 2009 at 9:26 AM, Chris Foley christopher.fo...@strath.ac.uk wrote: I'm afraid not. It appeared to work when the water molecule was selected. But all the atoms of HOH were selected. When I tried selecting a methyl group (select c13,h16,h17,h18) the whole caffeine molecule was rotated. In case it helps, I used Windows XP, Sun Java plugin 1.6.0_13 on Internet Explorer. Cheers, Chris. Robert Hanson wrote: Did it work at http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm # 30? On Thu, Apr 30, 2009 at 5:54 AM, Chris Foley christopher.fo...@strath.ac.uk wrote: Thanks for the reply Robert. I downloaded 11.7.33 but unfortunately I can't get the rotation to work. I can translate the atoms as you describe but can't rotate them. Also, is it possible to change the point the atoms rotate around? The kind of thing I want to do is rotate a group around the atom it is attached to. Thanks again, Chris. Robert Hanson wrote: It's in there, at least for Jmol 11.7. See http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm 30. selective atom rotation and translation # Using set dragSelected in Jmol 11.7.25 you can move selected atoms around, translating them with ALT-SHIFT-LEFT mouse and rotating them around their geometric center using ALT-LEFT or CTRL-ALT-RIGHT. Selection halos are automatically turned on during mouse-drag actions. (Still a few bugs there) load caffeine.xyz;load append water.xyz;frame 0;select 2.1;selectionHalos on set dragSelected !dragSelected On Wed, Apr 29, 2009 at 9:16 AM, Chris Foley christopher.fo...@strath.ac.uk wrote: Hi Jmol users, I would like to be rotate the selected atoms with the mouse. The rotateSelected command is almost perfect... but only works via scripting, not mouse interaction. The allowrotateselected = true setting is also close but rotates the entire molecule, not just the selected atoms. I was wondering (hoping) if I've missed something that would let me set this up quickly and easily. If not, no worries. I can write a small Java application that will do the job. Cheers, Chris Foley. -- Register Now Save for Velocity, the Web Performance Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- Register Now Save for Velocity, the Web Performance Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- Register Now Save for Velocity, the Web Performance Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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,
Re: [Jmol-users] Rotate selected atoms with the mouse
It's in there, at least for Jmol 11.7. See http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm 30. selective atom rotation and translation # Using set dragSelected in Jmol 11.7.25 you can move selected atoms around, translating them with ALT-SHIFT-LEFT mouse and rotating them around their geometric center using ALT-LEFT or CTRL-ALT-RIGHT. Selection halos are automatically turned on during mouse-drag actions. (Still a few bugs there) load caffeine.xyz;load append water.xyz;frame 0;select 2.1;selectionHalos on set dragSelected !dragSelected On Wed, Apr 29, 2009 at 9:16 AM, Chris Foley christopher.fo...@strath.ac.uk wrote: Hi Jmol users, I would like to be rotate the selected atoms with the mouse. The rotateSelected command is almost perfect... but only works via scripting, not mouse interaction. The allowrotateselected = true setting is also close but rotates the entire molecule, not just the selected atoms. I was wondering (hoping) if I've missed something that would let me set this up quickly and easily. If not, no worries. I can write a small Java application that will do the job. Cheers, Chris Foley. -- Register Now Save for Velocity, the Web Performance Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- Register Now Save for Velocity, the Web Performance Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
