Restoring view to normal axes orientation?

General Discussion
1

People,

Is there a quick way to restore the view to the standard axes
orientation? ie:

Y
^
|
|
(Z)------> X

  • I can’t find it if there is (I have Googled).

Thanks,

Phil.

Philip Rhoades

GPO Box 3411
Sydney NSW 2001
Australia
E-mail: phil@pricom.com.au

2

Hi Phil,

I don’t know if this is exactly what you want, but did you try the Center command under the View menu?

Steve

Dr. Steven P. Wathen
Associate Professor of Chemistry
Siena Heights University
1247 East Siena Heights Drive
Adrian, MI 49221

(517) 264-7657
swathen@sienaheights.edu

From: Philip Rhoades [phil@pricom.com.au]
Sent: Monday, August 02, 2010 8:22 PM
To: avogadro-discuss@lists.sourceforge.net
Subject: [Avogadro-Discuss] Restoring view to normal axes orientation?

People,

Is there a quick way to restore the view to the standard axes
orientation? ie:

Y
^
|
|
(Z)------> X

  • I can’t find it if there is (I have Googled).

Thanks,

Phil.

Philip Rhoades

GPO Box 3411
Sydney NSW 2001
Australia
E-mail: phil@pricom.com.au

The Palm PDK Hot Apps Program offers developers who use the
Plug-In Development Kit to bring their C/C++ apps to Palm for a share
of $1 Million in cash or HP Products. Visit us here for more details:
http://p.sf.net/sfu/dev2dev-palm

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https://lists.sourceforge.net/lists/listinfo/avogadro-discuss

3

Steve,

Yes, I did try that - it seems to center the molecule but does nothing
to the orientation of the axes eg I have adenine displayed and the axes are:

Z
^
|
|
(X)------> Y

and these do not change if I click “Center”

thanks,

Phil.

On 2010-08-03 11:12, Steven Wathen wrote:

Hi Phil,

I don’t know if this is exactly what you want, but did you try the
Center command under the View menu?

Steve ------------- Dr. Steven P. Wathen Associate Professor of
Chemistry Siena Heights University 1247 East Siena Heights Drive
Adrian, MI 49221

(517) 264-7657 swathen@sienaheights.edu
________________________________________ From: Philip Rhoades
[phil@pricom.com.au] Sent: Monday, August 02, 2010 8:22 PM To:
avogadro-discuss@lists.sourceforge.net Subject: [Avogadro-Discuss]
Restoring view to normal axes orientation?

People,

Is there a quick way to restore the view to the standard axes
orientation? ie:

Y ^ | | (Z)------> X

  • I can’t find it if there is (I have Googled).

Thanks,

Phil. – Philip Rhoades

GPO Box 3411 Sydney NSW 2001 Australia E-mail:
phil@pricom.com.au

The Palm PDK Hot Apps Program offers developers who use the

Plug-In Development Kit to bring their C/C++ apps to Palm for a
share of $1 Million in cash or HP Products. Visit us here for more
details: http://p.sf.net/sfu/dev2dev-palm
_______________________________________________ Avogadro-Discuss
mailing list Avogadro-Discuss@lists.sourceforge.net
avogadro-discuss List Signup and Options

–
Philip Rhoades

GPO Box 3411
Sydney NSW 2001
Australia
E-mail: phil@pricom.com.au

4

Is there a quick way to restore the view to the standard axes
orientation? ie:
…

There are two things which I think are mixed into your question:

  1. The camera (i.e., how the window looks at the molecule)
  2. The coordinate system of the molecule

As Steven mentioned, “Center” will restore the view to the “standard” camera view. This is a projection which maximizes the 2D plane to the screen.

You seem to ask about the axes, which show the coordinate system of the molecule. I’m not quite sure what you might want as a “standard” orientation. Can you be a bit more specific?

-Geoff

5

Geoff,

Is there a quick way to restore the view to the standard axes
orientation? ie:
…

There are two things which I think are mixed into your question:

  1. The camera (i.e., how the window looks at the molecule)
  2. The coordinate system of the molecule

As Steven mentioned, “Center” will restore the view to the “standard”
camera view. This is a projection which maximizes the 2D plane to the
screen.

OK - that clarifies something but doesn’t help doing what I want to do.

You seem to ask about the axes, which show the coordinate system of the
molecule. I’m not quite sure what you might want as a “standard”
orientation. Can you be a bit more specific?

If you create a molecule from scratch the axes look like this:

Y
^
|
|
|
(Z)------> X

After rotating and playing around with the molecule, the axes move to some
other position. I just want a quick way of returning to the original view
with the axes as above.

Is that clear? Maybe I am still misunderstanding something?

Thanks,

Phil.

Philip Rhoades

Pricom Pty Limited (ACN 003 252 275 ABN 91 003 252 275)
GPO Box 3411
Sydney NSW 2001
Australia
E-mail: phil@pricom.com.au

6

View → Center does that. If you are working with a unit cell it wont do it
until you make several cells.

Claudiu Bucur, PhD
USDA-NCAUR
850-566-1562

http://www.linkedin.com/in/claudiubucur

On Tue, Aug 3, 2010 at 10:21 PM, Philip Rhoades phil@pricom.com.au wrote:

Geoff,

Is there a quick way to restore the view to the standard axes
orientation? ie:
…

There are two things which I think are mixed into your question:

  1. The camera (i.e., how the window looks at the molecule)
  2. The coordinate system of the molecule

As Steven mentioned, “Center” will restore the view to the “standard”
camera view. This is a projection which maximizes the 2D plane to the
screen.

OK - that clarifies something but doesn’t help doing what I want to do.

You seem to ask about the axes, which show the coordinate system of the
molecule. I’m not quite sure what you might want as a “standard”
orientation. Can you be a bit more specific?

If you create a molecule from scratch the axes look like this:

Y
^
|
|
|
(Z)------> X

After rotating and playing around with the molecule, the axes move to some
other position. I just want a quick way of returning to the original view
with the axes as above.

Is that clear? Maybe I am still misunderstanding something?

Thanks,

Phil.

Philip Rhoades

Pricom Pty Limited (ACN 003 252 275 ABN 91 003 252 275)
GPO Box 3411
Sydney NSW 2001
Australia
E-mail: phil@pricom.com.au

The Palm PDK Hot Apps Program offers developers who use the
Plug-In Development Kit to bring their C/C++ apps to Palm for a share
of $1 Million in cash or HP Products. Visit us here for more details:
http://p.sf.net/sfu/dev2dev-palm

Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net
avogadro-discuss List Signup and Options

7

On Wed, 4 Aug 2010, Philip Rhoades wrote:

Geoff,

Is there a quick way to restore the view to the standard axes
orientation? ie:
…

There are two things which I think are mixed into your question:

  1. The camera (i.e., how the window looks at the molecule)
  2. The coordinate system of the molecule

As Steven mentioned, “Center” will restore the view to the “standard”
camera view. This is a projection which maximizes the 2D plane to the
screen.

OK - that clarifies something but doesn’t help doing what I want to do.

You seem to ask about the axes, which show the coordinate system of the
molecule. I’m not quite sure what you might want as a “standard”
orientation. Can you be a bit more specific?

If you create a molecule from scratch the axes look like this:

Y
^
|
|
|
(Z)------> X

After rotating and playing around with the molecule, the axes move to some
other position. I just want a quick way of returning to the original view
with the axes as above.

Is that clear? Maybe I am still misunderstanding something?

Thanks,

Phil.

Philip Rhoades

I agree with Philip. I think it would be useful to have a way of defining
certain views. One would be what Philip proposes. But there might be
others.

for example:

1st atom at center of coordinate system
2nd atom alog x axis
3rd atom on the X-Y plane

Or maybe a way of selecting 3 atoms and orienting the molecule the way
described before. I belive it can be very useful to have a way of
orienting molecules in case you need to compare similar molecules.

Maybe make shortcuts to get views perpendicular to XY, XZ or YZ planes, or
something like that.

In particular I find it a little baffling when I open Gaussian output
files of different runs on the same molecule, I never know how the
molecule is going to show up on the screen. Sometimes small changes in
geometry produce a completely different view of basically the same
molecular system. Maybe this is related to the way gaussian output files
are processed. In such cases a fast way to reorient the molecule could be
quite handy.

best regards
Kenneth

8

Claudiu,

On 2010-08-04 22:55, Claudiu Bucur wrote:

View → Center does that.

?? - not for me.

If you are working with a unit cell it wont do it until you make
several cells.

OK, a specific example:

I create a hexane molecule from scratch, optimize geometry and the axes
still look like this:

Y
^
|
|
|
(Z)------> X

I now rotate the molecule to an edge-on view of the ring - the axes have
also moved to reflect the new position of the hexane ring. Now,
clicking on the center button - does nothing at all - everything remains
exactly the same. I want to (preferably single click) return the view
to what it was before I rotated the ring so the axes are as above.

BTW, I am using: avogadro.x86_64 0:1.0.0-3.fc12

Regards,

Phil.

Philip Rhoades

GPO Box 3411
Sydney NSW 2001
Australia
E-mail: phil@pricom.com.au

9

Kenneth,

On 2010-08-04 23:00, Kenneth Irving wrote:

On Wed, 4 Aug 2010, Philip Rhoades wrote:

Geoff,

Is there a quick way to restore the view to the standard axes
orientation? ie:
…

There are two things which I think are mixed into your question:

  1. The camera (i.e., how the window looks at the molecule)
  2. The coordinate system of the molecule

As Steven mentioned, “Center” will restore the view to the “standard”
camera view. This is a projection which maximizes the 2D plane to the
screen.

OK - that clarifies something but doesn’t help doing what I want to do.

You seem to ask about the axes, which show the coordinate system of the
molecule. I’m not quite sure what you might want as a “standard”
orientation. Can you be a bit more specific?

If you create a molecule from scratch the axes look like this:

Y
^
|
|
|
(Z)------> X

After rotating and playing around with the molecule, the axes move to some
other position. I just want a quick way of returning to the original view
with the axes as above.

Is that clear? Maybe I am still misunderstanding something?

Thanks,

Phil.

Philip Rhoades

I agree with Philip. I think it would be useful to have a way of defining
certain views. One would be what Philip proposes. But there might be
others.

for example:

1st atom at center of coordinate system
2nd atom alog x axis
3rd atom on the X-Y plane

Yes, that is what I suggested in another post but for multiple molecules
so they could be lined up easily. I struggled trying to do this with
Avogadro but gave up. I then tried it in conjunction with packmol and
made more progress but it is still clumsy. I think you should able to do:

[
1st atom on x axis parallel
2nd atom on x axis parallel
3rd atom on X-Y plane
] * n times → click “align”

Or maybe a way of selecting 3 atoms and orienting the molecule the way
described before. I belive it can be very useful to have a way of
orienting molecules in case you need to compare similar molecules.

Exactly. I have just been trying to put the four DNA nucleotides in a
square - you would think it would be easy . .

Maybe make shortcuts to get views perpendicular to XY, XZ or YZ planes, or
something like that.

In particular I find it a little baffling when I open Gaussian output
files of different runs on the same molecule, I never know how the
molecule is going to show up on the screen. Sometimes small changes in
geometry produce a completely different view of basically the same
molecular system. Maybe this is related to the way gaussian output files
are processed. In such cases a fast way to reorient the molecule could be
quite handy.

I don’t know about gaussian output but when opening xyz files I would
prefer the view to correspond to the axes like:

Y
^
|
|
|
(Z)------> X

Regards,

Phil.

Philip Rhoades

GPO Box 3411
Sydney NSW 2001
Australia
E-mail: phil@pricom.com.au

10

On Thursday 05 August 2010 08:02:47 Philip Rhoades wrote:

Claudiu,

On 2010-08-04 22:55, Claudiu Bucur wrote:

View → Center does that.

?? - not for me.

If you are working with a unit cell it wont do it until you make
several cells.

OK, a specific example:

I create a hexane molecule from scratch, optimize geometry and the axes
still look like this:

Y
^

(Z)------> X

I now rotate the molecule to an edge-on view of the ring - the axes have
also moved to reflect the new position of the hexane ring. Now,
clicking on the center button - does nothing at all - everything remains
exactly the same. I want to (preferably single click) return the view
to what it was before I rotated the ring so the axes are as above.

BTW, I am using: avogadro.x86_64 0:1.0.0-3.fc12

This would be some new functionality in the navigation tool (or a new tool),
but I think it would be a great addition. It should not be too difficult to add,
if no one else gets to it I will see what I can do to get it in. I am very
busy right now with other things, and so can’t promise a time frame as
Avogadro development is all in my spare time at the moment.

Marcus

Marcus D. Hanwell, Ph.D.
R&D Engineer, Kitware Inc.
(518) 881-4937

11

Marcus,

On 2010-08-06 00:07, Marcus D. Hanwell wrote:

On Thursday 05 August 2010 08:02:47 Philip Rhoades wrote:

Claudiu,

On 2010-08-04 22:55, Claudiu Bucur wrote:

View → Center does that.

?? - not for me.

If you are working with a unit cell it wont do it until you make
several cells.

OK, a specific example:

I create a hexane molecule from scratch, optimize geometry and the axes
still look like this:

Y
^

(Z)------> X

I now rotate the molecule to an edge-on view of the ring - the axes have
also moved to reflect the new position of the hexane ring. Now,
clicking on the center button - does nothing at all - everything remains
exactly the same. I want to (preferably single click) return the view
to what it was before I rotated the ring so the axes are as above.

BTW, I am using: avogadro.x86_64 0:1.0.0-3.fc12

This would be some new functionality in the navigation tool (or a new tool),
but I think it would be a great addition. It should not be too difficult to add,
if no one else gets to it I will see what I can do to get it in. I am very
busy right now with other things, and so can’t promise a time frame as
Avogadro development is all in my spare time at the moment.

Would you be doing this in Python or C++?

Thanks,

Phil.

Philip Rhoades

GPO Box 3411
Sydney NSW 2001
Australia
E-mail: phil@pricom.com.au

12

Claudiu,

On my setup, yes View->Center does in fact turn the molecule so the
plane is in the plane of the screen but the axes now look like:

 X
^

/
/
/




>
Y

with the Z axis pointing away from the plane of the screen.

Thanks,

Phil.

On 2010-08-05 22:56, Claudiu Bucur wrote:

On avogadro version 1.0.1 i was able to use View → Center to “reset” a
hexane, optomized, molecule which i made sure to twirl around
beforehand. Maybe its a version issue.
Something else, clicking on the center button wont “Center” it, it will
just allow you to manipulate the molecule in a certain way described
over the cursor on hover. You actually have to go to View → Center from
the top.

Claudiu Bucur, PhD
USDA-NCAUR
850-566-1562
www.claudiubucur.com http://www.claudiubucur.com
Claudiu B. Bucur - Piersica | LinkedIn

On Thu, Aug 5, 2010 at 7:02 AM, Philip Rhoades <phil@pricom.com.au
mailto:phil@pricom.com.au> wrote:

Claudiu,


On 2010-08-04 22:55, Claudiu Bucur wrote:

    View --> Center does that.



?? - not for me.



    If you are working with a unit cell it wont do it until you make
    several cells.



OK, a specific example:

I create a hexane molecule from scratch, optimize geometry and the axes
still look like this:

Y
^
|
|
|
(Z)------> X


I now rotate the molecule to an edge-on view of the ring - the axes have
also moved to reflect the new position of the hexane ring.  Now,
clicking on the center button - does nothing at all - everything remains
exactly the same.  I want to (preferably single click) return the
view to what it was before I rotated the ring so the axes are as above.

BTW, I am using: avogadro.x86_64 0:1.0.0-3.fc12

Regards,

Phil.
--
Philip Rhoades


GPO Box 3411
Sydney NSW      2001
Australia
E-mail: phil@pricom.com.au <mailto:phil@pricom.com.au>

–
Philip Rhoades

GPO Box 3411
Sydney NSW 2001
Australia
E-mail: phil@pricom.com.au