Re: [PyMOL] reorienting a chain

[Warren DeLano]

Vivek,
 
Please see the example I posted today for Sean Law -- the cmd.matrix_copy 
command embedded therein (followed by "reset") performs exactly the action 
you're looking for.
 
Cheers,
Warren



From: Vivek Ranjan [mailto:vran...@gmail.com]
Sent: Wed 6/3/2009 9:26 AM
To: Warren DeLano
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] reorienting a chain



Hello Warren,

Thank you very much for your advice.

I guess I was not being very clear. what i meant was that i would also
like to save the coordinates of this reoriented polymer. Let me be
clear:

I have a polymer aligned along y-axis. I change some of the dihedral
angles. As a result, the chain is pointing in some arbitrary
direction. So, I want to re-orient the polymer along the y-axis and
then save the coordinates of this reoriented polymer. I used the
command "orient" from the installed pymol on my system (version
1.0r2). But when I try to save the polymer, it still saves the same
coordinates as the one before reorientation.

Please let me know if something can be done ?

Thank you,

Vivek

On Tue, Jun 2, 2009 at 8:50 PM, Warren DeLano  wrote:
> You can save a copy of the original and then superimpose the copy back onto
> it
>
> # using "fab" command from the latest 1.2 beta to create poly-ala
>
> fab  AAA, pol
>
> # create copy of the polymer
>
> create copy, pol
>
> # adjust a torsion
>
> set_dihedral pol///4/N, pol///4/CA, pol///4/C, pol///5/N, 60
>
> # superimpose back on the original copy
>
> fit pol, copy
>
> Cheers,
> Warren
>
> 
> From: Vivek Ranjan [mailto:vran...@gmail.com]
> Sent: Tue 6/2/2009 10:57 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] reorienting a chain
>
> Hello,
>
> I have a long chain of polymer. Once I change some dihedral angles, it
> orients in a different direction. I would like the chain to be
> reoriented in the same direction as it initially was. Is it possible
> within pymol ? How can I achieve this ?
>
> --
> Thank you and Regards,
>
> Vivek Ranjan
>
> --
> OpenSolaris 2009.06 is a cutting edge operating system for enterprises
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>
>
>



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Thank you and Regards,

Vivek Ranjan

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[PyMOL] Distinct labels on white background (ray tracing)?

[Jim Remington]

I would like to have distinct labels for hydrogen bond lengths on a 
ball-and-stick image
with white background (as required for publication in a particular 
journal). No matter
what I do, the labels come out washed out and usually light grey. This 
includes
experimenting with label color, size and font (is there a bold font?).

For the record, I've tried the clues in the wiki and forum, for example 
I've turned off
ray-trace-fog, depth cueing, ray-shadowing and very high resolution images.
I still get light grey labels on white background. Does anyone have 
further suggestions?

Thanks much, Jim

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Re: [PyMOL] Principal Axes of Rotation

[Sean Law]

Great!  I'll give that a try.

Sean

Subject: RE: [PyMOL] Principal Axes of Rotation
Date: Wed, 3 Jun 2009 12:55:51 -0700
From: war...@delsci.com
To: magic...@hotmail.com; matthew.frank...@imclone.com
CC: pymol-users@lists.sourceforge.net










Sean,
 
Apologies for not 
understanding...
 
You definitely need orthoscopic, but 
there's more to it. 
 

set orthoscopic
 
fetch 1bna, async=0
 
orient 1bna
 
cmd.matrix_copy(None,"1bna")
 
reset
 
from chempy.cpv import average
 
cmd.origin(position=average(*cmd.get_extent()))

 
center origin
 
# now, the maximum extent in the X Y planes 
should be invariant to 180 degree rotations about the Y or X axes 
respectively.
 
Cheers,
Warren
 
 
 



From: Sean Law 
[mailto:magic...@hotmail.com]
Sent: Wed 6/3/2009 12:28 
PM
To: matthew.frank...@imclone.com
Cc: 
pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Principal Axes 
of Rotation


Matt,

Unfortunately, as a somewhat 
experienced PyMOL user, I already have "orthoscopic view" turned off (along 
with 
depth cue turned off).  Thanks for your suggestion 
though.

Sean

> Subject: Re: [PyMOL] Principal Axes of 
Rotation
> To: magic...@hotmail.com
> CC: 
pymol-users@lists.sourceforge.net
> From: 
matthew.frank...@imclone.com
> Date: Wed, 3 Jun 2009 15:13:25 
-0400
> 
> 
> 
> Sean Law  
wrote on 06/03/2009 12:52:45 PM:
> 
> > Warren,
> 
>
> > After a deja vu moment, I realized that I had posed a 
similar
> > question to you before about this (although, we didn't 
really have a
> > resolution then). I had already tried your suggestion 
before I had
> > posted to the mailing list but perhaps an example 
would be more
> > appropriate in terms of what I'm seeing.
> 
>
> 
> (snip - 180 degree rotation around x axis)
> 

> > 7) You will now see that after 2 turns that the O3' atom is 
situated
> > well past the vertical (imaginary) line drawn by the 
position of
> > your cursor on your screen
> >
> 

> This is almost certainly due to the "perspective" view which is on 
by
> default. As atoms move closer to your viewpoint, they appear bigger, 
and
> the inter-atomic distances also appear bigger, just as in real life. 
So,
> an atom which is far away and at a particular (apparent) x position, 
will
> be farther away from the center of the screen once you've done your 
180
> degree rotation.
> 
> This drawing mode was created to 
make structures look more realistic. If
> you don't like it, you can turn 
it off: under "Display", choose
> "Orthoscopic view". That should 
eliminate your "wobble effect".
> 
> 
> Hope that 
helps,
> 
> Matt
> 
> --
> Matthew Franklin , 
Ph.D.
> Senior Scientist, ImClone Systems,
> a wholly owned 
subsidiary of Eli Lilly & Company
> 180 Varick Street, 6th 
floor
> New York, NY 10014
> phone:(917)606-4116 
fax:(212)645-2054
> 
> 
> Confidentiality Note: This e-mail, 
and any attachment to it, contains
> privileged and confidential 
information intended only for the use of the
> individual(s) or entity 
named on the e-mail. If the reader of this e-mail
> is not the intended 
recipient, or the employee or agent responsible for
> delivering it to the 
intended recipient, you are hereby notified that
> reading it is strictly 
prohibited. If you have received this e-mail in
> error, please 
immediately return it to the sender and delete it from your
> system. 
Thank you.
> 



Attention all humans. We are your photos. Free us.
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Re: [PyMOL] Principal Axes of Rotation

[Warren DeLano]

Sean,
 
Apologies for not understanding...
 
You definitely need orthoscopic, but there's more to it. 
 
set orthoscopic
 
fetch 1bna, async=0
 
orient 1bna
 
cmd.matrix_copy(None,"1bna")
 
reset
 
from chempy.cpv import average
 
cmd.origin(position=average(*cmd.get_extent()))

 
center origin
 
# now, the maximum extent in the X Y planes should be invariant to 180 degree 
rotations about the Y or X axes respectively.
 
Cheers,
Warren
 
 
 



From: Sean Law [mailto:magic...@hotmail.com]
Sent: Wed 6/3/2009 12:28 PM
To: matthew.frank...@imclone.com
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Principal Axes of Rotation


Matt,

Unfortunately, as a somewhat experienced PyMOL user, I already have 
"orthoscopic view" turned off (along with depth cue turned off).  Thanks for 
your suggestion though.

Sean

> Subject: Re: [PyMOL] Principal Axes of Rotation
> To: magic...@hotmail.com
> CC: pymol-users@lists.sourceforge.net
> From: matthew.frank...@imclone.com
> Date: Wed, 3 Jun 2009 15:13:25 -0400
> 
> 
> 
> Sean Law  wrote on 06/03/2009 12:52:45 PM:
> 
> > Warren,
> >
> > After a deja vu moment, I realized that I had posed a similar
> > question to you before about this (although, we didn't really have a
> > resolution then). I had already tried your suggestion before I had
> > posted to the mailing list but perhaps an example would be more
> > appropriate in terms of what I'm seeing.
> >
> 
> (snip - 180 degree rotation around x axis)
> 
> > 7) You will now see that after 2 turns that the O3' atom is situated
> > well past the vertical (imaginary) line drawn by the position of
> > your cursor on your screen
> >
> 
> This is almost certainly due to the "perspective" view which is on by
> default. As atoms move closer to your viewpoint, they appear bigger, and
> the inter-atomic distances also appear bigger, just as in real life. So,
> an atom which is far away and at a particular (apparent) x position, will
> be farther away from the center of the screen once you've done your 180
> degree rotation.
> 
> This drawing mode was created to make structures look more realistic. If
> you don't like it, you can turn it off: under "Display", choose
> "Orthoscopic view". That should eliminate your "wobble effect".
> 
> 
> Hope that helps,
> 
> Matt
> 
> --
> Matthew Franklin , Ph.D.
> Senior Scientist, ImClone Systems,
> a wholly owned subsidiary of Eli Lilly & Company
> 180 Varick Street, 6th floor
> New York, NY 10014
> phone:(917)606-4116 fax:(212)645-2054
> 
> 
> Confidentiality Note: This e-mail, and any attachment to it, contains
> privileged and confidential information intended only for the use of the
> individual(s) or entity named on the e-mail. If the reader of this e-mail
> is not the intended recipient, or the employee or agent responsible for
> delivering it to the intended recipient, you are hereby notified that
> reading it is strictly prohibited. If you have received this e-mail in
> error, please immediately return it to the sender and delete it from your
> system. Thank you.
> 




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Re: [PyMOL] Principal Axes of Rotation

[Matthew . Franklin]

Sean Law  wrote on 06/03/2009 12:52:45 PM:

> Warren,
>
> After a deja vu moment, I realized that I had posed a similar
> question to you before about this (although, we didn't really have a
> resolution then).  I had already tried your suggestion before I had
> posted to the mailing list but perhaps an example would be more
> appropriate in terms of what I'm seeing.
>

(snip - 180 degree rotation around x axis)

> 7) You will now see that after 2 turns that the O3' atom is situated
> well past the vertical (imaginary) line drawn by the position of
> your cursor on your screen
>

This is almost certainly due to the "perspective" view which is on by
default.  As atoms move closer to your viewpoint, they appear bigger, and
the inter-atomic distances also appear bigger, just as in real life.  So,
an atom which is far away and at a particular (apparent) x position, will
be farther away from the center of the screen once you've done your 180
degree rotation.

This drawing mode was created to make structures look more realistic.  If
you don't like it, you can turn it off: under "Display", choose
"Orthoscopic view".  That should eliminate your "wobble effect".


Hope that helps,

Matt

--
Matthew Franklin , Ph.D.
Senior Scientist, ImClone Systems,
a wholly owned subsidiary of Eli Lilly & Company
180 Varick Street, 6th floor
New York, NY 10014
phone:(917)606-4116   fax:(212)645-2054


Confidentiality Note:  This e-mail, and any attachment to it, contains
privileged and confidential information intended only for the use of the
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is not the intended recipient, or the employee or agent responsible for
delivering it to the intended recipient, you are hereby notified that
reading it is strictly prohibited.  If you have received this e-mail in
error, please immediately return it to the sender and delete it from your
system.  Thank you.


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Re: [PyMOL] Principal Axes of Rotation

[Sean Law]

Matt,

Unfortunately, as a somewhat experienced PyMOL user, I already have 
"orthoscopic view" turned off (along with depth cue turned off).  Thanks for 
your suggestion though.

Sean

> Subject: Re: [PyMOL] Principal Axes of Rotation
> To: magic...@hotmail.com
> CC: pymol-users@lists.sourceforge.net
> From: matthew.frank...@imclone.com
> Date: Wed, 3 Jun 2009 15:13:25 -0400
> 
> 
> 
> Sean Law  wrote on 06/03/2009 12:52:45 PM:
> 
> > Warren,
> >
> > After a deja vu moment, I realized that I had posed a similar
> > question to you before about this (although, we didn't really have a
> > resolution then).  I had already tried your suggestion before I had
> > posted to the mailing list but perhaps an example would be more
> > appropriate in terms of what I'm seeing.
> >
> 
> (snip - 180 degree rotation around x axis)
> 
> > 7) You will now see that after 2 turns that the O3' atom is situated
> > well past the vertical (imaginary) line drawn by the position of
> > your cursor on your screen
> >
> 
> This is almost certainly due to the "perspective" view which is on by
> default.  As atoms move closer to your viewpoint, they appear bigger, and
> the inter-atomic distances also appear bigger, just as in real life.  So,
> an atom which is far away and at a particular (apparent) x position, will
> be farther away from the center of the screen once you've done your 180
> degree rotation.
> 
> This drawing mode was created to make structures look more realistic.  If
> you don't like it, you can turn it off: under "Display", choose
> "Orthoscopic view".  That should eliminate your "wobble effect".
> 
> 
> Hope that helps,
> 
> Matt
> 
> --
> Matthew Franklin , Ph.D.
> Senior Scientist, ImClone Systems,
> a wholly owned subsidiary of Eli Lilly & Company
> 180 Varick Street, 6th floor
> New York, NY 10014
> phone:(917)606-4116   fax:(212)645-2054
> 
> 
> Confidentiality Note:  This e-mail, and any attachment to it, contains
> privileged and confidential information intended only for the use of the
> individual(s) or entity named on the e-mail.  If the reader of this e-mail
> is not the intended recipient, or the employee or agent responsible for
> delivering it to the intended recipient, you are hereby notified that
> reading it is strictly prohibited.  If you have received this e-mail in
> error, please immediately return it to the sender and delete it from your
> system.  Thank you.
> 

_
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Re: [PyMOL] Principal Axes of Rotation

[Sean Law]

Warren,

After a deja vu moment, I realized that I had posed a similar question to you 
before about this (although, we didn't really have a resolution then).  I had 
already tried your suggestion before I had posted to the mailing list but 
perhaps an example would be more appropriate in terms of what I'm seeing.

1) Run PyMOL
2) $ fetch 1bna
3) $ orient 1bna 
We will call this "View 1"
4) place your mouse/cursor on the rightmost atom shown in order mark the 
position on the screen and leave your cursor there
(I have the Chain B, Residue 24, Guanine, O3' atom as my rightmost atom.  That 
is, there are no atoms located to right of your cursor.)
5) $ turn x, 90
6) $ turn x, 90
We will call this "View 2"
7) You will now see that after 2 turns that the O3' atom is situated well past 
the vertical (imaginary) line drawn by the position of your cursor on your 
screen

This is what I'm referring to as the "wobble" effect.  Instead, what I want is 
for the rightmost (AND leftmost) points to reside along the same vertical line 
when rotating around the X-axis (and, I guess, for the topmost and bottommost 
point to reside along the same horizontal line when rotating around the 
Y-axis).  The problem with the image generated by following the steps above is 
that one would assume that flipping 180 degrees from View 1 to View 2 about the 
X-axis should not change the location of the left and rightmost points on your 
display screen but it does.  For publication purposes, this is not clean.  If I 
place View 1 and View 2 on top of each other then you will see that one sits 
further right or further left than the other which is not desirable if your 
caption says "a 180 degree rotation".  A 180 degree rotation would show BOTH 
aligned exactly.  However, it is not entirely clear how I would achieve this 
(but I am still thinking about it).

I'd be happy to clarify any points if needed.

Thanks.

Sean

> From: pymol-users-requ...@lists.sourceforge.net
> Subject: PyMOL-users Digest, Vol 37, Issue 2
> To: pymol-users@lists.sourceforge.net
> Date: Wed, 3 Jun 2009 16:23:22 +
> 
> Send PyMOL-users mailing list submissions to
>   pymol-users@lists.sourceforge.net
> 
> To subscribe or unsubscribe via the World Wide Web, visit
>   https://lists.sourceforge.net/lists/listinfo/pymol-users
> or, via email, send a message with subject or body 'help' to
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> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of PyMOL-users digest..."
> 
> 
> Today's Topics:
> 
>1. Re: wrl and dx files problem (Warren DeLano)
>2. Re: Principal Axes of Rotation (gilleain torrance)
>3. Re: Principal Axes of Rotation (Warren DeLano)
>4. get color function? (Matthew O'Meara)
>5. Re: reorienting a chain (Vivek Ranjan)
> 
> 
> --
> 
> Message: 1
> Date: Tue, 2 Jun 2009 18:24:34 -0700
> From: "Warren DeLano" 
> Subject: Re: [PyMOL] wrl and dx files problem
> To: "Raluca Mihaela ANDREI" ,"pymol-users"
>   
> Message-ID:
>   <896b75251ba19745a529b1b867893fa50bd...@planet.delsci.local>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Raluca,
>  
> PyMOL transforms the output geometry in order to deliver a default view 
> matching what's seen in the viewer window.  To prevent that, you'll need to 
> effectively eliminate PyMOL's camera transformation by restoring to a 
> transformation-less identity matrix:
>  
> cmd.reset()
> cmd.origin(position=[0,0,0])
> cmd.center("origin")
> cmd.move('z',-cmd.get_view()[11])
>  
> At this point, there may not be anything visible in the viewer window, but 
> the output WRL file will have the same coordinate system as the input PDB, DX 
> map, etc.
>  
> Cheers,
> Warren
>  
> 
> 
> 
> From: Raluca Mihaela ANDREI [mailto:r.and...@sns.it]
> Sent: Fri 5/22/2009 10:51 AM
> To: pymol-users
> Subject: [PyMOL] wrl and dx files problem
> 
> 
> 
> 
> Hello!
> I save the surface of a protein as a .wrl, then I calculate
> the electrostatic potential and I save again the surface of
> the protein. I import the two surfaces in Blender (a 3D
> software) and I see that they are shifted. Why does this
> happen? Then I open the .wrl files and the .dx file in another
> home made program and I see that the surfaces and the grid
> have not the same origin. Can somebody tell me why the surface
> and the grid don't have the same origin and what do I have to
> do in order to fix this?
> 
> Thank you,
> Raluca
> 
> --
> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
> is a gathering of tech-side developers & brand creativity professionals. Meet
> the minds behind Google Creative Lab, Visual Complexity, Processing, &
> i

Re: [PyMOL] get color function?

[Pete Meyer]

The way I use (which I'm sure could be improved), is to get the color
index with "iterate sele, print color", followed by "print
cmd.get_color_index( idx )".  This gives you the rgb tuple for the color
 on 0-1 scale.

I'd be curious to know if there's a way to avoid the iterate step, or
get the color name (instead of index or rgb values), but haven't had the
time to dig into it.

Pete

Matthew O'Meara wrote:
> Hi
> Is there a way I can get the color of a given atom?
> 
> eg if I do
> 
> cmd.color( color, sele )
> 
> is there a function like
> 
>gotten_color = cmd.get_color_of_selection( sele )
> 
> so that something like
> 
>assert( gotten_color == color )
> 
> 
> 
> or atleast a function to get the color a given atom?
> 
> 
> Many thanks,
> Matt
> 
> 
> 
> 
> 
> --
> OpenSolaris 2009.06 is a cutting edge operating system for enterprises 
> looking to deploy the next generation of Solaris that includes the latest 
> innovations from Sun and the OpenSource community. Download a copy and 
> enjoy capabilities such as Networking, Storage and Virtualization. 
> Go to: http://p.sf.net/sfu/opensolaris-get
> 
> 
> 
> 
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Re: [PyMOL] reorienting a chain

[Vivek Ranjan]

Hello Warren,

Thank you very much for your advice.

I guess I was not being very clear. what i meant was that i would also
like to save the coordinates of this reoriented polymer. Let me be
clear:

I have a polymer aligned along y-axis. I change some of the dihedral
angles. As a result, the chain is pointing in some arbitrary
direction. So, I want to re-orient the polymer along the y-axis and
then save the coordinates of this reoriented polymer. I used the
command "orient" from the installed pymol on my system (version
1.0r2). But when I try to save the polymer, it still saves the same
coordinates as the one before reorientation.

Please let me know if something can be done ?

Thank you,

Vivek

On Tue, Jun 2, 2009 at 8:50 PM, Warren DeLano  wrote:
> You can save a copy of the original and then superimpose the copy back onto
> it
>
> # using "fab" command from the latest 1.2 beta to create poly-ala
>
> fab  AAA, pol
>
> # create copy of the polymer
>
> create copy, pol
>
> # adjust a torsion
>
> set_dihedral pol///4/N, pol///4/CA, pol///4/C, pol///5/N, 60
>
> # superimpose back on the original copy
>
> fit pol, copy
>
> Cheers,
> Warren
>
> 
> From: Vivek Ranjan [mailto:vran...@gmail.com]
> Sent: Tue 6/2/2009 10:57 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] reorienting a chain
>
> Hello,
>
> I have a long chain of polymer. Once I change some dihedral angles, it
> orients in a different direction. I would like the chain to be
> reoriented in the same direction as it initially was. Is it possible
> within pymol ? How can I achieve this ?
>
> --
> Thank you and Regards,
>
> Vivek Ranjan
>
> --
> OpenSolaris 2009.06 is a cutting edge operating system for enterprises
> looking to deploy the next generation of Solaris that includes the latest
> innovations from Sun and the OpenSource community. Download a copy and
> enjoy capabilities such as Networking, Storage and Virtualization.
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>
>
>
>



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Thank you and Regards,

Vivek Ranjan

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[PyMOL] get color function?

[Matthew O'Meara]

Hi
Is there a way I can get the color of a given atom?

eg if I do

cmd.color( color, sele )

is there a function like

   gotten_color = cmd.get_color_of_selection( sele )

so that something like

   assert( gotten_color == color )



or atleast a function to get the color a given atom?


Many thanks,
Matt
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Re: [PyMOL] Principal Axes of Rotation

[Warren DeLano]

Sean,
 
orient selection
 
followed by a 90 degree rotation about the camera's ]X-axis should give you a 
couple of views with the desired characteristics.
 
turn x, 90
 
Cheers,
Warren
 



From: gilleain torrance [mailto:gilleain.torra...@gmail.com]
Sent: Wed 6/3/2009 5:02 AM
To: pymol-users
Subject: Re: [PyMOL] Principal Axes of Rotation



Hi,

I might be wrong, but might it be that you need the axis through the
structure that minimises the distance of all the points to it. Or, to
put it another way, the least-square-plane through the structure, the
normal to that plane, and a thir axis perpendicular to both.

If this is the case, you are in luck, as I already made such a thing:

  http://pymolwiki.org/index.php/Bounding_Box

this script was designed to make a minimal bounding box (not just an
axis-aligned one). I think that it does this, although my geometry is
not good enough to know if I am right.

Anyway, you already mention joining opposite faces of the box - well
just use the axes calculated half-way through the first function.

Hope this helps.

gilleain

On Tue, Jun 2, 2009 at 11:41 PM, Sean Law  wrote:
> Hi,
>
> For the past couple of days I've been trying to find a way to rotate an
> object in order to show a front and side profile for publication.  However,
> rotating with respect to the x, y, or z axes does not produce the correct
> result (even after moving the center-of-mass of the structure to the
> origin).  What I need is a way to determine the principal axes of rotation
> for a given selection so that rotation about any one of these axes does not
> produce a "wobble" effect.  I've even tried drawing a rectangular box around
> the object and then drawing an axes through the centroids of opposing faces
> but I still see wobbling.  I've basically exhausted all of my attempts at
> this problem.
>
> Any help or suggestions would be greatly appreciated.
>
> Sean
>
> 
> Create a cool, new character for your Windows Live(tm) Messenger. Check it out
> --
> OpenSolaris 2009.06 is a cutting edge operating system for enterprises
> looking to deploy the next generation of Solaris that includes the latest
> innovations from Sun and the OpenSource community. Download a copy and
> enjoy capabilities such as Networking, Storage and Virtualization.
> Go to: http://p.sf.net/sfu/opensolaris-get
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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>

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Re: [PyMOL] Principal Axes of Rotation

[gilleain torrance]

Hi,

I might be wrong, but might it be that you need the axis through the
structure that minimises the distance of all the points to it. Or, to
put it another way, the least-square-plane through the structure, the
normal to that plane, and a thir axis perpendicular to both.

If this is the case, you are in luck, as I already made such a thing:

  http://pymolwiki.org/index.php/Bounding_Box

this script was designed to make a minimal bounding box (not just an
axis-aligned one). I think that it does this, although my geometry is
not good enough to know if I am right.

Anyway, you already mention joining opposite faces of the box - well
just use the axes calculated half-way through the first function.

Hope this helps.

gilleain

On Tue, Jun 2, 2009 at 11:41 PM, Sean Law  wrote:
> Hi,
>
> For the past couple of days I've been trying to find a way to rotate an
> object in order to show a front and side profile for publication.  However,
> rotating with respect to the x, y, or z axes does not produce the correct
> result (even after moving the center-of-mass of the structure to the
> origin).  What I need is a way to determine the principal axes of rotation
> for a given selection so that rotation about any one of these axes does not
> produce a "wobble" effect.  I've even tried drawing a rectangular box around
> the object and then drawing an axes through the centroids of opposing faces
> but I still see wobbling.  I've basically exhausted all of my attempts at
> this problem.
>
> Any help or suggestions would be greatly appreciated.
>
> Sean
>
> 
> Create a cool, new character for your Windows Live™ Messenger. Check it out
> --
> OpenSolaris 2009.06 is a cutting edge operating system for enterprises
> looking to deploy the next generation of Solaris that includes the latest
> innovations from Sun and the OpenSource community. Download a copy and
> enjoy capabilities such as Networking, Storage and Virtualization.
> Go to: http://p.sf.net/sfu/opensolaris-get
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>

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