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 +0000
>
> Send PyMOL-users mailing list submissions to
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>
> 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" <war...@delsci.com>
> Subject: Re: [PyMOL] wrl and dx files problem
> To: "Raluca Mihaela ANDREI" <r.and...@sns.it>, "pymol-users"
> <pymol-users@lists.sourceforge.net>
> 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
>
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>
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> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 2
> Date: Wed, 3 Jun 2009 11:01:59 +0100
> From: gilleain torrance <gilleain.torra...@gmail.com>
> Subject: Re: [PyMOL] Principal Axes of Rotation
> To: pymol-users <pymol-users@lists.sourceforge.net>
> Message-ID:
> <d0d153660906030301k2467519m2b742192248fa...@mail.gmail.com>
> Content-Type: text/plain; charset=windows-1252
>
> 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 <magic...@hotmail.com> 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
> >
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 3 Jun 2009 06:05:26 -0700
> From: "Warren DeLano" <war...@delsci.com>
> Subject: Re: [PyMOL] Principal Axes of Rotation
> To: "gilleain torrance" <gilleain.torra...@gmail.com>, "pymol-users"
> <pymol-users@lists.sourceforge.net>
> Message-ID:
> <896b75251ba19745a529b1b867893fa50bd...@planet.delsci.local>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 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 <magic...@hotmail.com> 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
> > _______________________________________________
> > 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
> >
>
> ------------------------------------------------------------------------------
> 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
>
>
>
>
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 4
> Date: Wed, 3 Jun 2009 11:04:37 -0400
> From: "Matthew O'Meara" <mattjome...@gmail.com>
> Subject: [PyMOL] get color function?
> To: pymol-users@lists.sourceforge.net
> Message-ID:
> <e8e2f1300906030804l496ef03dl2e1f2fd5c6273...@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 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
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 5
> Date: Wed, 3 Jun 2009 12:23:15 -0400
> From: Vivek Ranjan <vran...@gmail.com>
> Subject: Re: [PyMOL] reorienting a chain
> To: Warren DeLano <war...@delsci.com>
> Cc: pymol-users@lists.sourceforge.net
> Message-ID:
> <1abcddff0906030923yd6513ccn468bb014bb3cd...@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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 <war...@delsci.com> 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? AAAAAAA, 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.
> > 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
> >
> >
> >
> >
>
>
>
> --
> 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.
> Go to: http://p.sf.net/sfu/opensolaris-get
>
> ------------------------------
>
> _______________________________________________
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
> End of PyMOL-users Digest, Vol 37, Issue 2
> ******************************************
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