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™ 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
Re: [PyMOL] Principal Axes of Rotation
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 -- 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
Re: [PyMOL] Principal Axes of Rotation
heavyweights like Barbarian Group, R/GA, Big Spaceship. http://www.creativitycat.com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- next part -- 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
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 magic...@hotmail.com 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. http://go.microsoft.com/?linkid=9666046-- 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
Re: [PyMOL] Principal Axes of Rotation
Sean Law magic...@hotmail.com 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. -- 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
Re: [PyMOL] Principal Axes of Rotation
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 magic...@hotmail.com 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. http://go.microsoft.com/?linkid=9666044 -- 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
Re: [PyMOL] Principal Axes of Rotation
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 magic...@hotmail.com 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. _ We are your photos. Share us now with Windows Live Photos. http://go.microsoft.com/?linkid=9666047-- 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
