Re: [PyMOL] moving objects
Hi Marcelo - Is Object 2 actually a pseudoatom? Or, if not, can it be placed separately from Object 1? If either of those are the case, it would be much easier to place the pseudoatom at a point equidistant from the two ends of Object 1 than mess with rotation matrices, etc. Here’s what I worked out. # get a long protein, e.g. collagen fetch 1bkv, async=0 as cartoon # place a couple helper pseudoatoms at the ends of the collagen (approximately) pseudoatom nterm, resi 2+31+61, vdw=2 pseudoatom cterm, resi 30+60+90, vdw=2 select ends, nterm or cterm show spheres, ends # orient the helper pseudoatoms along one of the display axes (usually ends up being x) orient ends # place another helper pseudoatom at the midpoint of the object pseudoatom obj_b, ends, vdw=4 show spheres, obj_b # move it (e.g.) 50Å away translate [0,0,-50], obj_b # make sure it looks right orient ends or obj_b You could then load your “real” Object 2 (if necessary) and move it to the obj_2 pseudoatom using a combination of `origin` and the COM script (http://www.pymolwiki.org/index.php/Com), for example. Haven’t tested that, but it should be possible. Hope that helps! Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Apr 28, 2015, at 1:57 PM, Marcelo Marcet mmar...@nait.camailto:mmar...@nait.ca wrote: Hi Pymol Users, I have 2 objects (objects 1 and 2) and I would like to re-orient object 1 so that the distance from either end of object 1 becomes the same to object 2 (see image). Is there a way to achieve this in PyMol? I have tried using the mouse in edit mode and I have tried using the rotate/translate commands. Neither method can move object 1 without altering the position of the lower end of object 1. Regards, Marcelo image.jpeg -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___ 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 -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___ 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
[PyMOL] moving objects
Hi Pymol Users, I have 2 objects (objects 1 and 2) and I would like to re-orient object 1 so that the distance from either end of object 1 becomes the same to object 2 (see image). Is there a way to achieve this in PyMol? I have tried using the mouse in edit mode and I have tried using the rotate/translate commands. Neither method can move object 1 without altering the position of the lower end of object 1. Regards, Marcelo -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___ 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
[PyMOL] moving objects freely
From time to time, I have a need to manually move objects relative to one another. For example, manual docking of a ligand requires that it the translated and rotated relative to its binding pocket. It there a simple, intuitive way to do this? Thank a lot, Tom Leyh Professor of Biochemistry The Albert Einstein College of Medicine
Re: [PyMOL] moving objects freely
Hi Tom, On Thu, 04 Oct 2007 11:20:35 -0700, Tom tl...@optonline.net wrote: From time to time, I have a need to manually move objects relative to one another. For example, manual docking of a ligand requires that it the translated and rotated relative to its binding pocket. It there a simple, intuitive way to do this? Put the mouse in editing mode (either through the Mouse menu in the external GUI or by clicking anywhere in the bottom right region of the graphics window where the mouse functions are described). Then while holding down the Shift button the left and middle mouse buttons can be used to rotate and translate an object. Just make sure your mouse is over the object you want to move when you press the mouse button. Just be careful that you haven't picked an atom within the moving object, or that atom will not move. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc
Re: [PyMOL] moving objects freely
The drag action provides an easier to use solution. Right click on the atom, select molecule/chain/object then drag. From that point on, shift-left, shift-middle, and shift-right click can be used to move those atoms. -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor! -WLD -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Robert Campbell Sent: Thursday, October 04, 2007 10:22 AM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] moving objects freely Hi Tom, On Thu, 04 Oct 2007 11:20:35 -0700, Tom tl...@optonline.net wrote: From time to time, I have a need to manually move objects relative to one another. For example, manual docking of a ligand requires that it the translated and rotated relative to its binding pocket. It there a simple, intuitive way to do this? Put the mouse in editing mode (either through the Mouse menu in the external GUI or by clicking anywhere in the bottom right region of the graphics window where the mouse functions are described). Then while holding down the Shift button the left and middle mouse buttons can be used to rotate and translate an object. Just make sure your mouse is over the object you want to move when you press the mouse button. Just be careful that you haven't picked an atom within the moving object, or that atom will not move. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.ca http://pldserver1.biochem.queensu.ca/~rlc -- --- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Moving Objects
Yes, Assuming you're running 0.95: Put the mouse into Editing Mode (Mouse menu or click on the mouse matrix). Insure that no atoms are currently picked (i.e. there are no pk selections). Click unpick if there are... You can now independently rotate and translate objects with shift-left-click-and-drag and shift-middle-click-and-drag. To rotate fragments of an object, pick one or atoms with ctrl-middle-click (or right-double-click). The picked atoms become the joints which separate fragments that are independently movable and rotatable. If you click and drag on a picked atom, then you will be able to independently translate or rotate the complete covalent system (molcule) which contains that atom. Instead of clicking unpick you can ctrl-middle-click (or double-right-click) away from any atom in order to clear the current picked atom set. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Tony Giannetti Sent: Wednesday, May 12, 2004 11:45 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Moving Objects Hey fellow PyMoler's, If you have multiple objects loaded and on screen at once, is it possible to rotate one without rotating the others? I've had success using rotate and translate commands with selections, and it works, but it can be slow with lots of objects. In Swiss-PDB viewer, you are allowed to lock layers and then continue working with the other ones with the mouse. This would also be similar to 'move-object-zone' in O where the dials are locked onto a single object. I was wondering if PyMol has a functionality like this and how it can be activated. I'm interested in this both for still frame images and for possible animations where one or two objects move relative to other ones. Thanks, Tony --- This SF.Net email is sponsored by: SourceForge.net Broadband Sign-up now for SourceForge Broadband and get the fastest 6.0/768 connection for only $19.95/mo for the first 3 months! http://ads.osdn.com/?ad_id=2562alloc_id=6184op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] moving objects independently?
Dear Pymolers, I am trying to manually superimpose a couple of structures that are simultaneously opened in Pymol. I can't figure out how to move one structure independent of the other. Is there a way to select just one object, move it with the mouse, deselect it, select the other object, move it, etc? Help would be much appreciated. Thank you! richard Triad Therapeutics, Inc. 9381 Judicial Dr., Suite 200 San Diego, CA 92121 r...@triadt.com 858-964-1575 858-457-7893 fax
