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From: Sampson, J. <Jar...@ny...> - 2015-04-29 17:14:55
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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 <MM...@na...<mailto:MM...@na...>> 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 (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... |