I think he means: "sheared" as in garden :) Creating a separate object is one route.
Another would be: flag ignore, not rep dots rebuild But do note that this would affect surfaces or meshs as well. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -----Original Message----- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Tsjerk Wassenaar Sent: Tuesday, August 12, 2008 7:17 AM To: O. J. Ganesh Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] sheared spheres for dots in dot representation Hi O.J., What exactly do you mean by 'sheared' (http://mathworld.wolfram.com/Shear.html). What you see is due to the fact that you show the 'exposed' part of the vdw sphere of an atom with substituents. I think that if you want to show them whole, you have to make them a separate object first. Assuming it's the phosphorous atoms: create phospho, elem p show dots, phospho Hope it helps, Tsjerk On Tue, Aug 12, 2008 at 2:58 PM, O. J. Ganesh <ojgan...@mbi.ufl.edu> wrote: > > > Hello again. I'm having a bit of trouble with the dot representation again. When I use the dot representation on an object, the sphere on which the dots reside ends up sheared; that is, I do not get a nice round sphere to hold up the dots. > I've adjusted vdw of the object I'd like to have in the dot representation, however no matter how small (or large) I make the spheres, the spheres are always sheared. I also played with the slab settings, and it doesn't matter how far back I move the 'camera' the spheres are still sheared. > Is there some setting that I'm missing? I'd like to end up with round spheres for the dots, as in: > http://www.pymolwiki.org/index.php/Image:Dots_ex.png > I've uploaded an example of my problem to the wiki as: > http://www.pymolwiki.org/index.php/Image:Sheared_dots.png > > Thanks! > > ---------------------------------------------------------------------- > --- This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge Build the coolest Linux based applications with Moblin SDK & > win great prizes Grand prize is a trip for two to an Open Source event > anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
