John, You're not doing anything wrong -- there's just a little confusion here about how settings work: they're global for an object or for the whole system. The current value is what is always used. To get different sphere sizes, use the alter command to change the vdw radii of the atoms for which you wish to change the radii, followed by a rebuild command.
alter selection, expression rebuild For example: alter name ca, vdw=vdw*0.5 alter resi 200, vdw=vdw*2.0 rebuild Cheers, Warren > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > John Berrisford > Sent: Thursday, February 26, 2004 2:13 AM > To: email@example.com > Subject: [PyMOL] sphere sizes > > I am trying to create a picture containing a metal ion and > water molecules. The problem that I am having is that I wish > to display them both as spheres, but of different sizes. > Pymol (version 0.93 and 0.95 beta 11 ) seems to only use the > last sphere size command i.e. "set sphere_scale, 0.1" in the > script and effectively ignore any previous sphere_scale command. > > Am I doing something wrong and there is another, better way > of doing this, for example linking the size command to an object? > > I have been so far unable to work out how to do this. > > Thanks > > John > > -- > John Berrisford > Department of Molecular Biology and Biotechnology University > of Sheffield > > email: j.berrisf...@sheffield.ac.uk > > > ------------------------------------------------------- > SF.Net is sponsored by: Speed Start Your Linux Apps Now. > Build and deploy apps & Web services for Linux with a free > DVD software kit from IBM. Click Now! > http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click > _______________________________________________ > PyMOL-users mailing list > PyMOLfirstname.lastname@example.org > https://lists.sourceforge.net/lists/listinfo/pymol-users >