PyMOL Users: For the record, do note that the current open-source code and latest beta executable builds (beta14) do support a few genuine per-atom and per-triangle settings.
Available per-bond setttings: valence, line_width, line_color, stick_radius, stick_transparency Available per-atom settings: sphere_color, sphere_scale, surface_color, mesh_color, label_color, dot_color, cartoon_color, ribbon_color, transparency, sphere_transparency. Note that per-bond settings require use of the new "set_bond" and "unset_bond" commands. For example: load $TUT/1hpv.pdb as surface show cartoon set transparency, 0.5, chain A And for bonds: as sticks set_bond stick_transparency, 0.8, not name N+CA+C, all ray Unfortunately, per-atom cartoon_transparency is not yet supported. Cheers, DeLano Scientific LLC Email Support Services > -----Original Message----- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of Andreas Forster > Sent: Wednesday, November 01, 2006 12:33 PM > To: Satinder Singh > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] differential helix transparency > > Hey Satinder, > > transparency can only be set for objects, not for selections. > Thus, you have to create different objects corresponding to > your helices. Like so: > > create helix1, i. 23:30 # wherever your first helix is > create helix2and3, i. 40:45 or i. 70:83 # the other two > helices show cartoon, helix1 or helix2and3 set > cartoon_transparency, 0.5, helix2and3 set > cartoon_transparency, 0, helix1 > > Since no transparency is the default, you might not have to > bother with > helix1 at all. > > Hope that helps. > > > Andreas > > > > > Satinder Singh wrote: > > Hello, > > > > I am showing three helices in my figure, and I would like > to make 2 of them semi-transparent while leaving the third > one opaque. I haven't been able to figure out how to do that. > Could someone tell me if this is even possible in PyMol and, > if so, what the command(s) are. Thanks. > > > > Satinder > > > > -------------------------------------------------------------- > ----------- > Using Tomcat but need to do more? Need to support web > services, security? > Get stuff done quickly with pre-integrated technology to make > your job easier > Download IBM WebSphere Application Server v.1.0.1 based on > Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&; > dat=121642 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
