Commands like setting transparency (for surfaces, spheres, sticks, etc) act on objects, not selections. Does something like the following work for you?
fetch 1t3r, async=0
create lig, resn 017
show sticks, lig
set stick_transparency, 0.7,lig
show sticks, byres (lig around 5) and not resn 017
For me, this shows the ligand as transparent sticks and nearby residues as solid sticks.
Actually it seems that for some reason the comma after the value (0.5)
invalidate the command line.
On Fri, 2010-05-21 at 11:40 -0500, Matthew Franklin wrote:
> (I'm putting this back on-list)
> That's too bad. It worked for me: PyMOL 1.2r2, Windows XP. Can you set other properties of this object: color, stick_radius, etc.?
> - Matt
> Matthew Franklin , Ph.D.
> Senior Scientist, ImClone Systems,
> a wholly owned subsidiary of Eli Lilly & Company
> 180 Varick Street, 6th floor
> New York, NY 10014
> phone:(917)606-4116 fax:(212)645-2054
> > -----Original Message-----
> > From: Ariel Talavera [mailto:firstname.lastname@example.org]
> > Sent: Friday, May 21, 2010 12:26 PM
> > To: Matthew Franklin
> > Subject: RE: [PyMOL] stick transparency
> > Thanks for the very quick answer, but it didn't succeed.
> > Best,
> > Ariel
> > On Fri, 2010-05-21 at 11:18 -0500, Matthew Franklin wrote:
> > Hi Ariel -
> > Try "set stick_transparency=0.5, peg_1"
> > - Matt
> > --
> > Matthew Franklin , Ph.D.
> > Senior Scientist, ImClone Systems,
> > a wholly owned subsidiary of Eli Lilly & Company
> > 180 Varick Street, 6th floor
> > New York, NY 10014
> > phone:(917)606-4116 fax:(212)645-2054
> > > -----Original Message-----
> > > From: Ariel Talavera [mailto:email@example.com]
> > > Sent: Friday, May 21, 2010 12:01 PM
> > > To: firstname.lastname@example.org
> > > Subject: [PyMOL] stick transparency
> > >
> > > Hi there,
> > >
> > > I am trying to set stick transparency using the following command:
> > > set stick_transparency, 0.5, peg_1, but with no success. The problem is
> > > with the selection, because if I use instead, set stick_transparency,
> > > 0.5, then every thing represented with stick get 50% transparent. Can
> > > you help with this? I am using Pymol 1.2 under Ubuntu 10.04.
> > >
> > > Thanks a lot in advanced,
> > >
> > > Best regards,
> > > Ariel
> > >
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