Hi Ariel,

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
hide everything
show cartoon
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.

Mike Z

On Fri, May 21, 2010 at 11:50 AM, Ariel Talavera <talavera@cim.sld.cu> wrote:
Hi again,

Actually it seems that for some reason the comma after the value (0.5)
invalidate the command line.

Ariel

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:talavera@cim.sld.cu]
> > 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:talavera@cim.sld.cu]
> > > Sent: Friday, May 21, 2010 12:01 PM
> > > To: pymol-users@lists.sourceforge.net
> > > 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
> > >
> Confidentiality Note:
> This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system.
>
> Thank you.



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--
Michael Zimmermann
Ph.D. student in Bioinformatics and Computational Biology
Department of Biochemistry, Biophysics and Molecular Biology
Iowa State University