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 <talav...@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:talav...@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:talav...@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. > > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Michael Zimmermann Ph.D. student in Bioinformatics and Computational Biology Department of Biochemistry, Biophysics and Molecular Biology Iowa State University
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