Mark, Your confusion arises from the new "set_bond" command, which must be used when setting bond-specific properties. Please see the official docs on "set_bond". Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info "Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor!" -WLD
_____ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Dr. Mark Mayer Sent: Tuesday, June 26, 2007 10:18 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Sticks and distances with individual transparencies - repost Apologies for prior post message font was nearly unreadable Dear All, I'm trying to write a Pymol script with which produces a mixture of both solid and transparent sticks I'm using the current 1.0 incentive release of MacPymol. After drawing all my sticks I issue following commands, but nothing changes although the log output suggests the change is being set. PyMOL>set stick_transparency=0.2, /sca//A/228 and !mc Setting: stick_transparency set for 5 atoms in object "mol1". I'd also like to draw selected H-bonds with control of transparency with the rest solid, but have no idea how to do this. -- Mark Mayer Ph.D. LCMN NICHD NIH DHHS Bldg 35, Room 3B 1002 MSC 3712 35 Lincoln Drive Bethesda MD 20892 3712 Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396 Lab web site: http://mayerlab.nichd.nih.gov Send packages, Fedex and anything requiring a signature to: Bldg 35, Room 3B 1004 35 Lincoln Drive Bethesda MD 20892
