Hi Kristoffer, The key is to set "cartoon skip" on the cartoon to hide:
#fetch a protein and make a copy fetch 1cll, async=0 create a_copy, 1cll # show them as cartoons set cartoon_transparency, 0.75, a_copy show_as cartoon # select the region of interest select to_hide, i. 103-111 orient to_hide # hide/skip this section in the original cartoon skip, to_hide and 1cll color marine color magenta, ss 'h' select none ray Cheers, -- Jason On Fri, Dec 2, 2011 at 4:05 AM, essolini <essol...@gmail.com> wrote: > Hello Jason, and thank you for the reply. > > I have tried the trick of creating a new object of the segment of interest, > and then independently adjust transparency of this object. However, when I > do this, the cartoon from the two objects are not perfectly aligned, so it > looks really weird in the "transition zones". Any other ideas? > > Regards, > > Kristoffer > > On Thu, Dec 1, 2011 at 6:04 PM, Jason Vertrees > <jason.vertr...@schrodinger.com> wrote: >> >> Hi Kristoffer, >> >> Cartoon transparency is an object-level property. You can use this >> trick though: >> http://pymolwiki.org/index.php/Cartoon#Various_Transparency_Levels. >> >> Cheers, >> >> -- Jason >> >> >> On Thu, Dec 1, 2011 at 10:34 AM, essolini <essol...@gmail.com> wrote: >> > Greetings! >> > >> > I have a problem with Pymol driving me crazy, and I hope someone is able >> > to >> > help me. >> > >> > Is there a way of displaying selected residues in a cartoon structure >> > with >> > another transparency than the rest? I have tried to make a selection of >> > residues from an object (let's call it sel), and then type: >> > >> > set cartoon_transparency = 0.8, sel >> > >> > After doing that, the following message comes up in the command window: >> > >> > Setting: cartoon_transparency set for 36 atoms in object "3FJQ". >> > >> > But nothing happens! >> > >> > I found this in the archives, describing a similar problem but regarding >> > sticks: >> > >> > https://sourceforge.net/mailarchive/message.php?msg_id=27522311 >> > >> > Is there a similar solution to the problem only regarding cartoon? >> > >> > >> > >> > Can someone tell me what I am doing wrong? Your help is very much >> > appreciated! >> > >> > Kristoffer >> > >> > ------------------------------------------------------------------------------ >> > All the data continuously generated in your IT infrastructure >> > contains a definitive record of customers, application performance, >> > security threats, fraudulent activity, and more. Splunk takes this >> > data and makes sense of it. IT sense. And common sense. >> > http://p.sf.net/sfu/splunk-novd2d >> > _______________________________________________ >> > 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 >> >> >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schrodinger, LLC >> >> (e) jason.vertr...@schrodinger.com >> (o) +1 (603) 374-7120 > > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d _______________________________________________ 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
