I suspect Afonso's talking about a moire / halftone dot pattern like the one at this link:
http://www.uvm.edu/~hag/presentations/maze2004/moire.html I have no idea what would cause this, but if you have two identical copies of a molecule, in the same representation, strange things can happen. For example: load myprotein.pdb hide everything show cartoon show spheres, residue 100 create myproteincopy, myprotein ray Sure enough, this creates a very odd speckled pattern on the raytraced cartoon surface, but not on the spheres. It's not really a regular moire pattern, but it could be considered a "newspaper pattern". So, Afonso, I think this is the culprit. Somewhere before you did your raytracing, you set up two identical objects, which are both visible at once. Try turning off the visibility of one of these (by clicking on its name in the list in the PyMOL viewer) and the effect should go away. Hope that helps, 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: Tsjerk Wassenaar [mailto:tsje...@gmail.com] > Sent: Tuesday, May 18, 2010 6:54 AM > To: Afonso Duarte > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Strange pattern on the cartoon representation > > Hi Afonso, > > Can you tell which newspaper? And does it show the date? :) > Seriously, it's difficult to make out more, unless you give more > information, like a link to the image, or the series of commands you > used to get to the point you're at. What you describe might be caused > by two interfering surfaces,e.g., trying to show two times the same > thing as cartoon. > > Cheers, > > Tsjerk > > On Tue, May 18, 2010 at 12:42 PM, Afonso Duarte > <afonsomdua...@gmail.com> wrote: > > Dear All, > > > > I am making some figures using ray. When the processing is finished I > get a > > strange pattern (like newspaper paper pattern) in my cartoon > > representations, Spheres and sticks representations are OK only the > cartoon. > > I have tried to change the options on the cartoon representation but > without > > any sucess. > > > > Did any body had such problem before? > > > > Best > > > > Afonso > > > > --------------------------------------------------------------------- > --------- > > > > > > _______________________________________________ > > 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- > us...@lists.sourceforge.net > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > Groningen Institute for Biomolecular Research and Biotechnology > University of Groningen > The Netherlands > > ----------------------------------------------------------------------- > ------- > > _______________________________________________ > 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 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
