I forgot a step in my command list before; the copy of the molecule has to be a different color from the parent molecule. (Perhaps that was obvious, but I thought I should state it.) This may be why you see it some times and not others: you have to have both copies with their visibility turned on and with colors different enough that you can see the speckling.
- 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
From: Afonso Duarte [mailto:afonsomduarte@...]
Sent: Tuesday, May 18, 2010 10:36 AM
To: Matthew Franklin
Cc: Tsjerk Wassenaar; pymol-users@...
Subject: Re: [PyMOL] Strange pattern on the cartoon representation
That's exactly what I just found out!
Thanks! but I don't understand why sometimes it happens and other times it does not happen.
Cheers
Afonso
On Tue, May 18, 2010 at 4:17 PM, Matthew Franklin <Matthew.Franklin@...>> wrote:
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<http://www.uvm.edu/%7Ehag/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:tsjerkw@...>]
> Sent: Tuesday, May 18, 2010 6:54 AM
> To: Afonso Duarte
> Cc: pymol-users@...>
> 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
> <afonsomduarte@...>> 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@...>)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-
> users@...>
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> Groningen Institute for Biomolecular Research and Biotechnology
> University of Groningen
> The Netherlands
>
> -----------------------------------------------------------------------
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