Re: [PyMOL] ribbon trace, visualizing polymers (resent)

Hi Erik,

This is a known bug introduced in OS X 10.8 and some video cards. To
fix this just type,

  set cylinder_shader_ff_workaround, 1

and all should be well. PyMOL uses an official rendering optimization
but some systems have difficulty with it, hence our workaround.

This is automatically fixed in PyMOL v1.5.0.5 and later (and in the
recent open-source code).

Cheers,

-- Jason



On Tue, Nov 27, 2012 at 11:23 AM, Erik Nelson <nel...@gm...> wrote:
>
> I use pymol to generate images of simple polymers by loading their
> coordinates as
> .pdb files. The 'polymer .pdb' files contain only alpha carbon coordinates.
> I connect
> them using the ribbon_trace option, and color them by varying b-factors in
> the .pdb
> file.
>
> I had created many different movies and figures this way, and I saved the
> sessions
> as .pse files. Just recently, I went back to view some of these sessions and
> they just
> loaded as blank screens.
>
> I tried creating more images as before - using the ribbon_trace option to
> connect the
> atoms - but it no longer works.
>
> I'm pretty sure I didn't change any options in pymol, so I'm wondering if
> pymol
> somehow updated itself, or some update of my mac airbook affected the pymol
> program. Neither of these seems very likely.
>
> What went wrong? Is there a way I can fix this?
>
> A more general question. It seems like there must be a better way to
> visualise a
> polymer, say as a ball an stick image. Is there a more straight forward way
> of doing
> this in pymol?
>
> Thanks, Erik
>
> --
> Erik Nelson
>
> Howard Hughes Medical Institute
> 6001 Forest Park Blvd., Room ND10.124
> Dallas, Texas 75235-9050
>
> p : 214 645 5981
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-- 
Jason Vertrees, PhD
Director of Core Modeling Product Management
Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120