Andreas,
That's an interesting find. PyMOL is clearly being fooled by the secondary
structure assignment. I don't think it's PyMOL's responsibility to address
egregious cases like this—rare and non-standard.
You can run 'dss' to update the secondary structure to something more
reasonable or you can use the 'alter' command to update the secondary
structure assignments. That should improve the result.
Cheers,
-- Jason
On Fri, Nov 1, 2013 at 7:33 AM, Andreas Förster <docandr...@gmail.com>wrote:
> Dear all,
>
> I've just been baffled for a while with a pdb that showed a strange
> behavior upon changing the representation from cylindrical cartoon
> helices to normal cartoon helices. It seemed to me that helices were
> disappearing.
>
> A picture of the effect is here:
> http://www.msf.bio.ic.ac.uk/images/helices.png
>
> The arrows show pairs of normal helices merged into single short
> cylindrical helices.
>
> At some point, I realized the problem was the definition of pairs of
> helices as one continuous secondary-structure element (encircled).
> Running dss on the file fixed everything.
>
> I'm left wondering whether PyMOL should realize it's being fooled by the
> secondary structure predictions in egregious cases like this. I looked
> hard at the structure with cylindrical helices and started to interpret
> differences to a homologous structure, which seemed to have additional
> helices, and in perpendicular orientations.
>
> Best regards.
>
>
> Andreas
>
>
>
>
> --
> Andreas Förster
> Crystallization and Xray Facility Manager
> Centre for Structural Biology
> Imperial College London
>
>
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--
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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