Hello,
This is only my opinion right...
But it seems to me that converting hbonds into secondary structure
elements (helices, strands, paperclips...) can be tricky at the
boundaries when bonds are just too short or just the other side of the
correct angle.
To illustrate this with 1m6q (which is a model, by the way, and has
some odd features, like not-quite-bonded sheets) I pick one of the
short sheets you circle (at least I think I do) : 379-383::423-427.
From the attached pictures, you can see that pymol does not consider
residue 381's oxygen to be bonded to residue 425's nitrogen. This may
well be justified, since the O->N distance is 3.69 - which is quite
long.
What I'm not sure is what can be done about this - ss assignment could
potentially have a lot of 'hacks' to deal with supposed corner cases
like this (phi-psi angles, ca-ca distances, etc) but it's a bit of a
judgement call.
gilleain torrance
On 3/3/06, oliverggmxde <oli...@us...> wrote:
> Hello all,
>
> I am using PyMOL V0.99pre06 (build from CVS repository)
>
> When viewing 1m6q.pdb (http://www.rcsb.org/pdb/files/1m6q.pdb) in
> cartoon mode, I think the arrows in beta sheet are rendered too short
> in comparison to other software (e.g. RasMOL). I posted this
> behavior already in the "bugs"-section (see comparison screenshot
> there
> https://sourceforge.net/tracker/index.php?func=3Ddetail&aid=3D1429665&gro=
up_id=3D4546&atid=3D104546).
>
> I'd like to use PyMOL of course. Is there any chance to get PyMol to
> display a larger version of these arrows?
>
> Oliver
>
>
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>
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>
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