Jason (or someone else),
Is there way in pymol to look for the following angle in a structure φ=-49o and
ψ=-26o ? Which is the definition of a 310 helix. And yes we'd have to search
for a few degrees plus of minus of those angles. They should all appear in
tight turns and last for about 3 or 4 amino acids (I don't think there wouldn't
be any cartoon helix shown).
I don't think there are any pdbs yet that contain pi helices (because of the
loose packing and steric hindrance of the side chains), does anyone know of any?
Thanks
Adam
On Apr 6, 2011, at 8:16 AM, Jason Vertrees wrote:
> Hi Ramiro,
>
> PyMOL doesn't differentiate helices, so it cannot color them
> differently. If you had the residue labels from some other program
> you could read them in and then color by type.
>
> Cheers,
>
> -- Jason
>
> On Wed, Apr 6, 2011 at 5:22 AM, Ramiro Téllez Sanz <urcind...@gmail.com>
> wrote:
>> Hi and thanks for reading this.
>>
>> I have googled for a way to achieve what I want and have gone through
>> the wiki, to no avail.
>>
>> I would like to color in a different way the different helix types:
>> alpha, pi and 310. When you open, for instance, 1pyg into Jmol, you get
>> distinct colors for each type by default. But if the same pdb file is
>> open with PyMOL all helices are treated the same way. Can't PyMOL
>> distinguish helix types?
>>
>> Thanks in advance,
>> Ramiro Téllez Sanz
>> Dept. Physical Chemistry
>> University of Almeria
>> Spain
>>
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>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>
> ------------------------------------------------------------------------------
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> It's a major breakthrough. An authentic gaming
> smartphone on the nation's most reliable network.
> And it wants your games.
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artforscience
H. Adam Steinberg
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