Hi Joel,
The preset commands make changes that are sometimes undoable. In this
case, PyMOL sets "cartoon_side_chain_helper" on a selection and then
deletes the selection. To do what you want, you need to perform the
actions in the command without the cartoon_side_chain_helper setting:
# fetch an example protein
fetch 1hpv, async=0
# detect ligand sites
preset.ligand_sites("1hpv")
# show the dashes in the polar contacts
show dashes, 1hpv_pol_conts
# show the cartoon
show cartoon, rep ribbon
# hide surface and ribbon
hide surface
hide ribbon
Should we add some more options for preset visualizations?
Cheers,
-- Jason
On Thu, Aug 4, 2011 at 6:22 PM, Joel Tyndall <joel.tynd...@otago.ac.nz> wrote:
> Hi folks/Jason,
>
>
>
> I have been playing with PyMOL again lately for teaching and have noticed
> that when you run the menu command Action>preset>ligand site >cartoon which
> looks great... if there are any H-bonds with a protein chain amide carbonyl,
> then the carbonyl is not displayed. If you use “Show>lines or sticks” this
> does not then show them. I’m sure there is a background (python) setting to
> adjust this but is it possible to include the carbonyl’s in question with
> the initial preset? HIV protease is a good example to show this.
>
>
>
> Cheers
> Joel
>
>
>
> _________________________________
>
> Joel Tyndall, PhD
>
> Senior Lecturer in Medicinal Chemistry
> National School of Pharmacy
> University of Otago
> PO Box 56 Dunedin 9054
> New Zealand
>
> Skype: jtyndall
> http://www.researcherid.com/rid/C-2803-2008
>
> Pukeka Matua
> Te Kura Taiwhanga Putaiao
> Te Whare Wananga o Otago
> Pouaka Poutapeta 56 Otepoti 9054
> Aotearoa
>
> Ph / Waea +64 3 4797293
> Fax / Waeawhakaahua +64 3 4797034
>
>
>
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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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