Re: [PyMOL] Display main chain amides after preset

[Joel T. <joe...@ot...>]

Hi Jason,

Thanks for that. From a teaching-learning perspective, I would like to see a "correct" option added, or indeed the current option updated to include amides (turning off the helper), but just a suggestion. 

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


-----Original Message-----
From: Jason Vertrees [mailto:jas...@sc...] 
Sent: Friday, 5 August 2011 3:24 p.m.
To: Joel Tyndall
Cc: pym...@li...
Subject: Re: [PyMOL] Display main chain amides after preset

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 <joe...@ot...> 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
>
>
>
> ----------------------------------------------------------------------
> -------- BlackBerry&reg; DevCon Americas, Oct. 18-20, San Francisco, 
> CA The must-attend event for mobile developers. Connect with experts.
> Get tools for creating Super Apps. See the latest technologies.
> Sessions, hands-on labs, demos & much more. Register early & save!
> http://p.sf.net/sfu/rim-blackberry-1
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: 
> http://www.mail-archive.com/pym...@li...
>



--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

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