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:jason.vertr...@schrodinger.com] Sent: Friday, 5 August 2011 3:24 p.m. To: Joel Tyndall Cc: pymol-users@lists.sourceforge.net 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 <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 > > > > ---------------------------------------------------------------------- > -------- BlackBerry® 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 (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: > http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ BlackBerry® 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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
