Hi Joel, You're right. I think we need some updated/additional preset visualizations. Can you please add this to the open-source tracker (http://sourceforge.net/tracker/?group_id=4546&atid=354546)?
Cheers, -- Jason On Mon, Aug 8, 2011 at 12:43 AM, Joel Tyndall <joel.tynd...@otago.ac.nz> wrote: > 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 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ uberSVN's rich system and user administration capabilities and model configuration take the hassle out of deploying and managing Subversion and the tools developers use with it. Learn more about uberSVN and get a free download at: http://p.sf.net/sfu/wandisco-dev2dev _______________________________________________ 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
