Re: [PyMOL] how can we make this kind of figure?
what’s the reference to the paper? > On Feb 12, 2016, at 1:39 AM, Albert wrote: > > > > Hello > > I found a very nice figure in an article but the author didn't mention > which software he used for render. I am just wondering is it possible to > render in the same way in Pymol? I've attached this figure. > > thx a lot > > Albert > > > > -- > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140___ > 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 H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 ___ 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
Re: [PyMOL] Can't build trans peptides ?
Hi Charbel, After you opened the builder panel, you can change the "secondary_structure" setting to 4 before you start building: PyMOL> set secondary_structure, 4 You may also like the "fab" command to build peptides: http://pymolwiki.org/index.php/Fab Extended poly-ALA example: PyMOL> fab , ss=4 Cheers, Thomas On 11 Feb 2016, at 06:48, R. Charbel MAROUN wrote: > Hello Pymolers, > > When trying to build a polypeptide chain with the Build Residue command, > I find no "trans" conformation for the phi and psi angles, only Helix > and Beta sheet. Is there a simple way of building a chain in the trans > (extended) conformation ? > > Thanks in advance. > > -- > R. Charbel MAROUN, Ph.D., H.D.R. > UMR-S INSERM U1204/UEVE > Structure et activité des biomolécules > normales et pathologiques > Université d'Evry-Val d'Essonne > Bâtiment Maupertuis > Rue du Père Jarlan > 91000 EVRY > FRANCE > Tél: +33 1 69 47 76 64 > FAX: +33 1 69 47 02 19 > e-mail charbel.mar...@inserm.fr -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 ___ 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
Re: [PyMOL] how can we make this kind of figure?
Albert, looks like it is from 'cutemol'. You can probably achieve a similar effect in Pymol -enable perspective -play around with occlusion (search in settings for occlusion) -display protein with 'cartoon loop' -show sidechains for selected residues -fog seems to have a tint of grey in there, you could play with that setting -not knowing the context of the figures it looks like they only displayed C-alphas as white spheres maybe with adjusted radii -There seems to be some light coming from back left, so playing around with light positions may also be appropriate Looks like it would require a lot of tinkering with settings, but you should be able to get to a similar figure. HTH Carsten -Original Message- From: Albert [mailto:mailmd2...@gmail.com] Sent: Friday, February 12, 2016 2:39 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] how can we make this kind of figure? Hello I found a very nice figure in an article but the author didn't mention which software he used for render. I am just wondering is it possible to render in the same way in Pymol? I've attached this figure. thx a lot Albert -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 ___ 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
[PyMOL] Can't build trans peptides ?
Hello Pymolers, When trying to build a polypeptide chain with the Build Residue command, I find no "trans" conformation for the phi and psi angles, only Helix and Beta sheet. Is there a simple way of building a chain in the trans (extended) conformation ? Thanks in advance. -- R. Charbel MAROUN, Ph.D., H.D.R. UMR-S INSERM U1204/UEVE Structure et activité des biomolécules normales et pathologiques Université d'Evry-Val d'Essonne Bâtiment Maupertuis Rue du Père Jarlan 91000 EVRY FRANCE Tél: +33 1 69 47 76 64 FAX: +33 1 69 47 02 19 e-mail charbel.mar...@inserm.fr -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 ___ 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
