[PyMOL] Re: Réf.: [PyMOL] Help! Color by atom/H-bond display/mouse on OSX
Le Wed, 31 July 2002, Luca Jovine a écrit snip BTW, do people on the PyMol bulletin boar normally post (or are at least expected to post) summaries of the answers they received to a particular problem? /snip Depends. On a low-traffic list like this one, everybody can easily check all the answers in a thread, so summaries are not relly necessary. Just if you get input from off the list (a flash of genius or so...) it would be nice to get this information, too. It will be stored on the sourceforge mail-archives and everybody can check it later. I hope the others see it the same way as I do. joerg Internet et mail gratuit AltaVista http://www.altavista.fr
Re: [PyMOL] Help! Color by atom/H-bond display/mouse on OSX
Luca Jovine wrote: 1) Is there any typed command one can use to color a selection by atom type (rather than manually doing so by using the internal GUI pop-up menus)? The util module contains a number of functions that color the atoms according to type, with different colors for the C atoms. For instance, util.cbay three in a .pml script will color object three by atom type, with the carbon atoms in yellow (color by atom yellow). Other functions from ../modules/pymol/util.py are cbag, cbac, cbas, cbap, cbak, cbaw and cbab (grey (carbon), cyan, salmon, purple, pink, white (hydrogen) and slate). -- Lieven Buts Brussels Free University
[PyMOL] Réf.: [PyMOL] Help! Color by atom/H-bond display/mouse on OSX
Le Tue, 30 July 2002, Luca Jovine a écrit Hello again PyMol users, I've now been playing with PyMol on OSX for 10 days or so and still love it. I also developed three more questions though ;) 1) Is there any typed command one can use to color a selection by atom type (rather than manually doing so by using the internal GUI pop-up menus) ? Hi Luca, I can just answer question 1.) color black, (*/CA) will paint all C\alpha atoms black (looks good on black background... ;) ) See the manual (page 13 in the pdf version, IIRC) for the other atom names, and the hierarchical selection method. hth joerg Internet et mail gratuit AltaVista http://www.altavista.fr
Re: [PyMOL] Help! Color by atom/H-bond display/mouse on OSX
Luca Jovine wrote: 3) And finally, how do people who use PyMol on Mac OSX cope with the mouse issue? Is any of you using a 3-button mouse, and, if so, which one? Hi Luca, A simple logitech wheel optical mouse works wonderfully with PyMol on MacOS X. MacOS X has basic built-in drivers for multi-button mice. It supports the 3 buttons + the wheel. I'm still wondering why Apple is not selling multi-button mice with their computers... Bye -- Florian NACHON, phDCRSSA Grenoble, France - UNMC Omaha, USA Every man has two nations, and one of them is France Benjamin Franklin Thomas Jefferson ICQ# 43686170
[PyMOL] Help! Color by atom/H-bond display/mouse on OSX
Hello again PyMol users, I've now been playing with PyMol on OSX for 10 days or so and still love it. I also developed three more questions though ;) 1) Is there any typed command one can use to color a selection by atom type (rather than manually doing so by using the internal GUI pop-up menus) ? 2) Is there any way to detect and display hydrogen bonds (say with nice dashed lines!)? 3) And finally, how do people who use PyMol on Mac OSX cope with the mouse issue? Is any of you using a 3-button mouse, and, if so, which one? Thanks a lot and ciao Luca Luca Jovine, Ph.D. Department of Molecular, Cell Developmental Biology Mount Sinai School of Medicine Annenberg Building, Room 25-18 One Gustave L. Levy Place, New York, NY 10029-6574, USA Voice: +1.212.241-8620 FAX: +1.509.356-2832 E-Mail: lucajov...@mac.com W3: http://www.mssm.edu/students/jovinl02
