[PyMOL] electrostatic potential as cartoon?

. Vincent -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug Resistance and Membrane Proteins Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.ibcp.fr -- Check

Re: [PyMOL] PyMOL-users Digest, Vol 116, Issue 15

ick.net/gampad/clk?id=272487151=/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 -- Vincent

[PyMOL] bonds in ligands for MD simulations?

... thank you for your help. best Vincent -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug-resistance modulation and mechanism Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 07 http://www.ibcp.fr

[PyMOL] white background is black when opaque_background is on

. It didn't happen on previous versions. (as a workaround, i could comment the opaque background off, and decomment it when I ray trace the image, but it would be nice to have the full settings working initially without having to edit too much the .pml ...) thanks Vincent -- Vincent Chaptal, PhD

Re: [PyMOL] white background is black when opaque_background is off

Sorry, I meant in the title, opaque_background set to off. Le 9/16/14 3:03 PM, vincent Chaptal a écrit : Hi all, when I use : cmd.set('''opaque_background''','''0''',quiet=0) cmd.bg_color('white') the background is black. If I set the background back to opaque, then it turns white

Re: [PyMOL] drawing arows, CONE cgo doesn't work. -- SOLVED

CONE in pymol? It looks very nice. Thank you Vincent -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug-resistance modulation and mechanism Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 tel:%2B33

[PyMOL] drawing arows, CONE cgo doesn't work.

draw anything. cmd.load_cgo( [ CONE, x0, y0, z0, x1, y1, z1, radius, r1, g1, b1, r1, g1, b1 ], cone_a ) Can someone tell me what is going on and how I can draw a cgo CONE in pymol? It looks very nice. Thank you Vincent -- Vincent Chaptal, PhD Institut de Biologie et Chimie des

[PyMOL] problem with distance

and atom o. For a proof, I'm pasting the top screen where the names of the atoms I clicked is: You clicked /molA//A/SER`53/O Selector: selection sele defined with 1 atoms. You clicked /molA//D/GLY`8/N) I was previously under 1.3 and didn't have this problem. Can you help me? Vincent -- Vincent

Re: [PyMOL] disconnected loop in pymol

) Thanks in advance, Tassos -- Vincent Chaptal Dept. of Physiology at UCLA http://www.physiology.ucla.edu/Labs/Abramson/index.html http://www.physiology.ucla.edu/Labs/Abramson/index.html/ Phone: 1-310-206-1399

[PyMOL] COVER image

Hello, I am trying to make a picture for a cover and I am wondering how to make a vertical image. (Pymol creates horizontal images, and journal covers are vertical) Is there a way to creates those vertical images other than turning the image 90 degrees with the 'turn z, 90' command? thanks

[PyMOL] manual docking problem

. any ideas to keep the protein as one single piece? I am using version 0.98 on windows xp. thanks vincent Vincent Chaptal CNRS, LEBS-bat 34 1 Av de la terrasse 91 198 gif sur Yvette tel: 01 69 82 42 04 fax: 01 69 82 31 29 http://www.lebs.cnrs-gif.fr/