[PyMOL] Delete Bonds
Hi I would like to know how can I break bonds that are wrongly drawn in pymol. I am only using a coordinate file with no connectivities. I know how to select the bond, but then I don't know how to delete the bond without deleting other correct bonds that involve one of the atoms in the incorrect bond. Thank you in advance Jose
Re: [PyMOL] Ray trace is freezing...
the command 'ray' initiates the raytracing which is not GPU-dependent, i.e. your gfx drivers won't increase your raytrace time, only upgrading your main CPU will. But it shouldn't freeze. Does it crash? Have you tried ray'ing a simple scene, i.e. just a few residue, stick representation, nothing special? my 2 cents' worth :) jp On Mon, 18 Aug 2003, naalas wrote: Dear everybody, I'm using the last version of PyMOL, which is very fast (!), but I encountered a problem with ray. I found a driver for my video card which makes programs like O a lot faster, and it also makes PyMOL faster in all the *preparation* process. But as soon as I want to ray my picture, then it freezes. I do not know if the problem is coming from my video card or from PyMOL (e.g. my configuration), so if you have any suggestion, I'd be thankful... I am using Red Hat 9; video card= Ge Force 2.MX; commercial driver from NVIDIA version 1.0.4496. Thank you in advance. Leo - cha...@post.kek.jp naa...@docomo.ne.jp hnaa...@hotmail.com - --- This SF.Net email sponsored by: Free pre-built ASP.NET sites including Data Reports, E-commerce, Portals, and Forums are available now. Download today and enter to win an XBOX or Visual Studio .NET. http://aspnet.click-url.com/go/psa0013ave/direct;at.aspnet_072303_01/01 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- JP Cartailler 3205 McGaugh Hall Dept. of Molecular Biology Biochemistry Irvine Research Unit in Macromolecular Structure UC Irvine Irvine, CA 92697-3900 USA (949) 824 4322 (T) j...@bragg.bio.uci.edu (email) www.cartailler.com (www)
[PyMOL] problem fixed
I had the following lines in the .cshrc file, which prevented pymol from starting up. ## source initPython script source /Applications/ADT/ppcDarwin6/bin/initPython These lines were added for the AutoDock program. After commenting out the line, both x-windows and the native versions of pymol started up normally. I should have looked more carefully. Wataru Kagawa, Ph. D. Special Postdoctoral Researcher Protein Research Group RIKEN (Physical and Chemical Research Institute) W221, West Research Bldg. 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama, Japan 230-0045 tel.045-503-9206 fax.045-503-9201
RE: [PyMOL] Delete Bonds
Jose, Select the bond using Ctrl-right-click, then either unbond pk1,pk2 or hit Ctrl-D. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Jose Avalos Sent: Monday, August 18, 2003 6:45 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Delete Bonds Hi I would like to know how can I break bonds that are wrongly drawn in pymol. I am only using a coordinate file with no connectivities. I know how to select the bond, but then I don't know how to delete the bond without deleting other correct bonds that involve one of the atoms in the incorrect bond. Thank you in advance Jose --- This SF.Net email sponsored by: Free pre-built ASP.NET sites including Data Reports, E-commerce, Portals, and Forums are available now. Download today and enter to win an XBOX or Visual Studio .NET. http://aspnet.click- url.com/go/psa0013ave/direct;at.aspnet_072303_01/01 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
