[Fwd: [PyMOL] Apple new version X11]
Richard Gillilan wrote: Sorry, intended this to go out to the whole group. Here goes again: Craig Smith wrote: I've installed X11 server through XDarwin. Will the installation of PyMOL for OS X described on your web page work with XDarwin's implementation of X11 or do I have to install Apple's version. Is there any advantage in installing Apple's X11? Will Apple X11 installation overwrite XDarwin? They have encountered some problems over in OpenDx land with the new X11 from Apple. I have my code running mostly, but I think it's important to keep in mind that this is a beta version. Here is a quote one of the developers forwarded to me. It may or may not effect PyMol (uses GLUT?). Anyhow here it is: Just to let you know, Apple's X11 is beta and there are problems with it and X apps. For one thing the window manager does not honor any window placement and window size requests. This can really make apps like DX unusable. It also is missing some of the hardware rendering implementation XGL and thus DX's hardware rendering will not work. The developers are aware of the problems and will hopefully be addressing these before the final release is finished. Richard Gillilan MacCHESS, Cornell
[PyMOL] new user
Hi all, I just installed PyMol last week on my Linux and PC and laptop and I love it! And v0.86 is of course better with its session-saving capability. There is a new thing (I'm pretty sure it's a bug, not a feature) in 0.86: When I Tab for command completion, the command ends with a comma when in fact = is expected. For example, set cartoon_fl(Tab)at_sheets, not set cartoon_fl(Tab)at_sheets= Print quality doesn't seem to be as high as the image on the display. Do I need to feed the PyMol output into something else first? Can (how) I annotate the pictures in PyMol? If it's not there yet, I hope it'll be soon as annotation is an indivisible right for any figure to have. Cheers, Nukri Ruslan Sanishvili (Nukri) Ph.D. GM/CA-CAT, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel (630)252-0665 Fax (630)252-0667 rsanishv...@anl.gov
RE: [PyMOL] how to control the density coverage in pymol
Rongjin, this works for me. You have to specify either buffer or carve with named variables (hope that is the right term). inh1 is the selection I defined the map to be centered on. # load maps load 2fofc.ccp4, 2fofc_map load fofc.ccp4, fofc_map isomesh 2fofc, 2fofc_map, 1.4, inh1, carve=2 color marine, 2fofc isomesh fofc1, fofc_map, 3.0, inh1, buffer=2 color forest, fofc1 isomesh fofc2, fofc_map, -3.0, inh1, buffer=2 color firebrick, fofc2 Hope it helps Carsten -Original Message- From: Rongjin Guan [mailto:gu...@umbi.umd.edu] Sent: Tuesday, January 14, 2003 11:22 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] how to control the density coverage in pymol Hi, all, I am new to this BB. In O we can use something like map_cover object radius to only display the density aroung the part model we are interested, and get rid of other densities neaby to make the figure clean. But in PyMOL, I tried insomesh den, map1, 1.0, (i;8,9), 3.0 to try to only display the density around residues 8 and 9, but there are still some additional densities neaby, which makes the figure a little dirty. Anybody has some ideas to deal with it? Thanks Rongjin Guan -- Rongjin Guan, Ph.D. Center for Advanced Research in Biotechnology 9600 Gudelsky Drive Rockville MD, 20850 Tel: 301-738-6210 Fax: 301-738-6255
RE: [PyMOL] new user
From: Nukri Sanishvili [mailto:rsanishv...@anl.gov] There is a new thing (I'm pretty sure it's a bug, not a feature) in 0.86: When I Tab for command completion, the command ends with a comma when in fact = is expected. For example, set cartoon_fl(Tab)at_sheets, not set cartoon_fl(Tab)at_sheets= Actually, that is a feature. Slowly, the PyMOL command language is becoming more consistent (and more Python like). set name,value is preferred over set name=value Since it follows the convention that arguments to PyMOL keywords are separated by commas. Nevertheless, I am a strong proponent of backwards compatibility. set parameter=value will continue to function for years to come so that old scripts will not break. Print quality doesn't seem to be as high as the image on the display. Do I need to feed the PyMol output into something else first? Increase the resolution: ray 2000,1500 etc. Can (how) I annotate the pictures in PyMol? If it's not there yet, I hope it'll be soon as annotation is an indivisible right for any figure to have. Sorry, your figures will continue to be oppressed with versions 0.86. Liberation will come in due time. Cheers, Warren
