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
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
[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
[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
[PyMOL] 0.86 session files and Ribbons-like RNA representation
Hello PyMOLers, These are maybe things only Warren will know, but other people might have some ideas: 1) It's really useful to be able to save sessions - thanks Warren! But why are .pse files created by PyMOL so big? (well, relatively speaking, that is!). Even when working with a single normally-sized PDB file, I always seem to end up with > 1 MB files... 2) Has anyone ever tried to generate a Ribbons-like representation of a nucleic acid with PyMOL? (for an example of what I mean, have a look at http://sgce.cbse.uab.edu/ribbons/imonth/index.html ) Displaying bases as cylinders as implemented in Ribbons is a very clear way of showing the overall folding of RNA/DNA, and it would be great to have a comparable feature in PyMOL. Thanks and best regards, 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 - luca.jov...@mssm.edu W3: http://www.mssm.edu/students/jovinl02
Re: [PyMOL] help compiling pymol on OSX
Craig, You'll have to install not only X11, but also its SDK. Go to: http://www.apple.com/macosx/x11 then scroll to the bottom of the page, and on the right hand side you'll see a small box with the title "Developer’s Kit"; inside this box are links to both of the installers you need. As far as glut-3.7-3 compilation is concerned, I'm not entirely sure what the problem is; have you tried re-running the job with "sudo fink install pymol" to make sure you (still) have writing permission? Best regards - Luca On Monday, January 13, 2003, at 09:52 PM, boiler...@mac.com wrote: I have installed the following: 1. Apple's X11 2. Apple Dev Tools Dec. 2002 3. Fink Typed fink install pymol. After about 30 min. of text scrolled up my page, I get the following fatal error: make: *** [glut_8x13.o] Error 1 ### execution of failed, exit code 2 Failed: compiling glut-3.7-3 failed So what does this mean and how do I get around it. Craig 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 - luca.jov...@mssm.edu W3: http://www.mssm.edu/students/jovinl02
[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
