Re: [PyMOL] wild card

2004-02-19 Thread Laurence Pearl
Beware of sweeping statements - I work with nucleic acids (mostly bound to proteins) and I am continually irritated by the use of * in nucleic acid names, and I think I qualify as anyone. Now that the ASCII code has settled down somewhat, ' could take it's rightful place in PDB files,

[PyMOL] Povray

2004-02-19 Thread Tsjerk Wassenaar
Hi Guys, I seem to have some trouble rendering with povray. The render starts and finishes fine, and the image is created, but Pymol crashes with a segmentation fault as soon as the rendering is done. The image is not loaded to the viewer. I'm using povray 3.5 with Pymol 0.93 on a laptop

Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

2004-02-19 Thread Robert Campbell
Michael, * Michael Banck mba...@gmx.net [2004-02-19 12:24] wrote: On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote: For me PyMol on SuSE 8.2 crashed always when raytracing a line element. That seems to be identical to Debian Bug #229080 (http://bugs.debian.org/229080)

Re: [PyMOL] Povray

2004-02-19 Thread Robert Campbell
* Tsjerk Wassenaar t.a.wassen...@chem.rug.nl [2004-02-19 04:30] wrote: Hi Guys, I seem to have some trouble rendering with povray. The render starts and finishes fine, and the image is created, but Pymol crashes with a segmentation fault as soon as the rendering is done. The image is not

[PyMOL] using the build function

2004-02-19 Thread Moriarty, Daniel
Hello everyone, I'm trying to build some model proteins for a diagram showing a protein unfolding over several steps. I'm using the build function in the 0.95beta10 release. The main problem is that I can't control the angle of the protein chain, so the chain just goes off in one direction

RE: [PyMOL] using the build function

2004-02-19 Thread Warren DeLano
Dan, I think it's fair to say that PyMOL's currently molecular building capabilities are at the stage of a technology demonstration/proof-of-concept, but very little effort has yet been expended toward making them useful for real work. Part of that is because we don't yet have

[PyMOL] drawing hydrogen bonds or dashes

2004-02-19 Thread John Berrisford
I have searched the manual and forum and cannot find how to draw a hydrogen bond between two specific atoms. I wish to do the equivalent to the following molscript command line position res-atom A97 OE1 to position res-atom M200 MN; which draws a line between two atoms A97 OE1 and Mn200. So not

[PyMOL] cartoons

2004-02-19 Thread ALEX DAJKOVIC
dear all, i am new to pymol and i have a question about cartoons. i saw the demo of cartoon ribbons and really liked it, but i haven't been able to get my protein displayed that way. when i give the command cartoon automatic all i get is a simple line that apparently traces the backbone of my

[PyMOL] Making the selection indicators bigger

2004-02-19 Thread Matthew Zimmerman
Hello -- So I've installed PyMOL onto a new system, and I'm having trouble with the little pink indicators that pop up when you make a selection. On this machine they appear to about a single pixel wide, which on a 1280x1024 resolution screen makes them practically invisible! I've tried

Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

2004-02-19 Thread Morri Feldman
Hi Michael, I downloaded pymol-0_93-bin-linux-libc6-i386.tgz to my Debian machine. When I run this copy rather than the .deb version I am able to ray trace lines without a crash. Best, Morri On Thu, 19 Feb 2004, Michael Banck wrote: On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund

RE: [PyMOL] Making the selection indicators bigger

2004-02-19 Thread Warren DeLano
Matt, Try: set selection_width, 6 set selection_width, 7 set selection_width, 8 Cheers, Warren -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Matthew Zimmerman Sent: Thursday,

RE: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

2004-02-19 Thread Warren DeLano
Morri has a good point: The standalone pymol-0_xx-bin-linux-libc6-i386.tgz binary builds should be capable of running on virtually any current x86-based Linux system: RH, SUSE, Debian, Fedora, or whatever. So, if you're having trouble with compilation or use of

RE: [PyMOL] molecular surface colored by hydrophobicity

2004-02-19 Thread Warren DeLano
Rongjin, PyMOL can certainly color surfaces by atom color and other properties. show surface color green, elem c color violet, elem n+o But Grasp's hydrophobicity function may be doing something more sophisticated then that... Cheers, Warren -Original Message- From:

[PyMOL] cartoons

2004-02-19 Thread Scott Classen
Alex try typing: dss this will assign secondary structure to your PDB and then the cartoon will show you the sheets and helices you desire. Scott On Feb 19, 2004, at 1:44 PM, ALEX DAJKOVIC wrote: dear all, i am new to pymol and i have a question about cartoons. i saw the demo of cartoon