Hi,
If you have the latest version of pymol and ANISOU in your pdb file, you
just have to type:
show ellipsoids,
http://www.pymolwiki.org/index.php/Ellipsoids
Mathieu
These kind of problems with r3d can usually be traced back to the
header. In fact, the rastep page has the following snippet:
Describe the same ellipsoids colored by Biso, and create an input
module with no header records for inclusion in a composite image:
rastep -h -Bcolor 10. 30. < infile.pdb > ellipsoids.r3d
cat header.r3d ellipsoids.r3d otherstuff.r3d | render -tiff
picture.tiff
If fancy0 (default) yields a proper header, you can probably extract
that, name it "header.r3d" and emulate the above commands.
James
On Dec 9, 2008, at 6:12 PM, Joseph Ho wrote:
Hello,
I would like to display thermal ellipsoids in pymol. What I did was
using rastep to make a r3d file and open it in pymol.
If I generate the r3d file with no extra options: rastep < infile.pdb
> outfile.r3d, pymol can open it.
But if I generate the file with rastep -auto -fancy1 < infile.pdb >
outfile.r3d, pymol cannot open it.
I know I can use render to make a picture, but I would like to be
able to view the picture in 3-D in pymol, so I need to make a r3d
file (with the -auto -fancy1 options in rastep) that pymol can read.
Is it possible? Any suggestions for other ways of doing the same thing?
Joe
--
James Stroud
UCLA-DOE Institute for Genomics and Proteomics
611 Charles E. Young Dr. S.
Los Angeles, CA 90095
http://www.jamesstroud.com
