[ccp4bb] rastep r3d file for pymol
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
Re: [ccp4bb] rastep r3d file for pymol
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
Re: [ccp4bb] rastep r3d file for pymol
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
