Dear Chimera developer, I am looking for a program to add hydrogen atoms to a pdb file. Chimera is a good tool to do it. After adding hydrogen atoms to a PDB file, I'd like to save the result file to a PDB file, not tiff image . Chimera can do that now? Thanks. Euna Jeong School of Computer Science and Engineering Inha University Inchon 402-751, South Korea 82-32-860-7388 (phone) 82-32-863-4386 (fax)
Dear Euna, If you have a UNIX system, the Midas emulator's "pdbrun" command should be able to do what you want. Only the transformed coordinates are written out. I recommend the "nouser" keyword to avoid getting a lot of extra information in USER records. If there are multiple models, they all get sent to one file with END records in between (some postprocessing may be required). example usage: pdbrun all nouser cat >file.pdb See: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/pdbrun.html The "write" command is much better for this purpose (and works for all of the platforms) but is not in the current release. It has been implemented in our working version and will be available in the next release. See: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html The next release should be out at the end of October. Finally, I should note that the current method of adding hydrogens uses appropriate bond angles and distances, but makes no real checks for steric clashes. It was written with the expectation that some kind of energy minimization would performed on the resulting model (outside Chimera). If you observe steric clashes but aren't going to minimize the model, you may have to relieve such clashes "by hand" by using bond rotations. We are working on a more sophisticated method of adding hydrogens that avoids steric clashes and preserves hydrogen bonding. This method may or may not make it into the next release. It definitely will be available by the release after that. Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu On Thursday, September 12, 2002, at 12:59 AM, Euna Jeong wrote:
Dear Chimera developer,
I am looking for a program to add hydrogen atoms to a pdb file. Chimera is a good tool to do it. After adding hydrogen atoms to a PDB file, I'd like to save the result file to a PDB file, not tiff image . Chimera can do that now? Thanks.
Euna Jeong School of Computer Science and Engineering Inha University Inchon 402-751, South Korea 82-32-860-7388 (phone) 82-32-863-4386 (fax)
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Eric Pettersen -
Euna Jeong