[chimera-dev] question about AddH

Eric Pettersen pett at cgl.ucsf.edu
Thu Sep 12 12:24:54 PDT 2002

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 

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 at 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)
> _______________________________________________
> Chimera-dev mailing list
> Chimera-dev at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev

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