Investigating the cause for this, but the workaround is to put "del H" in front of the "min" command.  For some reason, if Chimera has to add all the hydrogens it uses the name HO3' whereas if only that hydrogen is missing then it uses H3''.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Jan 18, 2012, at 12:08 PM, Tom Goddard wrote:

I'm trying to minimize a few RNA nucleotides using Chimera (Tools / Structure Editing / Minimize Structure) but I get the error message

    No MMTK name for atom H3" in standard residue C.

Chimera adds hydrogens and creates this H3" atom on the 3' terminus (O3' atom) of the RNA.  Is there some trick to terminate the 3' end of the RNA so MMTK minimization will work?  Here's an example of the problem

   open 2d1b
   del ~ :39.B
   min spec #0 nogui true

Thanks!

   Tom

_______________________________________________
Chimera-users mailing list
Chimera-users@cgl.ucsf.edu
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users