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
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