Fixed in the next daily build. The bug only affected residues where some hydrogens already existed before AddH was used. --Eric On Jan 18, 2012, at 1:05 PM, Eric Pettersen wrote:
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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