[Chimera-users] Minimizing RNA, no MMTK name for H3"

Eric Pettersen pett at cgl.ucsf.edu
Wed Jan 18 13:05:27 PST 2012

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 Pettersen
                         UCSF Computer Graphics Lab

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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