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

Tom Goddard goddard at sonic.net
Wed Jan 18 12:39:52 PST 2012

Hi Elaine,

   Thanks for pointing me to bug report #9062 which gives an RNA example 
2ixz where minimization works.


PDB 2ixz terminates the 3' end of the RNA with a hydrogen named HO3' 
instead of the name Chimera adds which is H3".

   I'll submit a bug report to either get Chimera hydrogen adding to 
name this atom HO3' or get Chimera MMTK to accept H3" as a synonym for 
HO3'.  The hydrogen on the O2' sugar atom has IUPAC name HO2' and that 
is what the PDB uses.  But I didn't see anything on the web for the 
naming of the O3' hydrogen.


> Hmm, I thought I had reported that and it was fixed, but no, it was different RNA atom problem!
> http://plato.cgl.ucsf.edu/trac/chimera/ticket/9062
> If you find a way to run the minimization, I would be curious as to whether minimization actually improved the structure.  In general (with frustrated structures) I find minimization gets stuck and doesn't do much, possibly makes the structure worse.
> Elaine
> 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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