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

[Eric Pettersen]

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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>
>
>
>
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