[Chimera-users] Minimizing RNA, no MMTK name for H3"
pett at cgl.ucsf.edu
Wed Jan 18 13:56:30 PST 2012
Fixed in the next daily build. The bug only affected residues where
some hydrogens already existed before AddH was used.
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 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
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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