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
Hi Elaine, Thanks for pointing me to bug report #9062 which gives an RNA example 2ixz where minimization works. http://plato.cgl.ucsf.edu/trac/chimera/ticket/9062 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. Tom
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
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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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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Eric Pettersen -
Tom Goddard