[Chimera-users] building peptide with ornithine

Elaine Meng meng at cgl.ucsf.edu
Thu Oct 6 16:40:37 PDT 2016

P.S.  I assumed you already knew about peptide-building in Chimera… to clarify, it can be done with the Build Structure tool (in menu under Tools… Structure Editing), the “Start Structure” section:



> On Oct 6, 2016, at 4:30 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Jesse,
> After building the peptide with some other amino acid at the positions where you want ornithine, you could use the SwissSidechain plugin to “mutate” them to ornithine.  This plugin is available (separately from Chimera) here:
> <http://www.swisssidechain.ch/visualization/chimera.php>
> …and I did check that their database includes ornithine (ORN):
> <http://www.swisssidechain.ch/browse/family/table.php?family=lysine>
> I see that that table header says “D-form” but they have both L- and D-forms available.  There are two separate plugins available from the swisssidechain link above for mutating into L- and D- amino acids.
> If you don’t want to deal with a plugin:
> The other way you suggest is also possible but because the C would need to change from sp2 to sp3 if you start with glutamine, a better starting point would be lysine.  Then you’d just delete the terminal N on the sidechain and change the remaining terminal C to a tetrahedral N in Build Structure, Modify Structure.  
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On Oct 6, 2016, at 1:22 PM, Jaynes, Jesse <jjaynes at mytu.tuskegee.edu> wrote:
>> Hi Folks:
>> I am interested in generating a 23 amino acid peptide with several ornithines present.  Is it possible? If not can I construct it with glutamine as a replacement for ornithine and then just take the carbonyl group and replace the oxygen with 2 hydrogens.
>> Thank You, Jesse Jaynes

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