[Chimera-users] Attaching a Probe to Modify an Existing Amino Acid

Shana Burstein sburstei at haverford.edu
Wed Jun 18 06:50:58 PDT 2014

I am an undergraduate student at Haverford College and I am attempting to
attach thiocyanate probes onto different sites along a protein by first
replacing the existing amino acid with a cysteine and then by adding a C
and N onto the S- of the Cys residue. I know it is possible to carry this
out manually using Tools>Structure Editing>Modify Structure, but I am
hoping to automate this process by calling an external .py script that will
primarily contain a list of preexisting Chimera commands.

I have been successful at converting the targeted amino acid to Cys using
"swapaa," building a CN residue called MSCN (using the createMolecule.py as
a guide), combining the two models into one ("combine selected close True")
and forming a bond between the Cys S and CN C atoms ("bond").

At this point, I am seeking help in automating the renaming of the modified
residue to MSCN. Currently, Chimera sees this residue as two different
separate residues called CYS and MSCN. Is there a way to combine these two
structures so that the label corresponds to MSCN and the residue number
corresponds to CYS?


Shana Burstein
Haverford College '15
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