On Apr 23, 2015, at 8:42 AM, Repic Matej <matej.repic@epfl.ch> wrote:
Hello,
I wonder if it is possible to construct a composite residue from two existing residues in Chimera?
What I would like to do is concatenate residues ALA100 (mid chain) and GLY200 (end of chain) to make a composite residue AGL100.
Chimera won't let me set the same residue number via the "resrenumber" command. Preferably, the composite residue would have all the atoms listed where ALA100 was in the original pdb.
While I realize there are trivial text editor-based workarounds I would like to know if there is a native way.
Hi Matej, This is kind of an unusual request, and I don't think there's any way to do it with the standard tools or commands. Nonetheless, almost anything is possible via Chimera's Python interface, so I believe this Python code will do what you want: # find the two residues; assumes they're in chain A and that only one structure is open from chimera import openModels, Molecule mol = openModels.list(modelTypes=[Molecule])[0] for r in mol.residues: if r.id.chainId == 'A' and r.id.position == 100: a100 = r if r.id.chainId == 'A' and r.id.position == 200: g200 = r # transfer the GLY200 atoms into ALA100 for a in g200.atoms: g200.removeAtom(a) a100.addAtom(a) # delete the now empty GLY200 residue, which would otherwise be problematic mol.deleteResidue(g200) # change the combined residue's type to "AGL" a100.type = "AGL" So if you put the above in a file that ends with '.py' then you can run it simply by opening it (either with File->Open or with the "open" command). I hope this helps somehow. :-) --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu