Hi Nicole,

you could  note the pdb name of the old structure and use the homology modelling tool provided in Chimera (it is based on Modeller then you need a password to access the server) to model the new sequence, using the old one as a template. Check that the alignment is correct (identical alignment except the new region) and let the server prepare your structure.

Hope it helps,

Regards,

Marco

Hello,

I have a structure which I've cut a section out of and I am working on connecting the two loose ends together. I wanted to connect them with two glycine residues - since they are easiest to work with and have no side chains. I am doing this using the Modify Structure option under the Build structure tool and adding one atom at a time. However, when I try to minimize my newly created glycine, I get the error message "No MMTK name for atom "H1" in standard residue "GLY"" (I've attached a picture of my reply log). I'm not sure how to troubleshoot this.

Is there a better way to connect two ends of a peptide, or should I change the way I am using the modify structure tool?

Thank you.

Nicole Ostrovsky

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Dr.Marco Sette, Ph.D.
Department of Chemical Sciences and Technology
University of Rome, "Tor Vergata"
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