I have a subset of a protein active site containing a metal and its coordinating residues. Is there a tool to automatically measure all bond length, all angles and dihedrals in the subset.
Hi, Bakary Ntji Diallo!
I do not fully understand your question. Do you have a crystal structure of the protein's active site with a metal center? If you do, just open it in a crystallographic data program and measure by hand (there cannot be that many coordinating atoms!), since automation will give you all atoms within a certain radius of which many (most?) will not be truly bonding. Did I interpret your question correctly?
regards,
Daniel
Thank you for your reply
Avogadro is good tool to use. It will give all bonds, angles and dihedrals properties on a loaded .pdb file for example.
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