Protein Structure Regularization

goldman at mbcl.rutgers.edu goldman at mbcl.rutgers.edu
Wed Apr 1 07:36:37 EST 1992


In article <887 at alsys1.aecom.yu.edu>, reiner at medusa.bioc.aecom.yu.edu (Peter D. Reiner) writes:
> I'm looking for a program to correct bond lengths and rotations
> of a protein after they've been mangled to fit an electron density.
> This program must allow me to fix certain atoms in space and then
> manover all other atoms.

The tool you want is in Frodo.  It's called REFI (accessible through the
onscreen menu as .REFI).  You can use .FIX to fix particular atoms,
constrain to certain types of backbone geometry, (alpha, beta, some turns)
and then do Hermans-style regularisation.  Do about 20 cycles at a time and
(this is my approach) do short pieces (say 4-8 residues). Keep the ends
fixed, because the regularisation appears to be an N-to-C affair.  (There
is an option in CHAT to fix the ends.)  Don't accept anything worse than
(say) an rmsd on bond lengths of 0.1 A, and on bond angles of 3 degrees. 
If the numbers ARE worse than that, then that portion of the
protein/nucleic acid has been fitted incorrectly.  If you can't see how to
fix it, you should at least note it down as a place to go back to later.

               Adrian Goldman

Goldman at MBCL.Rutgers.Edu



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