The idea of a MUTATE command has been rattling around in my brain for a
while, and last night it hit me that we have all the pieces to do this
right -- structural comparison using Jmol bioSMARTS, flexible fit using
compare() and ROTATE BRANCH, atom alignment using COMPARE...ROTATE
TRANSLATE, easy ways to reconfigure bonds with CONNECT, and a very
serviceable MINIMIZE command. A few added tweaks, and nine hours work, and
what do you know? Jmol has a new command today!
Do try it out!
Bob
http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.12_2015.01.28.zip
Jmol.___JmolVersion="14.3.12_2015.01.28"
new feature: MUTATE command
-- operates only on last model present if multiple models are loaded
-- replaces one amino acid group with another
-- can read from RCSB or from user-specified file
-- examples:
mutate 33 lys // uses last occurrence of resno=33
mutate @3 arg // replaces group of atom 3
mutate @r @fname // replaces resno in variable r with file data
(use "==XXX" for RCSB)
mutate {r} his // same as above; r must be an atom selection
mutate 22 "myfile.cif" // user-defined replacement
bug fix: write "t.pdb" now correctly sequences groups and atoms, even after
mutation
new feature: resno is user settable
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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