OK, some adjustments.
http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.12_2015.01.30.zip
Jmol.___JmolVersion="14.3.12_2015.01.30"
new feature: MUTATE command
-- operates only on last model present if multiple models are loaded
-- replaces one *or more *amino acids group with others
-- can read from RCSB or from user-specified file
-- examples:
mutate 33 lys // replace resno=33 with lysine
mutate @3 arg // replaces group of atom 3 with arginine
mutate @r gly // replaces groups in variable r with glycine
mutate 22 "myfile.cif" // user-defined replacement
mutate {1-3} ala // replace first three residues with alanine
mutate {1-5} GLVAG // (sequence codes) replace residues 1-5 with
gly-leu-val-ala-gly
mutate {1-3} ~LYS // (force 1-character sequence codes) replace
1-3 with leu-tyr-ser
mutate {1-3} A?L // replace 1 with ala, 3 with leu; skip 2
mutate {within(sequence, "GAT")} GYT // replace locations of GAT with
GYT (needs testing)
mutate 35 @fname // replaces resno=35 with file data (use
"==ALA" or "~A" for RCSB)
mutate {r} his // same as above; r must be an atom selection
bug fix: code fixes relating to calculate structure in 01.29
On Fri, Jan 30, 2015 at 9:30 AM, Robert Hanson <hans...@stolaf.edu> wrote:
> alt-loc should be fine; the entire group is being replaced, so there is no
> problem with names. Can't help with the 400 -- even if you could do that,
> you would not want to using Jmol, I think. Better tools for that. But for
> small numbers, we could add mutations as alt-loc. Actually, that's a lot
> easier that creating a whole new group. Way before 400 you will run into
> the problem that the allowed number of bonds that link residues will be
> exceeded (20? something like that).
>
>
--
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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