Re: [Jmol-users] Amino Acid Mutation Is Finally in Jmol

[Robert H. <ha...@st...>]

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 <ha...@st...> 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