From: Robert H. <ha...@st...> - 2015-01-30 16:16:14
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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 |