Cool!
After a long period of not having time, I just started looking again at getting
the jsmol2wp Wordpress plugin into wordpress.org. How does this fit with jsmol?
I'm assuming that some of the stuff requires Jmol to do the processing.
Jim
On Jan 28, 2015, at 11:21 AM, Robert Hanson <hans...@stolaf.edu> wrote:
> 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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=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054
------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
_______________________________________________
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