MUTATION works the same in JavaScript as Java. Just
mutate 20 ARG
like that. Done.
No special minimization going on here, though. That's the next phase.
Bob
On Wed, Jan 28, 2015 at 2:18 PM, Jim Hu <jim.hu.bio...@gmail.com> wrote:
> 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/
> _______________________________________________
> Jmol-users mailing list
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>
>
--
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
------------------------------------------------------------------------------
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/
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
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