Is the mmtf file supposed top be a part of the release, or is it only on your
server? I do not find it in the jsmol directory.
> On Apr 20, 2016, at 2:07 AM, Robert Hanson <hans...@stolaf.edu> wrote:
>
> see http://chemapps.stolaf.edu/jmol/jsmol/mmtf.htm
> <http://chemapps.stolaf.edu/jmol/jsmol/mmtf.htm> and
> http://chemapps.stolaf.edu/jmol/zip/jmol-14.5.4_2016.04.19.zip
> <http://chemapps.stolaf.edu/jmol/zip/jmol-14.5.4_2016.04.19.zip>
>
> needs testing; highly experimental.
>
> Bob
>
>
> Jmol.___JmolVersion="14.5.4_2016.04.19"
>
> FEATURE NOTE: DSSP calculation at http://www.cmbi.ru.nl/dssp.html
> <http://www.cmbi.ru.nl/dssp.html> as changed
> from the original version, now emphasizing pi-helices (type
> "helix-5")
> insteda of alpha. The pi-helix set is determined first, then
> alpha helices
> (helix-4), then 3-10 helices (helix-3). I am not changing the
> order of
> determination in Jmol because I think this is a bug in that
> algorithm.
>
> new feature: preliminary MMTF reader
> -- MacroMolecular Transmission Format (MMTF, from RTSB)
> -- see https://github.com/rcsb/mmtf/blob/master/spec.md#overview
> <https://github.com/rcsb/mmtf/blob/master/spec.md#overview>
> -- binary format for file transfer and molecule construction
> -- uses MessagePack binary JSON format
> -- entirely experimental; not for general consumption
> -- biomolecule processing works
> -- DSSP secondary structure is read
> -- use LOAD =xxxx.mmtf for quick loading
>
> *
> * JmolData RCSB MMTF (macromolecular transmission format) file reader
> *
> * see https://github.com/rcsb/mmtf/blob/master/spec.md
> <https://github.com/rcsb/mmtf/blob/master/spec.md>
> *
> * /full/ specification as of 2016.4.18 is implemented,including:
> *
> * reading atoms, bonds, and DSSR secondary structure
> *
> * load =1f88.mmtf
> *
> *
> * reading space groups and unit cells, and using those as per other readers
> *
> * load =1crn.mmtf {1 1 1}
> *
> * reading bioassemblies (biomolecules) and applying those transformations
> *
> * load =1auy.mmtf FILTER "biomolecule 1;*.CA,*.P"
> *
> * reading biomolecules and lattices, and loading course-grained
> *
> * load =1auy.mmtf {2 2 1} filter "biomolecule 1;bychain";spacefill 30.0;
> color property symop
> *
> *
>
> bug fix: certain viral capsid CIF files will fail to load due to this line:
> XAU '(X0)(1-10,21-25)' A,B,C
>
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr <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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Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu
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