see http://chemapps.stolaf.edu/jmol/jsmol/mmtf.htm and
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 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
-- 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
*
* /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
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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