Note that our numbering system now clicks higher in the second number every
time there is a new feature. The third number just indicates bug fixes. In
this case, the new features have to do with nucleic acids -- abilities to
color them using new schemes and also a new option "backboneBlocks" that
renders nucleic acids as abstract blocks similar to what DSSR can do
natively.
Bob
* Download Jmol-14.11.0-binary.zip (70.0 MB)
<https://sourceforge.net/projects/jmol/files/latest/download?source=files> *
Jmol.___JmolVersion="14.11.0" // released 4/1/2017
new feature: color NUCLEIC
-- for nucleic only (others will be grey)
-- based on DSSR nucleic color scheme:
G green, C yellow, A red, T blue, U cyan
new feature: set backboneBlocks; set backboneBlockHeight x.x
-- for nucleic only
-- overrides set backboneSteps
-- uses DSSR data if present (using calculate structure DSSR or load
=xxxx/dssr)
-- displays a DSSR block for each base based on dssr.nts.frame
-- x.x is height of box in Angstroms (default 0.5)
new feature: color property DSSR type
-- where type is one of:
bulges
coaxStacks
hairpins
hbonds
helicies
iloops
isoCanonPairs
junctions
kissingLoops
multiplets
nonStack
nts
pairs
ssSegments
stacks
stems
-- color is based on index into the list of the given structures
-- 0 (not of that structure), 1 (first entry), 2 (second entry), etc.
-- for example:
load =4fe5/dssr
backbone -0.5;set backboneSteps;
color property dssr junctions
color {color=red} grey // just making "not this type" grey
instead of red
[ most bases are grey, but one region is green and one region is blue ]
bug fix: drag-drop of PDB file with isolated nucleic acids gives odd
unbonded look
bug fix: set drawPicking TRUE does not report pending measurement
bug fix: DSSR calculation should reset after atom coordinate changes
bug fix: using Jmol.scriptWait() within a callback will not work, as it
will overwrite the currently running eval object
--
Robert M. Hanson
Larson-Anderson Professor 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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