I’m trying to diagnose scripts written a few years ago that are no longer
working in the latest version of JSmol.
The same scripts work correctly in an older version of JSmol: ver. 14.2.4
(2014-08-03).
After updating JSmol, there is no error in the JSmol console, just a blank
JSmol canvas (no atoms appear).
I suspect that it’s syntax related to ‘select’? because nothing is being
selected for color or style, but not sure.
Here are a few excerpts: (I’ll just include an example of each type of call).
Does any of this look problematic or need fixes?
I can post the full scripts if helpful.
model 1
rotate z -108
rotate y 130
rotate z 32
zoom 100
restrict not :a and not solvent
select 147-157 and :a
define switch1a selected
select switch1a or switch2a or switch3a
define allswitcha selected
select :i and (177,179,181,192,198,199,200,202,205,211) #numbers are
less by 1 than those in the Nature 379 article
define ihb selected
#alpha subunit residues hbonding with beta
elect (switch1b and backbone) and not (173-176) #these sw1b
residues interact w/beta
select selected or (177,179,181) and :i
define subset1b selected
select :a and (172,173,174,176,179,185) or (switch2a and backbone)
define subset2a selected
select :a
color [xFFAD00] #orange
select gtp
color [x00C000] #guanine green
select gdp
color [xFF0000]
select :i or :b or :g or :d
spacefill on
select atomno=644 and :i
label "\u03b1"
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