I have noticed that a script that worked with a version that was current
in March 2015 (14.2.13_2015.03.23) does not work with the latest two (or
more) versions.
Briefly, I have a short DNA fragment in a png file that loads with the
following commands:
load DNAH-2.png;
set showHydrogens TRUE;
moveto 1.0 { -289 956 53 43.88} 100.0 0.0 0.0;
calculate STRUCTURE DSSR;
pairsCG = getProperty("auxiliaryinfo.models[1].dssr.basepairs[select
res1,res2 where bp='C-G' or bp='G-C']");
pairsAT = getProperty("auxiliaryinfo.models[1].dssr.basepairs[select
res1,res2 where bp='A-T' or bp='T-A']");
The load script does not generate any visible errors (in Java script in
a browser or in Java on the desktop) and the structure loads fine.
and then I have a script that "hides" base pairs, leaving just one that
is "zoomed into" user view and centered.
select @{pairsCG[1].res1},@{pairsCG[1].res2}; color translucent 9;
select @{pairsCG[12].res1},@{pairsCG[12].res2}; color translucent 9;
select @{pairsCG[11].res1},@{pairsCG[11].res2}; color translucent 9;
delay 0.1;
select @{pairsCG[2].res1},@{pairsCG[2].res2}; color translucent 9;
select @{pairsCG[10].res1},@{pairsCG[10].res2}; color translucent 9;
select @{pairsAT[5].res1},@{pairsAT[5].res2}; color translucent 9;
delay 0.1;
select @{pairsCG[3].res1},@{pairsCG[3].res2}; color translucent 9;
select @{pairsCG[9].res1},@{pairsCG[9].res2}; color translucent 9;
select @{pairsCG[8].res1},@{pairsCG[8].res2}; color translucent 9;
delay 0.1;
select @{pairsAT[1].res1},@{pairsAT[1].res2}; color translucent 9;
select @{pairsAT[4].res1},@{pairsAT[4].res2}; color translucent 9;
delay 0.1;
select @{pairsCG[4].res1},@{pairsCG[4].res2}; color translucent 9;
select @{pairsCG[7].res1},@{pairsCG[7].res2}; color translucent 9;
delay 0.1;
select @{pairsCG[5].res1},@{pairsCG[5].res2}; color translucent 9;
select @{pairsAT[3].res1},@{pairsAT[3].res2}; color translucent 9;
delay 0.1;
select @{pairsCG[6].res1},@{pairsCG[6].res2}; color translucent 9;
select @{pairsAT[2].res1},@{pairsAT[2].res2};
moveto 1.0 { 944 144 296 71.87} 300.24 0.0 0.0 {31.878408 48.3921
30.248789} 38.85318;
center@989; hbonds calculate; hbonds 0.2; hbonds 0.2; color hbonds
yellow;
That script worked fine with the old JSmol,, but it fails on the first
line with the newer versions. The error happens in the first line:
script ERROR: unexpected end of script command
----
select { @ { pairsCG [ 1 ] . res1 } << or @ { pairsCG [ 1 ] .
res2 } }
Any help is solving that puzzle would be appreciated (DNAH-2.png is
available upon request).
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