On 01/20/2016 07:37 PM, Pshemak Maslak wrote:
> 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).
>
The data structure below 'dssr' has changed (at least in my example
below), shown by printing the hash keys:
---- Example ---------
load =3cro;
calculate STRUCTURE DSSR;
x=getProperty("auxiliaryinfo");
y=x.models[1].dssr;
print y.keys;
----- Output in Jmol 14.2.9 -----------------
basePairs
dbn
hBonds
helices
seq
singleStranded
stems
summary
----- Output in Jmol 14.4.1 -----------------
counts
dbn
hbonds
helices
metadata
nts
num_hbonds
num_helices
num_nts
num_pairs
num_ssSegments
num_stacks
num_stems
pairs
paths
ssSegments
stacks
stems
---------------------------------------------
The 'basePairs' substructure from Jmol 14.2.9 might be resembled by the
'pairs' substructure from Jmol 14.4.1 but the 'res1' and 'res2'
properties are missing:
----- 'basePairs' entry -----------------
{
DSSR : "cW-W"
LW : "cWW"
Saenger : 20
bp : "A-T"
bpBuckle : -11.52
bpChi1 : -101.6
bpChi2 : -99.1
bpDistC1C1 : 10.51
bpDistC6C8 : 9.22
bpDistNN : 8.56
bpLambda1 : 53.1
bpLambda2 : 43.6
bpOpening : -13.25
bpPropeller : -5.68
bpShear : 0.68
bpStagger : 0.32999998
bpStretch : -0.68
bpTorCNNC : -12.0
g1 : "A"
g2 : "T"
heIncl : 3.48
heRise : 3.2
heRiseC1 : 3.2
heTip : 3.6399999
heTwist : 30.34
heTwistC1 : 32.16
heXDisp : -1.42
heYDisp : -0.84
helixId : 1
id : 1
info : " =-101.6 anti) ~C2'-endo lambda=53.1 =-99.1 anti)
~C2'-endo lambda=43.6 \n d C1'-C1')=10.51 d N1-N9)=8.56 d
C6-C8)=9.22 tor C1'-N1-N9-C1')=-12.0\n H-bonds[2]:
\"N6(amino)-O4(carbonyl)[2.24],N1-N3(imino)[2.38]\"\n
interBase-angle=13 Simple-bpParams: Shear=0.73 Stretch=-0.63
Buckle=-4.8 Propeller=-11.9\n bp-pars: [0.68 -0.68 0.33
-5.68 -11.52 -13.25]\n"
key : "[DA]2:A [DT]20:B"
name : "WC"
nt1 : "[DA]2:A"
nt2 : "[DT]20:B"
res1 : "2:A"
res2 : "20:B"
stRise : 3.26
stRiseC1 : 3.26
stRoll : 1.8199999
stShift : 0.24
stSlide : -0.56
stTilt : -1.9
stTwist : 30.23
stTwistC1 : 32.05
stemId : 1
}
----- 'pairs' entry----------------------
{
"DSSR" : "cW-W"
"LW" : "cWW"
"Saenger" : "20-XX"
"bp" : "A-T"
"index" : 1
"name" : "WC"
"nt1" : "|1|A|DA|2||||"
"nt2" : "|1|B|DT|20||||"
}
-----------------------------------------
If you are lucky, there might be an option to go back to the former
'DSSR' calculation method (which seems to have changed).
Or you could build the 'res1' and 'res2' information by reformatting the
'nt1' and 'nt2' information.
Regards,
Rolf
--
Rolf Huehne
Postdoc
Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany
Phone: +49 3641 65 6205
Fax: +49 3641 65 6210
E-Mail: rhue...@leibniz-fli.de
Website: http://www.leibniz-fli.de
Scientific Director: Prof. Dr. K. Lenhard Rudolph
Head of Administration: Dr. Daniele Barthel
Chairman of Board of Trustees: Burkhard Zinner
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