Thanks Rolf. That helps.
PM
On 1/20/2016 2:51 PM, Rolf Huehne wrote:
> 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
>
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