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 > ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. 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