Dear Bob,
Here are the answers to your queries:
Q: Is this the Jmol applet or the application?
This is in Jmol Application not the applet.
You are sure there are not two models (two frames) showing? That your
modelIndex parameter is not -1?
I can confirm that the model index parameter is not -1, I loaded to two PDB
files simultaneously and two models were created with index 0 & 1 respectively.
See below, a dumb from the debugger of the auxilaryInfo hash table for one of
the models. If you search for fileName in the dumb you’ll notice that it
contains the string “null". Note: this problem doesn’t occur when PDB files are
loaded one after the other and superposed, it only happens when multiple files
are loaded simultaneously.
{PDB_CONECT_bonds=[[I@6f0c9d40, [I@368664f8, [I@5eb59e05, [I@3c208a9e,
[I@37cde6c7, [I@3269f562, [I@40de109c, [I@78121663, [I@20312c78, [I@5d0e0ff9,
[I@6de4be34, [I@52d1ce5, [I@2cd6a2d4, [I@10a0170, [I@49570a7b, [I@24f0fd80,
[I@3d293bc8, [I@6c79bc9c, [I@1d8c67ba, [I@3e339576, [I@4ab01e03, [I@6b8cd695,
[I@15c3cde9, [I@37f97202, [I@7d7322f8, [I@70c66bbd, [I@7b615cc9, [I@77448c5,
[I@63f4de31, [I@20acca71, [I@51da4db9, [I@74cd1527, [I@310d48d9, [I@7734e3cb,
[I@7400df11, [I@6878889b, [I@33e85ecd, [I@6312c9c0, [I@11187ae4, [I@3d08140c,
[I@4c673b56, [I@394ea7d3, [I@6b533544, [I@1686f456, [I@634ed05b, [I@2f7283de,
[I@5df97a61, [I@7c7c01cc, [I@6925ca10, [I@5272c899, [I@444e8ac4, [I@58a081e0,
[I@1f12b5ae, [I@5b6090d5, [I@6bc839d7, [I@373b1acf, [I@3d8e6643, [I@62b7bf1f,
[I@489b241f, [I@2799b2a1, [I@696b746f, [I@367b711a, [I@27d11016, [I@4d37a2f7,
[I@7fcd7f32, [I@12d33270, [I@3d2dc19c, [I@4d7decd4, [I@59dd2ea6, [I@5216d75f,
[I@1e4cda0, [I@23dd9a04, [I@13c528c7, [I@770db9cf, [I@50a3e343, [I@1f614ee9,
[I@2558ded2, [I@3f01c877, [I@70778d2f, [I@657483ce, [I@6b97ffc, [I@37ca5d2c,
[I@7b98a00f, [I@3ab32641, [I@77b8e874, [I@127ee892, [I@2cd8aa0a, [I@f7a00fe,
[I@3fb1b22d, [I@5a6ef731, [I@330f9e8c, [I@6cad15e3, [I@5e3ff281, [I@73455108,
[I@3cf14a12, [I@38775262, [I@197d0417, [I@4069cb21, [I@76feb8e4, [I@7498101b,
[I@5b4ef23, [I@b8a0c77, [I@830bc7a, [I@3c1c6daf, [I@1ef350f8, [I@45c10ee5,
[I@489fa94b, [I@1731c4e2, [I@13c1326c, [I@5ebaa0d7, [I@6bda9fba, [I@72d550f7,
[I@689d5e93, [I@632af74f, [I@5cb293df, [I@4383256, [I@6d39d84, [I@3277929e,
[I@7a13c364, [I@3f7cf4f2, [I@25597124, [I@2bb4f473, [I@4fd81a82, [I@17dbacef,
[I@79e53f61, [I@757e4b42, [I@7afd5365, [I@300b3401, [I@60451b56, [I@67666847,
[I@779079b5, [I@1e52f07a, [I@5685d74d, [I@2f5b98a, [I@76dc25b0, [I@7f04ca31,
[I@7c35523, [I@28d585b8, [I@3f33d4b7, [I@66bfc422, [I@7bc8ff9b, [I@7fb45d1f,
[I@5e83a832, [I@4605f914, [I@7a8df268, [I@270c0483, [I@640dea68, [I@d2972a4,
[I@1822cfdb, [I@5fcde840, [I@5498177b, [I@12e2f31e, [I@1c30aa8e, [I@2c8fcea0,
[I@38382785, [I@3dc7499f, [I@243af073, [I@7692d09a, [I@fefc5c2, [I@863ee11,
[I@7ba92e06, [I@1bdf27e9, [I@6aef2085, [I@7d6b58af, [I@4f00801a, [I@2d82067c,
[I@3e7ae041, [I@19736901, [I@52382a65, [I@6fb467b8, [I@625eae7, [I@41cb043,
[I@1764d9a7, [I@5ba1f554, [I@72fa5e15, [I@138566a1, [I@221d3c97, [I@764276d5,
[I@56e894fe, [I@6ee040ec, [I@25522023, [I@40431e82, [I@521e3d10, [I@3e15f09f,
[I@a728c46, [I@529d2484, [I@71c8757a, [I@6048e2d4, [I@7e464227, [I@45c4f06f,
[I@77953e08, [I@50ec2c6c, [I@1cf70b2c, [I@7ed2c755, [I@2069d3f9, [I@11d704d4,
[I@35ddd3a9, [I@5ddd5228, [I@33c5a471, [I@1a1df779, [I@41862f08, [I@76fd6902],
initialBondCount=202, fileType=array, compoundSource=[{EC=1.8.7.1,
EXPRESSION_SYSTEM=ESCHERICHIA COLI, ORGANISM_TAXID=4577, MOL_ID=1, GENE=SIR,
EXPRESSION_SYSTEM_TAXID=562, SYNONYM=ZMSIR, ENGINEERED=YES, CHAIN=A, B,
ORGANISM_SCIENTIFIC=ZEA MAYS, select=(:A,:B), MOLECULE=SULFITE REDUCTASE
[FERREDOXIN], CHLOROPLASTIC, ORGANISM_COMMON=MAIZE},
{EXPRESSION_SYSTEM=ESCHERICHIA COLI, ORGANISM_TAXID=4577, MOL_ID=2, GENE=FDX1,
PFD1, EXPRESSION_SYSTEM_TAXID=562, SYNONYM=FERREDOXIN I,FD I, ENGINEERED=YES,
CHAIN=C, ORGANISM_SCIENTIFIC=ZEA MAYS, select=(:C), MOLECULE=FERREDOXIN-1,
CHLOROPLASTIC, ORGANISM_COMMON=MAIZE}], biomolecules=[{molecule=1, biomts=[[
[1.0 0.0 0.0 0.0]
[0.0 1.0 0.0 0.0]
[0.0 0.0 1.0 0.0]
[0.0 0.0 0.0 1.0] ]], name=biomolecule 1, chains=[:A;:C;], atomCount=5467,
title=REMARK 350 BIOMOLECULE: 1}, {molecule=2, biomts=[[
[1.0 0.0 0.0 0.0]
[0.0 1.0 0.0 0.0]
[0.0 0.0 1.0 0.0]
[0.0 0.0 0.0 1.0] ]], name=biomolecule 2, chains=[:B;], atomCount=4690,
title=REMARK 350 BIOMOLECULE: 2}],
pdbSites={AC9={groups=[SER]38:C,[CYS]39:C,[ARG]40:C,[GLY]42:C,[SER]43:C,[CYS]44:C,[CYS]47:C,[LEU]75:C,[CYS]77:C,
nResidues=9},
AC8={groups=[VAL]424:B,[ASN]453:B,[ASN]455:B,[HOH]832:B,[HOH]890:B,
nResidues=5},
AC7={groups=[ARG]124:B,[ARG]193:B,[LYS]276:B,[LYS]278:B,[SRM]702:B,
nResidues=5},
AC6={groups=[TYR]106:B,[GLN]108:B,[ARG]124:B,[ARG]153:B,[THR]155:B,[THR]156:B,[ARG]157:B,[THR]159:B,[GLN]161:B,[HIS]163:B,[ARG]275:B,[LYS]276:B,[LYS]278:B,[GLY]318:B,[MET]319:B,[GLY]320:B,[ARG]368:B,[GLN]454:B,[ALA]493:B,[CYS]494:B,[PRO]495:B,[LEU]499:B,[CYS]500:B,[PRO]501:B,[LEU]502:B,[ASN]542:B,[GLY]543:B,[CYS]544:B,[ARG]546:B,[SF4]701:B,[PO4]703:B,[HOH]805:B,[HOH]807:B,[HOH]811:B,[HOH]812:B,[HOH]836:B,[HOH]849:B,[HOH]895:B,[HOH]898:B,[HOH]909:B,
nResidues=40},
AC5={groups=[CYS]494:B,[PRO]495:B,[CYS]500:B,[ALA]503:B,[THR]538:B,[GLY]539:B,[CYS]540:B,[ASN]542:B,[GLY]543:B,[CYS]544:B,[SRM]702:B,
nResidues=11},
AC4={groups=[VAL]424:A,[ASN]453:A,[ASN]455:A,[HOH]825:A,[HOH]884:A,
nResidues=5},
AC3={groups=[ARG]124:A,[ARG]193:A,[LYS]276:A,[LYS]278:A,[SRM]702:A,[HOH]804:A,
nResidues=6},
AC2={groups=[TYR]106:A,[GLN]108:A,[ARG]124:A,[ARG]153:A,[THR]155:A,[THR]156:A,[ARG]157:A,[THR]159:A,[GLN]161:A,[HIS]163:A,[ARG]275:A,[LYS]276:A,[LYS]278:A,[GLY]318:A,[MET]319:A,[GLY]320:A,[ARG]368:A,[GLN]454:A,[ALA]493:A,[CYS]494:A,[PRO]495:A,[CYS]500:A,[PRO]501:A,[LEU]502:A,[ASN]542:A,[GLY]543:A,[CYS]544:A,[ARG]546:A,[SF4]701:A,[PO4]703:A,[HOH]816:A,[HOH]817:A,[HOH]849:A,[HOH]879:A,[HOH]889:A,[HOH]899:A,[HOH]904:A,[HOH]932:A,[HOH]969:A,[HOH]993:A,
nResidues=40},
AC1={groups=[CYS]494:A,[CYS]500:A,[ALA]503:A,[THR]538:A,[GLY]539:A,[CYS]540:A,[ASN]542:A,[GLY]543:A,[CYS]544:A,[SRM]702:A,
nResidues=10}}, modelNumber=1, modelNumberDotted=1.1, modelFileNumber=1000001,
PDB_CONECT_firstAtom_count_max=[I@6805bd80, hetNames={FES=FE2/S2 (INORGANIC)
CLUSTER, MG=MAGNESIUM ION, PO4=PHOSPHATE ION, SRM=SIROHEME, SF4=IRON/SULFUR
CLUSTER}, modelName=5H92, initialAtomCount=10157, unitCellParams=[F@1d5639c6,
isPDB=true, spaceGroup=P 21 21 21, fileName=null, title=5H92, name=5H92}
Regards,
Charles
Ofoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu
www.jalview.org<http://www.jalview.org/>
www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/>
On 26 Aug 2016, at 12:49, Robert Hanson
<[email protected]<mailto:[email protected]>> wrote:
Q: Is this the Jmol applet or the application?
Q: You are sure there are not two models (two frames) showing? That your
modelIndex parameter is not -1?
If two frames are showing and you use viewer.there are, then you must ensure
that you have not gotten modelIndex from viewer.am.cmi, because that will be
-1. Instead, you have to decide which of those superimposed models you want to
see the file name of -- 0 or 1.
Bob
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