Many thanks Bob, I’ve created a patch which uses the commands you hinted below for loading multiple files and it works ok now.
there is never a need to load files simultaneously. With JMol 14.2.14, loading multiple files simultaneously with the command: [Load FILES “fileX” “fileY” “fileZ” “file…”] used to work ok. 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 29 Aug 2016, at 14:03, Robert Hanson <[email protected]<mailto:[email protected]>> wrote: ps - there is never a need to load files simultaneously. Just use: load xxxx.pdb; load append yyyy.pdb On Mon, Aug 29, 2016 at 8:02 AM, Robert Hanson <[email protected]<mailto:[email protected]>> wrote: simultaneously -- that's the tip I needed. Thank you! On Mon, Aug 29, 2016 at 7:16 AM, Charles Ofoegbu (Staff) <[email protected]<mailto:[email protected]>> wrote: 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 _______________________________________________ Jalview-dev mailing list [email protected]<mailto:[email protected]> http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev The University of Dundee is a registered Scottish Charity, No: SC015096 -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 The University of Dundee is a registered Scottish Charity, No: SC015096
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