OK. Charles .. Can you check what happens when you save a superimposed pair of structures and reload ? Hopefully we don't hit the same issue when restoring views.
On Mon, Aug 29, 2016, 2:03 PM Robert Hanson <[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]> wrote: > >> simultaneously -- that's the tip I needed. Thank you! >> >> On Mon, Aug 29, 2016 at 7:16 AM, Charles Ofoegbu (Staff) < >> [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 >>> www.compbio.dundee.ac.uk >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> On 26 Aug 2016, at 12:49, Robert Hanson <[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] >>> 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 > > _______________________________________________ > Jalview-dev mailing list > [email protected] > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev >
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