getModelFileName() in ModelSet returns null string

Dear Bob,

We are updating Jalview’s Jmol from version 14.2.14_2015 to 14.6.1_2016.08.11. So far everything seems to work well. However, a new bug showed up when superposing structures. I’ve tracked it down to the method getModelFileName(modelIndex) in ModelSet class which usually returns the absolute file path in version 14.2.14_2015 but now returns a null string in 14.6.1_2016.08.11.

I’m wondering if this is a bug or if a there is a new method for getting the FileName for a loaded model?

Thanks and 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

The University of Dundee is a registered Scottish Charity, No: SC015096

Hmm. I don’t think it’s Jmol. The only way that can happen is if the file reader somehow has no file path. But we have in AtomSetCollectionReader:

filePath = “” + htParams.get(“fullPathName”);

Ah, wait, this could be:

public Object getInfo(int modelIndex, String key) {
return (modelIndex < 0 ? null : am[modelIndex].auxiliaryInfo.get(key));
}

maybe your modelIndex < 0.

So I don’t see how that can become null.

Try taking a look at viewer.ms.msInfo and seeing what its keys are.

It’s public. You are basically saying that in that Hashtable there is no “modelFile” key.

Hard to believe…

···

On Thu, Aug 25, 2016 at 12:23 PM, Charles Ofoegbu (Staff) <t.c.n.ofoegbu@dundee.ac.uk> wrote:

Dear Bob,

We are updating Jalview’s Jmol from version 14.2.14_2015 to 14.6.1_2016.08.11. So far everything seems to work well. However, a new bug showed up when superposing structures. I’ve tracked it down to the method getModelFileName(modelIndex) in ModelSet class which usually returns the absolute file path in version 14.2.14_2015 but now returns a null string in 14.6.1_2016.08.11.

I’m wondering if this is a bug or if a there is a new method for getting the FileName for a loaded model?

Thanks and 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

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

[sorry, that got messed up with my paste of of the modelIndex < 0 idea.]

Hmm. I don’t think it’s Jmol. The only way that can happen is if the file reader somehow has no file path. But we have in AtomSetCollectionReader:

filePath = “” + htParams.get(“fullPathName”);

So I don’t see how that can become null.

Try taking a look at viewer.ms.msInfo and seeing what its keys are.
It’s public. You are basically saying that in that Hashtable there is no “modelFile” key.
Hard to believe…

Ah, wait, this could be:

public Object getInfo(int modelIndex, String key) {
return (modelIndex < 0 ? null : am[modelIndex].auxiliaryInfo.get(key));
}

maybe your modelIndex < 0.

sorry – pps: modelIndex will be -1 if multiple models (frames) are visible. Could that be it?

···

On Thu, Aug 25, 2016 at 10:25 PM, Robert Hanson <hansonr@stolaf.edu> wrote:

[sorry, that got messed up with my paste of of the modelIndex < 0 idea.]

Hmm. I don’t think it’s Jmol. The only way that can happen is if the file reader somehow has no file path. But we have in AtomSetCollectionReader:

filePath = “” + htParams.get(“fullPathName”);

So I don’t see how that can become null.

Try taking a look at viewer.ms.msInfo and seeing what its keys are.
It’s public. You are basically saying that in that Hashtable there is no “modelFile” key.
Hard to believe…

Ah, wait, this could be:

public Object getInfo(int modelIndex, String key) {
return (modelIndex < 0 ? null : am[modelIndex].auxiliaryInfo.get(key));
}

maybe your modelIndex < 0.

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

Dear Bob,

I checked the auxiliaryInfo hash table while debugging this yesterday and it had a null string for the fileName key. I’m pretty sure about that.

Regards,
Charles

Hi Bob -

···

On 26/08/2016 06:57, Charles Ofoegbu (Staff) wrote:

I checked the auxiliaryInfo hash table while debugging this yesterday
and it had a null string for the fileName key. I'm pretty sure about that.

Just to clarify - that's a String called "null" as the key :slight_smile:

j.

Ah! OK. Good. So then htParams.get(“fullPathName”) is null. OK…

···

On Fri, Aug 26, 2016 at 4:36 AM, Jim Procter <foreveremain@gmail.com> wrote:

Hi Bob -

On 26/08/2016 06:57, Charles Ofoegbu (Staff) wrote:

I checked the auxiliaryInfo hash table while debugging this yesterday
and it had a null string for the fileName key. I’m pretty sure about that.

Just to clarify - that’s a String called “null” as the key :slight_smile:

j.

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

OK, this is set in FileManager, in getAtomSetCollectionFromFile. It is the first element of the names[] array returned from getClassifiedName, which comes from the nameAsGiven variable.

Look for a message in the Jmol console that comes from this:

Logger.info("\nFileManager.getAtomSetCollectionFromFile(" + nameAsGiven

  • “)” + (name.equals(nameAsGiven) ? “” : " //" + name));

Q: Is this an unsigned applet running on a local machine? If so, you might be hitting:

String s = file.getFullPath();
// local unsigned applet may have access control issue here and get a null return
String fname = file.getName();
names = new String[] { (s == null ? fname : s), fname,
(s == null ? fname : “file:/” + s.replace(’\’, ‘/’)) };

although that’s for the file.getFullPath() call, not file.getName(), and so s would be null, not fname.

You must be using the signed applet, though. Can’t be the unsigned. So if that’s not it…

···

On Fri, Aug 26, 2016 at 6:23 AM, Robert Hanson <hansonr@stolaf.edu> wrote:

Ah! OK. Good. So then htParams.get(“fullPathName”) is null. OK…

On Fri, Aug 26, 2016 at 4:36 AM, Jim Procter <foreveremain@gmail.com> wrote:

Hi Bob -

On 26/08/2016 06:57, Charles Ofoegbu (Staff) wrote:

I checked the auxiliaryInfo hash table while debugging this yesterday
and it had a null string for the fileName key. I’m pretty sure about that.

Just to clarify - that’s a String called “null” as the key :slight_smile:

j.

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

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

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 <hansonr@stolaf.edu> 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
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev

The University of Dundee is a registered Scottish Charity, No: SC015096

simultaneously – that’s the tip I needed. Thank you!

···

On Mon, Aug 29, 2016 at 7:16 AM, Charles Ofoegbu (Staff) <t.c.n.ofoegbu@dundee.ac.uk> 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 <hansonr@stolaf.edu> 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
Jalview-dev@jalview.org
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

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 <hansonr@stolaf.edu> wrote:

simultaneously – that’s the tip I needed. Thank you!

On Mon, Aug 29, 2016 at 7:16 AM, Charles Ofoegbu (Staff) <t.c.n.ofoegbu@dundee.ac.uk> 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 <hansonr@stolaf.edu> 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
Jalview-dev@jalview.org
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

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 at 8:02 AM, Robert Hanson <hansonr@stolaf.edu> wrote:

simultaneously – that’s the tip I needed. Thank you!

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

On Mon, Aug 29, 2016 at 7:16 AM, Charles Ofoegbu (Staff) <t.c.n.ofoegbu@dundee.ac.uk> 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 <hansonr@stolaf.edu> 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
Jalview-dev@jalview.org
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

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
www.compbio.dundee.ac.uk

···

On Mon, Aug 29, 2016 at 8:02 AM, Robert Hanson <hansonr@stolaf.edu> wrote:

simultaneously – that’s the tip I needed. Thank you!

On Mon, Aug 29, 2016 at 7:16 AM, Charles Ofoegbu (Staff) <t.c.n.ofoegbu@dundee.ac.uk> 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 <hansonr@stolaf.edu> 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
Jalview-dev@jalview.org
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