Re: [Jmol-users] New path for RCSB files causes Jmol error

[Andreas Prlic]

Thanks, Bob!

Andreas

On Wednesday, March 23, 2016, Robert Hanson  wrote:

> I have made changes to Jmol and JSmol to direct PDB default loading to be
> from files.rcsb.org
>
> see
> https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.4/Version%2014.4.4/
>
> * Download Jmol-14.4.4_2016.03.24-binary.zip (61.2 MB)
> *
>
>
>
> On Wed, Mar 23, 2016 at 10:53 AM, Dave Howorth  > wrote:
>
>> I'm probably way behind the times but I only just noticed that the path
>> to RCSB files has changed. I loaded an mmCIF file into Jmol and noticed
>> in Firebug that the request got redirected. So I went to update my
>> jmolscript, which started like this:
>>
>>script: 'set loadFormat "http://www.rcsb.org/pdb/files/%FILE.cif;;'
>>  + 'load =' + pdbid + ';',
>>
>> so it now reads:
>>
>>script: 'set loadFormat "http://files.rcsb.org/view/%FILE.cif;;'
>>  + 'load =' + pdbid + ';',
>>
>> But when I run the script now I get an error box saying:
>>
>>Error connecting to server: http://your.server.here
>>/jsmol.php?call=getRawDataFromDatabase=_=http%3A%2F
>>%2Ffiles.rcsb.org%2Fview%2F3qq5.cif
>>
>> I can retrieve the file http://files.rcsb.org/view/3qq5.cif with wget,
>> so I'm fairly sure I've got the correct URL and the problem is somewhere
>> in my usage of Jmol.
>>
>> Hopefully somebody can advise me. I've copied Andreas just in case this
>> is somehow connected with their changes.
>>
>> Cheers, Dave
>>
>>
>> --
>> Transform Data into Opportunity.
>> Accelerate data analysis in your applications with
>> Intel Data Analytics Acceleration Library.
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>> Jmol-users@lists.sourceforge.net
>> 
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department 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
>
>

-- 
---
Dr. Andreas Prlic
RCSB PDB Protein Data Bank
Technical & Scientific Team Lead
University of California, San Diego

Editor Software Section
PLOS Computational Biology

BioJava Project Lead
---
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Re: [Jmol-users] Resolver SMILES input errors

[Robert Hanson]

got it!

I have made changes to Jmol and JSmol to direct PDB default loading to be
from files.rcsb.org

see
https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.4/Version%2014.4.4/

* Download Jmol-14.4.4_2016.03.24-binary.zip (61.2 MB)
*


Jmol.___JmolVersion="14.5.4_2016.03.24"

bug fix: NCI requires stereochemistry to rings to be prior to a branch:
 C\1(/C)=C\C=C.C/1=C not C(/C)\1=C\C=C.C/1=C


​
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Re: [Jmol-users] New path for RCSB files causes Jmol error

[Robert Hanson]

I have made changes to Jmol and JSmol to direct PDB default loading to be
from files.rcsb.org

see
https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.4/Version%2014.4.4/

* Download Jmol-14.4.4_2016.03.24-binary.zip (61.2 MB)
*



On Wed, Mar 23, 2016 at 10:53 AM, Dave Howorth 
wrote:

> I'm probably way behind the times but I only just noticed that the path
> to RCSB files has changed. I loaded an mmCIF file into Jmol and noticed
> in Firebug that the request got redirected. So I went to update my
> jmolscript, which started like this:
>
>script: 'set loadFormat "http://www.rcsb.org/pdb/files/%FILE.cif;;'
>  + 'load =' + pdbid + ';',
>
> so it now reads:
>
>script: 'set loadFormat "http://files.rcsb.org/view/%FILE.cif;;'
>  + 'load =' + pdbid + ';',
>
> But when I run the script now I get an error box saying:
>
>Error connecting to server: http://your.server.here
>/jsmol.php?call=getRawDataFromDatabase=_=http%3A%2F
>%2Ffiles.rcsb.org%2Fview%2F3qq5.cif
>
> I can retrieve the file http://files.rcsb.org/view/3qq5.cif with wget,
> so I'm fairly sure I've got the correct URL and the problem is somewhere
> in my usage of Jmol.
>
> Hopefully somebody can advise me. I've copied Andreas just in case this
> is somehow connected with their changes.
>
> Cheers, Dave
>
>
> --
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785351=/4140
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department 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
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Re: [Jmol-users] fun with Jmol -- xxxx.find("chemical",...)

[Robert Hanson]

Nothing stops you from adding that to your pages, Pierluigi! :)

In answer to the question, the name/SMILES, SMILES/name and
SMILES/structure conversion is going through the NCI CACTVS resolver, which
is just a fantastic resource.

structure/SMILES conversion is done within Jmol unless it is

 print {*}.find("SMILES/NCI")
 print {*}.find("SMILES/canonical")

(these are just two ways of requesting the same thing)

 in which case it goes through NCI


Bob

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Re: [Jmol-users] Retrieve Temperature Factor Annotation via JMOL API

[Robert Hanson]

Charles, I would be more than happy to help you with that. Give me a hint
at hans...@stolaf.edu what you have going right now for the other data, and
I will fill you in.

Bob
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Re: [Jmol-users] New path for RCSB files causes Jmol error

[Robert Hanson]

The issue is that JSmol.min.js doesn't recognize your new url as one that
can be used for direct AJAX transfer. If you want to fix this yourself,
look in JSmol.min.js for

"www.rcsb.org":"%URL",

or

"www.rcsb.org":null,

and ADD to that a similar entry for files.rcsb.org


​
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Re: [Jmol-users] New path for RCSB files causes Jmol error

[Vinushka Schalk]

I know this got changed relatively recently in JSmol due to issues with
HTTPS requests. Since HTTPS pages cannot easily fire AJAX to HTTP pages, in
particular with certain firewall setups like the ones used at my lab, the
jsmol.php file that is used to fetch files from foreign sources must be
provided from your server rather than obtained from Rob's page, which was
the old default setting. I believe this was changed in JSmolCore itself, so
it's a major shift if you were running an old version of JSmol before.

To fix this in JSmol, you would add add the following to your Info variable
where you create your JSmol instance:

serverURL: '/jsmol-scripts/jsmol.php'

Where you would replace "/jsmol-scripts/" with the path, relative or
absolute, to the place on your server where jsmol.php is located. jsmol.php
is included with the JSmol zip file on sourceforge.

However, I don't know how this change affects Jmol itself, and it seems odd
to me that base Jmol would be calling for jsmol.php.

On Wed, Mar 23, 2016 at 11:53 AM, Dave Howorth 
wrote:

> I'm probably way behind the times but I only just noticed that the path
> to RCSB files has changed. I loaded an mmCIF file into Jmol and noticed
> in Firebug that the request got redirected. So I went to update my
> jmolscript, which started like this:
>
>script: 'set loadFormat "http://www.rcsb.org/pdb/files/%FILE.cif;;'
>  + 'load =' + pdbid + ';',
>
> so it now reads:
>
>script: 'set loadFormat "http://files.rcsb.org/view/%FILE.cif;;'
>  + 'load =' + pdbid + ';',
>
> But when I run the script now I get an error box saying:
>
>Error connecting to server: http://your.server.here
>/jsmol.php?call=getRawDataFromDatabase=_=http%3A%2F
>%2Ffiles.rcsb.org%2Fview%2F3qq5.cif
>
> I can retrieve the file http://files.rcsb.org/view/3qq5.cif with wget,
> so I'm fairly sure I've got the correct URL and the problem is somewhere
> in my usage of Jmol.
>
> Hopefully somebody can advise me. I've copied Andreas just in case this
> is somehow connected with their changes.
>
> Cheers, Dave
>
>
> --
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
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> ___
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> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
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[Jmol-users] New path for RCSB files causes Jmol error

[Dave Howorth]

I'm probably way behind the times but I only just noticed that the path 
to RCSB files has changed. I loaded an mmCIF file into Jmol and noticed 
in Firebug that the request got redirected. So I went to update my 
jmolscript, which started like this:

   script: 'set loadFormat "http://www.rcsb.org/pdb/files/%FILE.cif;;'
 + 'load =' + pdbid + ';',

so it now reads:

   script: 'set loadFormat "http://files.rcsb.org/view/%FILE.cif;;'
 + 'load =' + pdbid + ';',

But when I run the script now I get an error box saying:

   Error connecting to server: http://your.server.here
   /jsmol.php?call=getRawDataFromDatabase=_=http%3A%2F
   %2Ffiles.rcsb.org%2Fview%2F3qq5.cif

I can retrieve the file http://files.rcsb.org/view/3qq5.cif with wget, 
so I'm fairly sure I've got the correct URL and the problem is somewhere 
in my usage of Jmol.

Hopefully somebody can advise me. I've copied Andreas just in case this 
is somehow connected with their changes.

Cheers, Dave

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Re: [Jmol-users] Resolver SMILES input errors

[Robert Hanson]

On Wed, Mar 23, 2016 at 10:15 AM, Otis Rothenberger 
wrote:

> Bob,
>
> C(\C)/1=C/C=C.C\1=C
>
> Resolver cannot read this, and I’m now thinking that it’s, understandably,
> geometry confused. I don’t know how to read these things, so I’m not sure.
> Interestingly, if I send the molfile to the new inchi.js, it creates an
> inchi, but NIST reports the resulting structure as being geometry
> ambiguous. That’s the nice thing about NIST. It fails gracefully with a
> valid inchi, simply showing connectivity structures with links to NIST
> possibilities.
>
>
This has to do with the ordering of the terms in the SMILES that Jmol is
generating and sending to NCI.


$ load $C(\C)/1=C/C=C.C\1=C
script ERROR: java.io.FileNotFoundException:
http://cactus.nci.nih.gov/chemical/structure/C(\C)/1=C/C=C.C\1=C/file?format=sdf=True

 load "$C(\C)/1=C/C=C.C\1=C"

$ load $C/1(\C)=C/C=C.C\1=C
C7H10


So it appears that the connector /1 has to come before the branch (C). This
is not specified in the SMILES documentation,  as far as I can tell, but I
can consider it a bug in Jmol anyway, since NCI does not read it.

Bob
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[Jmol-users] Resolver SMILES input errors

[Otis Rothenberger]

Bob,

The CORINA documentation that I sent in my last email made me start thinking 
about an old problem. At the end of the CORINA documentation there is an 
extensive list of SMILES and stereochemistry input errors that CORINA throws. 
Over the years, the Jmol SMILES Resolver input problems that I have seen 
resulted from edited models - it’s a model kit! I encounter them when I want to 
clean up an edited structure with Resolver.

Some of these edited structures are a geometric mess. For example if I break 
the single C-C bond on the para carbon of toluene, I get a geometric mess and 
this SMILES after correcting H and using an MMFF94 hit:

C(\C)/1=C/C=C.C\1=C

Resolver cannot read this, and I’m now thinking that it’s, understandably, 
geometry confused. I don’t know how to read these things, so I’m not sure. 
Interestingly, if I send the molfile to the new inchi.js, it creates an inchi, 
but NIST reports the resulting structure as being geometry ambiguous. That’s 
the nice thing about NIST. It fails gracefully with a valid inchi, simply 
showing connectivity structures with links to NIST possibilities.

Otis

--
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o...@chemagic.org
http://chemagic.org


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[Jmol-users] Retrieve Temperature Factor Annotation via JMOL API

[Charles Ofoegbu (Staff)]

Dear All,

I am new to Jmol's Java API and I’m using it to integrate mmCIF into Jalview.

Currently, I can load PDB/mmCIF files via the API and retrieve residues, atoms, 
and secondary structure annotation data. However, I’ve not found a way to 
retrieve temperature factor annotation with the API. I’d be very delighted if 
someone could point me in the right direction (API docs or code snippets).

Thanks in advance.

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
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Re: [Jmol-users] fun with Jmol -- xxxx.find("chemical",...)

[Pierluigi Quagliotto]

Dear Bob and dear all,

is it possible to use the same feature in JSmol associating it to a
button?. It would be interesting to use it to help students during
nomenclature exercises.

Thanks!

Pierluigi


2016-03-22 19:04 GMT+01:00 Luciano Abriata :

> Robert, no, I didn't know. And it's amazing!
>
> Can you briefly and very plainly explain how the find() works? I mean,
> what's at the core of the formula-name-smile-etc conversions?
> Luciano
>
>
> --
> *De:* Robert Hanson 
> *Para:* "jmol-users@lists.sourceforge.net" <
> jmol-users@lists.sourceforge.net>
> *Enviado:* Martes, 22 de marzo, 2016 15:39:24
> *Asunto:* [Jmol-users] fun with Jmol -- .find("chemical",...)
>
> Did you know that this is now possible in Jmol:
>
> $ print "C1=CC=CC1=O".find("chemical","name")
> cyclopenta-2,4-dien-1-one
> $ print "succinic anhydride".find("chemical","SMILES")
> O=C1CCC(=O)O1
> $ print "maleic anhydride".find("chemical","SMILES")
> O=C1OC(=O)C=C1
> $ print "maleic anhydride".find("chemical","inchikey")
> FPYJFEHAWHCUMM-UHFFFAOYNA-N
> $ print "cholesterol".find("chemical","inchi")
>
> 1S/C27H46O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h9,18-19,21-25,28H,6-8,10-17H2,1-5H3/t19-,21+,22+,23-,24+,25+,26+,27-/m1/s1
>
> Bob
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department 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
>
>
>
> --
> Transform Data into Opportunity.
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>
>
>
>
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