Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Jeff Hansen]

Not seeing that behavior on my Mac.


***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***


On Apr 24, 2012, at 12:02 PM, Philip Bays wrote:

> Again on a macbook pro.   All works except y1237 when using not chemdoodle 
> (no webgl).  The right third of the image is green.
> 
>  


--
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Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Robert Hanson]

say again??

On Tue, Apr 24, 2012 at 11:02 AM, Philip Bays  wrote:

> Again on a macbook pro.   All works except y1237 when using not chemdoodle
> (no webgl).  The right third of the image is green.
>
>
> On Apr 24, 2012, at 10:49 AM, Robert Hanson wrote:
>
> the :smiles:C/C=C/C business was indeed my forgetting to upload the latest
> JAR files.
>
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm?SIGNED
>
> should work now, provided your browser uses the proper file, with
> timestamp 2012-04-24 07:22 in the "about" menu.
>
> Bob
>
>
> On Tue, Apr 24, 2012 at 8:56 AM, Otis Rothenberger 
> wrote:
>
>> Bob,
>>
>> I just cleared cache on Firefox Mac, and now the only "direct database
>> calls - no server" error I still see is:
>>
>> load :smiles:CC/C=C/CC (PubChem SMILES)
>>
>> Otis
>>
>>
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>>
>>
>>
>>
>> On Apr 24, 2012, at 9:44 AM, Robert Hanson wrote:
>>
>> Phil, could this be a local caching problem? I'm not seeing any problem
>> with a vanilla Mac running Safari. All the .js files have been changed
>> recently, and there are also new .jar files as well specifically for those
>> actions.
>>
>> Other Mac users?  http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>>
>>
>>
>> On Tue, Apr 24, 2012 at 6:21 AM, Philip Bays wrote:
>>
>>> Bob:
>>> On my Mac, I am getting some java i/o errors using the signed applet and
>>> the direct database calls; eg caffeine with map, 2-hexene smiles, aspirin.
>>>
>>>
>>> On Apr 24, 2012, at 12:51 AM, Robert Hanson wrote:
>>>
>>> Dear Jmol users,
>>>
>>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>>>
>>> Needs testing on iPads, iPhones, and Android tablet.
>>>
>>> I have all file types loading now, I think, including direct tapping
>>> into PubChem, NCI Resolver, and RCSB models and ligands all in Jmol and a
>>> slightly adapted subset of ChemDoodle. No links should cause errors. (Still
>>> waiting for one little hosting* *tweak at RCSB, which is requiring a
>>> bit of indirect server action for keyword searches.)
>>>
>>> In a Java applet environment, I can load PubChem models with charges
>>> (for MEP) directly from PubChem using a great new service they are rolling
>>> out soon. Most happy to beta test that for them! Interesting to compare the
>>> results with NCI.
>>>
>>> Full action requires a couple of files on a server. Which in this case
>>> is at St. Olaf.
>>>
>>> Paul Pillot and I are fast-tracking getting the rest of Jmol into an
>>> Object JavaScript format. A bit tricky, but one problem will be history: No
>>> more worry about waiting for the applet to load before sending it scripts.
>>> We'll just cache them until the applet is ready, then send them off
>>> automatically. That will be nice!
>>>
>>> Bob
>>>
>>>
>>> On Fri, Apr 13, 2012 at 12:03 AM, Robert Hanson wrote:
>>>
 OK. Please test!

 http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm

 -- adds loading of host-local file using

   MolGrabberJmol.loadFile(fileName,loadParams)

 of course, the loadParams business doesn't work with ChemDoodle, but
 perhaps it will supply reason to add such :)

 I notice that this does not work for machine-local (hard-drive-based)
 files in Chrome. I'm guessing that's a security setting.

 Also, actually, I couldn't get most of these to load into ChemDoodle.
 The CIF files seem to be unreadable in all cases, and when there is no
 WebGL, only MOL files are readable, not XYZ, PDB, or CIF.

 Kevin, now you have something to do! I'm hoping you can check that over
 and tell me what I'm doing wrong (actually, send me a corrected
 JmolCD.js!). Something odd in xxxInterpreters, I think. But I don't know
 what it would be.

 Bob


 --
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107


 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
>>> Professor of Chemistry
>>> St. Olaf College
>>> 1520 St. Olaf Ave.
>>> Northfield, MN 55057
>>> http://www.stolaf.edu/people/hansonr
>>> phone: 507-786-3107
>>>
>>>
>>> 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
>>> --
>>> Live Security Virtual Conference
>>> Exclusive live event will cover all the ways today's security and
>>> threat landscape has changed and how IT managers can respond.
>>> Discussions
>>> will include endpoint security, mobile security and the latest in
>>> malware
>>> threats.
>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/__

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Philip Bays]

Again on a macbook pro.   All works except y1237 when using not chemdoodle (no 
webgl).  The right third of the image is green.

 
On Apr 24, 2012, at 10:49 AM, Robert Hanson wrote:

> the :smiles:C/C=C/C business was indeed my forgetting to upload the latest 
> JAR files. 
> 
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm?SIGNED
> 
> should work now, provided your browser uses the proper file, with timestamp 
> 2012-04-24 07:22 in the "about" menu.
> 
> Bob
> 
> 
> On Tue, Apr 24, 2012 at 8:56 AM, Otis Rothenberger  
> wrote:
> Bob,
> 
> I just cleared cache on Firefox Mac, and now the only "direct database calls 
> - no server" error I still see is:
> 
> load :smiles:CC/C=C/CC (PubChem SMILES)
> 
> Otis
> 
> 
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
> 
> 
> 
> 
> On Apr 24, 2012, at 9:44 AM, Robert Hanson wrote:
> 
>> Phil, could this be a local caching problem? I'm not seeing any problem with 
>> a vanilla Mac running Safari. All the .js files have been changed recently, 
>> and there are also new .jar files as well specifically for those actions. 
>> 
>> Other Mac users?  http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>> 
>> 
>> 
>> On Tue, Apr 24, 2012 at 6:21 AM, Philip Bays  wrote:
>> Bob:
>> On my Mac, I am getting some java i/o errors using the signed applet and the 
>> direct database calls; eg caffeine with map, 2-hexene smiles, aspirin.
>> 
>> 
>> On Apr 24, 2012, at 12:51 AM, Robert Hanson wrote:
>> 
>>> Dear Jmol users,
>>> 
>>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>>> 
>>> Needs testing on iPads, iPhones, and Android tablet.
>>> 
>>> I have all file types loading now, I think, including direct tapping into 
>>> PubChem, NCI Resolver, and RCSB models and ligands all in Jmol and a 
>>> slightly adapted subset of ChemDoodle. No links should cause errors. (Still 
>>> waiting for one little hosting tweak at RCSB, which is requiring a bit of 
>>> indirect server action for keyword searches.)  
>>> 
>>> In a Java applet environment, I can load PubChem models with charges (for 
>>> MEP) directly from PubChem using a great new service they are rolling out 
>>> soon. Most happy to beta test that for them! Interesting to compare the 
>>> results with NCI. 
>>> 
>>> Full action requires a couple of files on a server. Which in this case is 
>>> at St. Olaf. 
>>> 
>>> Paul Pillot and I are fast-tracking getting the rest of Jmol into an Object 
>>> JavaScript format. A bit tricky, but one problem will be history: No more 
>>> worry about waiting for the applet to load before sending it scripts. We'll 
>>> just cache them until the applet is ready, then send them off 
>>> automatically. That will be nice!
>>> 
>>> Bob
>>> 
>>> 
>>> On Fri, Apr 13, 2012 at 12:03 AM, Robert Hanson  wrote:
>>> OK. Please test!
>>> 
>>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>>> 
>>> -- adds loading of host-local file using
>>> 
>>>   MolGrabberJmol.loadFile(fileName,loadParams)
>>> 
>>> of course, the loadParams business doesn't work with ChemDoodle, but 
>>> perhaps it will supply reason to add such :)
>>> 
>>> I notice that this does not work for machine-local (hard-drive-based) files 
>>> in Chrome. I'm guessing that's a security setting. 
>>> 
>>> Also, actually, I couldn't get most of these to load into ChemDoodle. The 
>>> CIF files seem to be unreadable in all cases, and when there is no WebGL, 
>>> only MOL files are readable, not XYZ, PDB, or CIF. 
>>> 
>>> Kevin, now you have something to do! I'm hoping you can check that over and 
>>> tell me what I'm doing wrong (actually, send me a corrected JmolCD.js!). 
>>> Something odd in xxxInterpreters, I think. But I don't know what it would 
>>> be.
>>> 
>>> Bob
>>> 
>>> 
>>> -- 
>>> Robert M. Hanson
>>> Professor of Chemistry
>>> St. Olaf College
>>> 1520 St. Olaf Ave.
>>> Northfield, MN 55057
>>> http://www.stolaf.edu/people/hansonr
>>> phone: 507-786-3107
>>> 
>>> 
>>> 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
>>> Professor of Chemistry
>>> St. Olaf College
>>> 1520 St. Olaf Ave.
>>> Northfield, MN 55057
>>> http://www.stolaf.edu/people/hansonr
>>> phone: 507-786-3107
>>> 
>>> 
>>> 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
>>> --
>>> Live Security Virtual Conference
>>> Exclusive live event will cover all the ways today's security and 
>>> threat landscape has changed and how IT managers can respond. Discussions 
>>> will include endpoint security, mobile security and the latest in malware 
>>> threats. 
>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
>>> 
>>> Jmol-users mailing list

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Otis Rothenberger]

Bob,

This works now on my Mac Firefox.

Otis

--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com




On Apr 24, 2012, at 10:49 AM, Robert Hanson wrote:

> the :smiles:C/C=C/C business was indeed my forgetting to upload the latest 
> JAR files. 
> 
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm?SIGNED
> 
> should work now, provided your browser uses the proper file, with timestamp 
> 2012-04-24 07:22 in the "about" menu.
> 
> Bob
> 
> 
> On Tue, Apr 24, 2012 at 8:56 AM, Otis Rothenberger  
> wrote:
> Bob,
> 
> I just cleared cache on Firefox Mac, and now the only "direct database calls 
> - no server" error I still see is:
> 
> load :smiles:CC/C=C/CC (PubChem SMILES)
> 
> Otis
> 
> 
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
> 
> 
> 
> 
> On Apr 24, 2012, at 9:44 AM, Robert Hanson wrote:
> 
>> Phil, could this be a local caching problem? I'm not seeing any problem with 
>> a vanilla Mac running Safari. All the .js files have been changed recently, 
>> and there are also new .jar files as well specifically for those actions. 
>> 
>> Other Mac users?  http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>> 
>> 
>> 
>> On Tue, Apr 24, 2012 at 6:21 AM, Philip Bays  wrote:
>> Bob:
>> On my Mac, I am getting some java i/o errors using the signed applet and the 
>> direct database calls; eg caffeine with map, 2-hexene smiles, aspirin.
>> 
>> 
>> On Apr 24, 2012, at 12:51 AM, Robert Hanson wrote:
>> 
>>> Dear Jmol users,
>>> 
>>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>>> 
>>> Needs testing on iPads, iPhones, and Android tablet.
>>> 
>>> I have all file types loading now, I think, including direct tapping into 
>>> PubChem, NCI Resolver, and RCSB models and ligands all in Jmol and a 
>>> slightly adapted subset of ChemDoodle. No links should cause errors. (Still 
>>> waiting for one little hosting tweak at RCSB, which is requiring a bit of 
>>> indirect server action for keyword searches.)  
>>> 
>>> In a Java applet environment, I can load PubChem models with charges (for 
>>> MEP) directly from PubChem using a great new service they are rolling out 
>>> soon. Most happy to beta test that for them! Interesting to compare the 
>>> results with NCI. 
>>> 
>>> Full action requires a couple of files on a server. Which in this case is 
>>> at St. Olaf. 
>>> 
>>> Paul Pillot and I are fast-tracking getting the rest of Jmol into an Object 
>>> JavaScript format. A bit tricky, but one problem will be history: No more 
>>> worry about waiting for the applet to load before sending it scripts. We'll 
>>> just cache them until the applet is ready, then send them off 
>>> automatically. That will be nice!
>>> 
>>> Bob
>>> 
>>> 
>>> On Fri, Apr 13, 2012 at 12:03 AM, Robert Hanson  wrote:
>>> OK. Please test!
>>> 
>>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>>> 
>>> -- adds loading of host-local file using
>>> 
>>>   MolGrabberJmol.loadFile(fileName,loadParams)
>>> 
>>> of course, the loadParams business doesn't work with ChemDoodle, but 
>>> perhaps it will supply reason to add such :)
>>> 
>>> I notice that this does not work for machine-local (hard-drive-based) files 
>>> in Chrome. I'm guessing that's a security setting. 
>>> 
>>> Also, actually, I couldn't get most of these to load into ChemDoodle. The 
>>> CIF files seem to be unreadable in all cases, and when there is no WebGL, 
>>> only MOL files are readable, not XYZ, PDB, or CIF. 
>>> 
>>> Kevin, now you have something to do! I'm hoping you can check that over and 
>>> tell me what I'm doing wrong (actually, send me a corrected JmolCD.js!). 
>>> Something odd in xxxInterpreters, I think. But I don't know what it would 
>>> be.
>>> 
>>> Bob
>>> 
>>> 
>>> -- 
>>> Robert M. Hanson
>>> Professor of Chemistry
>>> St. Olaf College
>>> 1520 St. Olaf Ave.
>>> Northfield, MN 55057
>>> http://www.stolaf.edu/people/hansonr
>>> phone: 507-786-3107
>>> 
>>> 
>>> 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
>>> Professor of Chemistry
>>> St. Olaf College
>>> 1520 St. Olaf Ave.
>>> Northfield, MN 55057
>>> http://www.stolaf.edu/people/hansonr
>>> phone: 507-786-3107
>>> 
>>> 
>>> 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
>>> --
>>> Live Security Virtual Conference
>>> Exclusive live event will cover all the ways today's security and 
>>> threat landscape has changed and how IT managers can respond. Discussions 
>>> will include endpoint security, mobile security and the latest in malware 
>>> threats. 
>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
>>> 
>>> Jmol-users mailing list
>>> Jmol-users@lists.

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Robert Hanson]

Right -- obviously there will be some differences, and your comments
relative to these are helpful. Good to see that your Mac, Jeff, is showing
the WebGL version of ChemDoodle. Give us all the feedback you can about
that experience.

There are two sorts of CIF examples -- some from RCSB and some from other
sources. They will render very differently because ChemDoodle has quite a
different reader than Jmol.

On Tue, Apr 24, 2012 at 9:48 AM, Jeff Hansen  wrote:

>
>
>
> I wasn't commenting on whether it looks ok or not, just reporting what I
> was seeing.  On my Mac the cif examples all have a box drawn around them
> with ChemDoodle though not with Jmol and they are ball and stick.  It looks
> different on the iPod Touch.  Not saying it is better or worse, just not
> the same behavior.  I figured you all would like to know how it compares.
>
>
> ***
> Jeff Hansen
> Department of Chemistry and Biochemistry
> DePauw University
> 602 S. College Ave.
> Greencastle, IN 46135
> jhan...@depauw.edu
> ***
>
>
>
> --
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Robert Hanson]

the :smiles:C/C=C/C business was indeed my forgetting to upload the latest
JAR files.

http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm?SIGNED

should work now, provided your browser uses the proper file, with timestamp
2012-04-24 07:22 in the "about" menu.

Bob


On Tue, Apr 24, 2012 at 8:56 AM, Otis Rothenberger wrote:

> Bob,
>
> I just cleared cache on Firefox Mac, and now the only "direct database
> calls - no server" error I still see is:
>
> load :smiles:CC/C=C/CC (PubChem SMILES)
>
> Otis
>
>
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>
>
>
> On Apr 24, 2012, at 9:44 AM, Robert Hanson wrote:
>
> Phil, could this be a local caching problem? I'm not seeing any problem
> with a vanilla Mac running Safari. All the .js files have been changed
> recently, and there are also new .jar files as well specifically for those
> actions.
>
> Other Mac users?  http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>
>
>
> On Tue, Apr 24, 2012 at 6:21 AM, Philip Bays  wrote:
>
>> Bob:
>> On my Mac, I am getting some java i/o errors using the signed applet and
>> the direct database calls; eg caffeine with map, 2-hexene smiles, aspirin.
>>
>>
>> On Apr 24, 2012, at 12:51 AM, Robert Hanson wrote:
>>
>> Dear Jmol users,
>>
>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>>
>> Needs testing on iPads, iPhones, and Android tablet.
>>
>> I have all file types loading now, I think, including direct tapping into
>> PubChem, NCI Resolver, and RCSB models and ligands all in Jmol and a
>> slightly adapted subset of ChemDoodle. No links should cause errors. (Still
>> waiting for one little hosting* *tweak at RCSB, which is requiring a bit
>> of indirect server action for keyword searches.)
>>
>> In a Java applet environment, I can load PubChem models with charges (for
>> MEP) directly from PubChem using a great new service they are rolling out
>> soon. Most happy to beta test that for them! Interesting to compare the
>> results with NCI.
>>
>> Full action requires a couple of files on a server. Which in this case is
>> at St. Olaf.
>>
>> Paul Pillot and I are fast-tracking getting the rest of Jmol into an
>> Object JavaScript format. A bit tricky, but one problem will be history: No
>> more worry about waiting for the applet to load before sending it scripts.
>> We'll just cache them until the applet is ready, then send them off
>> automatically. That will be nice!
>>
>> Bob
>>
>>
>> On Fri, Apr 13, 2012 at 12:03 AM, Robert Hanson wrote:
>>
>>> OK. Please test!
>>>
>>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>>>
>>> -- adds loading of host-local file using
>>>
>>>   MolGrabberJmol.loadFile(fileName,loadParams)
>>>
>>> of course, the loadParams business doesn't work with ChemDoodle, but
>>> perhaps it will supply reason to add such :)
>>>
>>> I notice that this does not work for machine-local (hard-drive-based)
>>> files in Chrome. I'm guessing that's a security setting.
>>>
>>> Also, actually, I couldn't get most of these to load into ChemDoodle.
>>> The CIF files seem to be unreadable in all cases, and when there is no
>>> WebGL, only MOL files are readable, not XYZ, PDB, or CIF.
>>>
>>> Kevin, now you have something to do! I'm hoping you can check that over
>>> and tell me what I'm doing wrong (actually, send me a corrected
>>> JmolCD.js!). Something odd in xxxInterpreters, I think. But I don't know
>>> what it would be.
>>>
>>> Bob
>>>
>>>
>>> --
>>> Robert M. Hanson
>>> Professor of Chemistry
>>> St. Olaf College
>>> 1520 St. Olaf Ave.
>>> Northfield, MN 55057
>>> http://www.stolaf.edu/people/hansonr
>>> phone: 507-786-3107
>>>
>>>
>>> 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
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>>
>>
>> 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
>> --
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and
>> threat landscape has changed and how IT managers can respond. Discussions
>> will include endpoint security, mobile security and the latest in malware
>> threats.
>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
>>
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>>  J. Philip Bays
>> Emeritus Professor of Chemistry
>> Department of Chemistry and Physics
>> Saint Mary's College
>> Notre Dame, IN 46556
>> pb...@saintmarys.edu
>>
>>
>>
>>
>>
>>
>>
>> 

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Jeff Hansen]

On Apr 24, 2012, at 9:31 AM, Kevin Theisen wrote:

> Hi Jeff,
> 
>> 1blu takes a long time to load and when it finally loads does not show a 
>> cartoon. 
> 
> The majority of the delay is probably in the download. Cartoons are for WebGL 
> canvases only, so not in the 2D components which some mobile devices will 
> default to.
> 
>> It shows just the bonds.  :caffeine (PubChem, with map) loads but does not 
>> show a surface. 
> 
> Surfaces are coming, although only to the WebGL canvases.
> 
>>  If the .cif examples are supposed to show anything other than bonds they do 
>> not.
> 
> We can also show a "Ball and Stick" like representation here. I can also add 
> in a unit cell rendering to 2D components. Would that improve the depiction?
> 
> Bests,
> Kevin

I wasn't commenting on whether it looks ok or not, just reporting what I was 
seeing.  On my Mac the cif examples all have a box drawn around them with 
ChemDoodle though not with Jmol and they are ball and stick.  It looks 
different on the iPod Touch.  Not saying it is better or worse, just not the 
same behavior.  I figured you all would like to know how it compares.


***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***


--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Jeff Hansen]

No problem on my MacBook Pro with Safari.  Tried both with Jmol unsigned and 
ChemDoodle.  Also fine with FireFox.


***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***


On Apr 24, 2012, at 9:44 AM, Robert Hanson wrote:

> Phil, could this be a local caching problem? I'm not seeing any problem with 
> a vanilla Mac running Safari. All the .js files have been changed recently, 
> and there are also new .jar files as well specifically for those actions. 
> 
> Other Mac users?  http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
> 
> 
> 
> On Tue, Apr 24, 2012 at 6:21 AM, Philip Bays  wrote:
> Bob:
> On my Mac, I am getting some java i/o errors using the signed applet and the 
> direct database calls; eg caffeine with map, 2-hexene smiles, aspirin.
> 
> 
> On Apr 24, 2012, at 12:51 AM, Robert Hanson wrote:
> 
>> Dear Jmol users,
>> 
>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>> 
>> Needs testing on iPads, iPhones, and Android tablet.
>> 
>> I have all file types loading now, I think, including direct tapping into 
>> PubChem, NCI Resolver, and RCSB models and ligands all in Jmol and a 
>> slightly adapted subset of ChemDoodle. No links should cause errors. (Still 
>> waiting for one little hosting tweak at RCSB, which is requiring a bit of 
>> indirect server action for keyword searches.)  
>> 
>> In a Java applet environment, I can load PubChem models with charges (for 
>> MEP) directly from PubChem using a great new service they are rolling out 
>> soon. Most happy to beta test that for them! Interesting to compare the 
>> results with NCI. 
>> 
>> Full action requires a couple of files on a server. Which in this case is at 
>> St. Olaf. 
>> 
>> Paul Pillot and I are fast-tracking getting the rest of Jmol into an Object 
>> JavaScript format. A bit tricky, but one problem will be history: No more 
>> worry about waiting for the applet to load before sending it scripts. We'll 
>> just cache them until the applet is ready, then send them off automatically. 
>> That will be nice!
>> 
>> Bob
>> 
>> 
>> On Fri, Apr 13, 2012 at 12:03 AM, Robert Hanson  wrote:
>> OK. Please test!
>> 
>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>> 
>> -- adds loading of host-local file using
>> 
>>   MolGrabberJmol.loadFile(fileName,loadParams)
>> 
>> of course, the loadParams business doesn't work with ChemDoodle, but perhaps 
>> it will supply reason to add such :)
>> 
>> I notice that this does not work for machine-local (hard-drive-based) files 
>> in Chrome. I'm guessing that's a security setting. 
>> 
>> Also, actually, I couldn't get most of these to load into ChemDoodle. The 
>> CIF files seem to be unreadable in all cases, and when there is no WebGL, 
>> only MOL files are readable, not XYZ, PDB, or CIF. 
>> 
>> Kevin, now you have something to do! I'm hoping you can check that over and 
>> tell me what I'm doing wrong (actually, send me a corrected JmolCD.js!). 
>> Something odd in xxxInterpreters, I think. But I don't know what it would be.
>> 
>> Bob
>> 
>> 
>> -- 
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>> 
>> 
>> 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
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>> 
>> 
>> 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
>> --
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and 
>> threat landscape has changed and how IT managers can respond. Discussions 
>> will include endpoint security, mobile security and the latest in malware 
>> threats. 
>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
>> 
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
> 
> J. Philip Bays
> Emeritus Professor of Chemistry
> Department of Chemistry and Physics
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu
> 
> 
> 
> 
> 
> 
> --
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile securi

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Robert Hanson]

another problem I'm having here is that on some browsers when you make a
selection from a keyword search, where the applet has been "minimized" (to
a 1x1 pixel frame) it won't rejuvinate itself. That's going to be a tough
one to track down.

Is everyone having that problem? (It's the set of links at the bottom left
of the list of links.)

On Tue, Apr 24, 2012 at 9:29 AM, Robert Hanson  wrote:

> I probably forgot to update the signed applet after making that work. I
> can reproduce that one here on my Mac. OK. Thanks.
>
>
> On Tue, Apr 24, 2012 at 8:56 AM, Otis Rothenberger 
> wrote:
>
>> Bob,
>>
>> I just cleared cache on Firefox Mac, and now the only "direct database
>> calls - no server" error I still see is:
>>
>> load :smiles:CC/C=C/CC (PubChem SMILES)
>>
>> Otis
>>
>>
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>>
>>
>>
>>
>> On Apr 24, 2012, at 9:44 AM, Robert Hanson wrote:
>>
>> Phil, could this be a local caching problem? I'm not seeing any problem
>> with a vanilla Mac running Safari. All the .js files have been changed
>> recently, and there are also new .jar files as well specifically for those
>> actions.
>>
>> Other Mac users?  http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>>
>>
>>
>> On Tue, Apr 24, 2012 at 6:21 AM, Philip Bays wrote:
>>
>>> Bob:
>>> On my Mac, I am getting some java i/o errors using the signed applet and
>>> the direct database calls; eg caffeine with map, 2-hexene smiles, aspirin.
>>>
>>>
>>> On Apr 24, 2012, at 12:51 AM, Robert Hanson wrote:
>>>
>>> Dear Jmol users,
>>>
>>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>>>
>>> Needs testing on iPads, iPhones, and Android tablet.
>>>
>>> I have all file types loading now, I think, including direct tapping
>>> into PubChem, NCI Resolver, and RCSB models and ligands all in Jmol and a
>>> slightly adapted subset of ChemDoodle. No links should cause errors. (Still
>>> waiting for one little hosting* *tweak at RCSB, which is requiring a
>>> bit of indirect server action for keyword searches.)
>>>
>>> In a Java applet environment, I can load PubChem models with charges
>>> (for MEP) directly from PubChem using a great new service they are rolling
>>> out soon. Most happy to beta test that for them! Interesting to compare the
>>> results with NCI.
>>>
>>> Full action requires a couple of files on a server. Which in this case
>>> is at St. Olaf.
>>>
>>> Paul Pillot and I are fast-tracking getting the rest of Jmol into an
>>> Object JavaScript format. A bit tricky, but one problem will be history: No
>>> more worry about waiting for the applet to load before sending it scripts.
>>> We'll just cache them until the applet is ready, then send them off
>>> automatically. That will be nice!
>>>
>>> Bob
>>>
>>>
>>> On Fri, Apr 13, 2012 at 12:03 AM, Robert Hanson wrote:
>>>
 OK. Please test!

 http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm

 -- adds loading of host-local file using

   MolGrabberJmol.loadFile(fileName,loadParams)

 of course, the loadParams business doesn't work with ChemDoodle, but
 perhaps it will supply reason to add such :)

 I notice that this does not work for machine-local (hard-drive-based)
 files in Chrome. I'm guessing that's a security setting.

 Also, actually, I couldn't get most of these to load into ChemDoodle.
 The CIF files seem to be unreadable in all cases, and when there is no
 WebGL, only MOL files are readable, not XYZ, PDB, or CIF.

 Kevin, now you have something to do! I'm hoping you can check that over
 and tell me what I'm doing wrong (actually, send me a corrected
 JmolCD.js!). Something odd in xxxInterpreters, I think. But I don't know
 what it would be.

 Bob


 --
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107


 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
>>> Professor of Chemistry
>>> St. Olaf College
>>> 1520 St. Olaf Ave.
>>> Northfield, MN 55057
>>> http://www.stolaf.edu/people/hansonr
>>> phone: 507-786-3107
>>>
>>>
>>> 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
>>> --
>>> Live Security Virtual Conference
>>> Exclusive live event will cover all the ways today's security and
>>> threat landscape has changed and how IT managers can respond.
>>> Discussions
>>> will include endpoint security, mobile security and the latest in
>>> malware
>>> threats.
>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/__

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Robert Hanson]

I probably forgot to update the signed applet after making that work. I can
reproduce that one here on my Mac. OK. Thanks.

On Tue, Apr 24, 2012 at 8:56 AM, Otis Rothenberger wrote:

> Bob,
>
> I just cleared cache on Firefox Mac, and now the only "direct database
> calls - no server" error I still see is:
>
> load :smiles:CC/C=C/CC (PubChem SMILES)
>
> Otis
>
>
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>
>
>
> On Apr 24, 2012, at 9:44 AM, Robert Hanson wrote:
>
> Phil, could this be a local caching problem? I'm not seeing any problem
> with a vanilla Mac running Safari. All the .js files have been changed
> recently, and there are also new .jar files as well specifically for those
> actions.
>
> Other Mac users?  http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>
>
>
> On Tue, Apr 24, 2012 at 6:21 AM, Philip Bays  wrote:
>
>> Bob:
>> On my Mac, I am getting some java i/o errors using the signed applet and
>> the direct database calls; eg caffeine with map, 2-hexene smiles, aspirin.
>>
>>
>> On Apr 24, 2012, at 12:51 AM, Robert Hanson wrote:
>>
>> Dear Jmol users,
>>
>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>>
>> Needs testing on iPads, iPhones, and Android tablet.
>>
>> I have all file types loading now, I think, including direct tapping into
>> PubChem, NCI Resolver, and RCSB models and ligands all in Jmol and a
>> slightly adapted subset of ChemDoodle. No links should cause errors. (Still
>> waiting for one little hosting* *tweak at RCSB, which is requiring a bit
>> of indirect server action for keyword searches.)
>>
>> In a Java applet environment, I can load PubChem models with charges (for
>> MEP) directly from PubChem using a great new service they are rolling out
>> soon. Most happy to beta test that for them! Interesting to compare the
>> results with NCI.
>>
>> Full action requires a couple of files on a server. Which in this case is
>> at St. Olaf.
>>
>> Paul Pillot and I are fast-tracking getting the rest of Jmol into an
>> Object JavaScript format. A bit tricky, but one problem will be history: No
>> more worry about waiting for the applet to load before sending it scripts.
>> We'll just cache them until the applet is ready, then send them off
>> automatically. That will be nice!
>>
>> Bob
>>
>>
>> On Fri, Apr 13, 2012 at 12:03 AM, Robert Hanson wrote:
>>
>>> OK. Please test!
>>>
>>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>>>
>>> -- adds loading of host-local file using
>>>
>>>   MolGrabberJmol.loadFile(fileName,loadParams)
>>>
>>> of course, the loadParams business doesn't work with ChemDoodle, but
>>> perhaps it will supply reason to add such :)
>>>
>>> I notice that this does not work for machine-local (hard-drive-based)
>>> files in Chrome. I'm guessing that's a security setting.
>>>
>>> Also, actually, I couldn't get most of these to load into ChemDoodle.
>>> The CIF files seem to be unreadable in all cases, and when there is no
>>> WebGL, only MOL files are readable, not XYZ, PDB, or CIF.
>>>
>>> Kevin, now you have something to do! I'm hoping you can check that over
>>> and tell me what I'm doing wrong (actually, send me a corrected
>>> JmolCD.js!). Something odd in xxxInterpreters, I think. But I don't know
>>> what it would be.
>>>
>>> Bob
>>>
>>>
>>> --
>>> Robert M. Hanson
>>> Professor of Chemistry
>>> St. Olaf College
>>> 1520 St. Olaf Ave.
>>> Northfield, MN 55057
>>> http://www.stolaf.edu/people/hansonr
>>> phone: 507-786-3107
>>>
>>>
>>> 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
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>>
>>
>> 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
>> --
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and
>> threat landscape has changed and how IT managers can respond. Discussions
>> will include endpoint security, mobile security and the latest in malware
>> threats.
>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
>>
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>>  J. Philip Bays
>> Emeritus Professor of Chemistry
>> Department of Chemistry and Physics
>> Saint Mary's College
>> Notre Dame, IN 46556
>> pb...@saintmarys.edu
>>
>>
>>
>>
>>
>>
>>
>> --
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and
>> threat landscape h

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Otis Rothenberger]

Bob,

I just cleared cache on Firefox Mac, and now the only "direct database calls - 
no server" error I still see is:

load :smiles:CC/C=C/CC (PubChem SMILES)

Otis


--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com




On Apr 24, 2012, at 9:44 AM, Robert Hanson wrote:

> Phil, could this be a local caching problem? I'm not seeing any problem with 
> a vanilla Mac running Safari. All the .js files have been changed recently, 
> and there are also new .jar files as well specifically for those actions. 
> 
> Other Mac users?  http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
> 
> 
> 
> On Tue, Apr 24, 2012 at 6:21 AM, Philip Bays  wrote:
> Bob:
> On my Mac, I am getting some java i/o errors using the signed applet and the 
> direct database calls; eg caffeine with map, 2-hexene smiles, aspirin.
> 
> 
> On Apr 24, 2012, at 12:51 AM, Robert Hanson wrote:
> 
>> Dear Jmol users,
>> 
>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>> 
>> Needs testing on iPads, iPhones, and Android tablet.
>> 
>> I have all file types loading now, I think, including direct tapping into 
>> PubChem, NCI Resolver, and RCSB models and ligands all in Jmol and a 
>> slightly adapted subset of ChemDoodle. No links should cause errors. (Still 
>> waiting for one little hosting tweak at RCSB, which is requiring a bit of 
>> indirect server action for keyword searches.)  
>> 
>> In a Java applet environment, I can load PubChem models with charges (for 
>> MEP) directly from PubChem using a great new service they are rolling out 
>> soon. Most happy to beta test that for them! Interesting to compare the 
>> results with NCI. 
>> 
>> Full action requires a couple of files on a server. Which in this case is at 
>> St. Olaf. 
>> 
>> Paul Pillot and I are fast-tracking getting the rest of Jmol into an Object 
>> JavaScript format. A bit tricky, but one problem will be history: No more 
>> worry about waiting for the applet to load before sending it scripts. We'll 
>> just cache them until the applet is ready, then send them off automatically. 
>> That will be nice!
>> 
>> Bob
>> 
>> 
>> On Fri, Apr 13, 2012 at 12:03 AM, Robert Hanson  wrote:
>> OK. Please test!
>> 
>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>> 
>> -- adds loading of host-local file using
>> 
>>   MolGrabberJmol.loadFile(fileName,loadParams)
>> 
>> of course, the loadParams business doesn't work with ChemDoodle, but perhaps 
>> it will supply reason to add such :)
>> 
>> I notice that this does not work for machine-local (hard-drive-based) files 
>> in Chrome. I'm guessing that's a security setting. 
>> 
>> Also, actually, I couldn't get most of these to load into ChemDoodle. The 
>> CIF files seem to be unreadable in all cases, and when there is no WebGL, 
>> only MOL files are readable, not XYZ, PDB, or CIF. 
>> 
>> Kevin, now you have something to do! I'm hoping you can check that over and 
>> tell me what I'm doing wrong (actually, send me a corrected JmolCD.js!). 
>> Something odd in xxxInterpreters, I think. But I don't know what it would be.
>> 
>> Bob
>> 
>> 
>> -- 
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>> 
>> 
>> 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
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>> 
>> 
>> 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
>> --
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and 
>> threat landscape has changed and how IT managers can respond. Discussions 
>> will include endpoint security, mobile security and the latest in malware 
>> threats. 
>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
>> 
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
> 
> J. Philip Bays
> Emeritus Professor of Chemistry
> Department of Chemistry and Physics
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu
> 
> 
> 
> 
> 
> 
> --
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> 

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Robert Hanson]

On Tue, Apr 24, 2012 at 8:44 AM, Otis Rothenberger wrote:

> I'm seeing pretty much the same thing on Mac Firefox that Phil reports. I
> also see what Jeff sees on his iPod Touch on my iPad 2. Notably:
>
> load :smiles:CC/C=C/CC (PubChem SMILES)
>
> chokes on my Mac Firefox per Phil's note, but loads on the iPad, albeit
> with some delay.
>
> Bob, out of curiosity, how are you going after that PubChem SMILES load?
>
>
You have to put /smiles/ in the URL and then POST smiles=xx  along with
that. So it's sort of a combination of get and post. The Jmol call is

http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/SDF?record_type=3d?POST?smiles=C/C=C/C

In Jmol now you designate PubChem with ":" instead of "$":

load :name:tylenol(or just load :tylenol)
load :smiles:C/C=C/C
load :cas:102-94-3  (or just load :102-94-3)
load :cid:1983  (or just load :1983)

Bob







> Otis
>
>
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>
>
>
> On Apr 24, 2012, at 12:51 AM, Robert Hanson wrote:
>
> Dear Jmol users,
>
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>
> Needs testing on iPads, iPhones, and Android tablet.
>
> I have all file types loading now, I think, including direct tapping into
> PubChem, NCI Resolver, and RCSB models and ligands all in Jmol and a
> slightly adapted subset of ChemDoodle. No links should cause errors. (Still
> waiting for one little hosting* *tweak at RCSB, which is requiring a bit
> of indirect server action for keyword searches.)
>
> In a Java applet environment, I can load PubChem models with charges (for
> MEP) directly from PubChem using a great new service they are rolling out
> soon. Most happy to beta test that for them! Interesting to compare the
> results with NCI.
>
> Full action requires a couple of files on a server. Which in this case is
> at St. Olaf.
>
> Paul Pillot and I are fast-tracking getting the rest of Jmol into an
> Object JavaScript format. A bit tricky, but one problem will be history: No
> more worry about waiting for the applet to load before sending it scripts.
> We'll just cache them until the applet is ready, then send them off
> automatically. That will be nice!
>
> Bob
>
>
> On Fri, Apr 13, 2012 at 12:03 AM, Robert Hanson wrote:
>
>> OK. Please test!
>>
>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>>
>> -- adds loading of host-local file using
>>
>>   MolGrabberJmol.loadFile(fileName,loadParams)
>>
>> of course, the loadParams business doesn't work with ChemDoodle, but
>> perhaps it will supply reason to add such :)
>>
>> I notice that this does not work for machine-local (hard-drive-based)
>> files in Chrome. I'm guessing that's a security setting.
>>
>> Also, actually, I couldn't get most of these to load into ChemDoodle. The
>> CIF files seem to be unreadable in all cases, and when there is no WebGL,
>> only MOL files are readable, not XYZ, PDB, or CIF.
>>
>> Kevin, now you have something to do! I'm hoping you can check that over
>> and tell me what I'm doing wrong (actually, send me a corrected
>> JmolCD.js!). Something odd in xxxInterpreters, I think. But I don't know
>> what it would be.
>>
>> Bob
>>
>>
>> --
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>>
>>
>> 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
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
> --
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats.
> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> --
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/list

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Robert Hanson]

Phil, could this be a local caching problem? I'm not seeing any problem
with a vanilla Mac running Safari. All the .js files have been changed
recently, and there are also new .jar files as well specifically for those
actions.

Other Mac users?  http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm



On Tue, Apr 24, 2012 at 6:21 AM, Philip Bays  wrote:

> Bob:
> On my Mac, I am getting some java i/o errors using the signed applet and
> the direct database calls; eg caffeine with map, 2-hexene smiles, aspirin.
>
>
> On Apr 24, 2012, at 12:51 AM, Robert Hanson wrote:
>
> Dear Jmol users,
>
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>
> Needs testing on iPads, iPhones, and Android tablet.
>
> I have all file types loading now, I think, including direct tapping into
> PubChem, NCI Resolver, and RCSB models and ligands all in Jmol and a
> slightly adapted subset of ChemDoodle. No links should cause errors. (Still
> waiting for one little hosting* *tweak at RCSB, which is requiring a bit
> of indirect server action for keyword searches.)
>
> In a Java applet environment, I can load PubChem models with charges (for
> MEP) directly from PubChem using a great new service they are rolling out
> soon. Most happy to beta test that for them! Interesting to compare the
> results with NCI.
>
> Full action requires a couple of files on a server. Which in this case is
> at St. Olaf.
>
> Paul Pillot and I are fast-tracking getting the rest of Jmol into an
> Object JavaScript format. A bit tricky, but one problem will be history: No
> more worry about waiting for the applet to load before sending it scripts.
> We'll just cache them until the applet is ready, then send them off
> automatically. That will be nice!
>
> Bob
>
>
> On Fri, Apr 13, 2012 at 12:03 AM, Robert Hanson wrote:
>
>> OK. Please test!
>>
>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>>
>> -- adds loading of host-local file using
>>
>>   MolGrabberJmol.loadFile(fileName,loadParams)
>>
>> of course, the loadParams business doesn't work with ChemDoodle, but
>> perhaps it will supply reason to add such :)
>>
>> I notice that this does not work for machine-local (hard-drive-based)
>> files in Chrome. I'm guessing that's a security setting.
>>
>> Also, actually, I couldn't get most of these to load into ChemDoodle. The
>> CIF files seem to be unreadable in all cases, and when there is no WebGL,
>> only MOL files are readable, not XYZ, PDB, or CIF.
>>
>> Kevin, now you have something to do! I'm hoping you can check that over
>> and tell me what I'm doing wrong (actually, send me a corrected
>> JmolCD.js!). Something odd in xxxInterpreters, I think. But I don't know
>> what it would be.
>>
>> Bob
>>
>>
>> --
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>>
>>
>> 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
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
> --
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats.
> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
>
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> J. Philip Bays
> Emeritus Professor of Chemistry
> Department of Chemistry and Physics
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu
>
>
>
>
>
>
>
> --
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Will

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Otis Rothenberger]

I'm seeing pretty much the same thing on Mac Firefox that Phil reports. I also 
see what Jeff sees on his iPod Touch on my iPad 2. Notably:

load :smiles:CC/C=C/CC (PubChem SMILES)

chokes on my Mac Firefox per Phil's note, but loads on the iPad, albeit with 
some delay.

Bob, out of curiosity, how are you going after that PubChem SMILES load?

Otis


--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com




On Apr 24, 2012, at 12:51 AM, Robert Hanson wrote:

> Dear Jmol users,
> 
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
> 
> Needs testing on iPads, iPhones, and Android tablet.
> 
> I have all file types loading now, I think, including direct tapping into 
> PubChem, NCI Resolver, and RCSB models and ligands all in Jmol and a slightly 
> adapted subset of ChemDoodle. No links should cause errors. (Still waiting 
> for one little hosting tweak at RCSB, which is requiring a bit of indirect 
> server action for keyword searches.)  
> 
> In a Java applet environment, I can load PubChem models with charges (for 
> MEP) directly from PubChem using a great new service they are rolling out 
> soon. Most happy to beta test that for them! Interesting to compare the 
> results with NCI. 
> 
> Full action requires a couple of files on a server. Which in this case is at 
> St. Olaf. 
> 
> Paul Pillot and I are fast-tracking getting the rest of Jmol into an Object 
> JavaScript format. A bit tricky, but one problem will be history: No more 
> worry about waiting for the applet to load before sending it scripts. We'll 
> just cache them until the applet is ready, then send them off automatically. 
> That will be nice!
> 
> Bob
> 
> 
> On Fri, Apr 13, 2012 at 12:03 AM, Robert Hanson  wrote:
> OK. Please test!
> 
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
> 
> -- adds loading of host-local file using
> 
>   MolGrabberJmol.loadFile(fileName,loadParams)
> 
> of course, the loadParams business doesn't work with ChemDoodle, but perhaps 
> it will supply reason to add such :)
> 
> I notice that this does not work for machine-local (hard-drive-based) files 
> in Chrome. I'm guessing that's a security setting. 
> 
> Also, actually, I couldn't get most of these to load into ChemDoodle. The CIF 
> files seem to be unreadable in all cases, and when there is no WebGL, only 
> MOL files are readable, not XYZ, PDB, or CIF. 
> 
> Kevin, now you have something to do! I'm hoping you can check that over and 
> tell me what I'm doing wrong (actually, send me a corrected JmolCD.js!). 
> Something odd in xxxInterpreters, I think. But I don't know what it would be.
> 
> Bob
> 
> 
> -- 
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
> 
> 
> 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
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
> 
> 
> 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
> --
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and 
> threat landscape has changed and how IT managers can respond. Discussions 
> will include endpoint security, mobile security and the latest in malware 
> threats. 
> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Robert Hanson]

Thanks, Phil. I may have forgotten to check that.

On Tue, Apr 24, 2012 at 6:21 AM, Philip Bays  wrote:

> Bob:
> On my Mac, I am getting some java i/o errors using the signed applet and
> the direct database calls; eg caffeine with map, 2-hexene smiles, aspirin.
>
>
> On Apr 24, 2012, at 12:51 AM, Robert Hanson wrote:
>
> Dear Jmol users,
>
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>
> Needs testing on iPads, iPhones, and Android tablet.
>
> I have all file types loading now, I think, including direct tapping into
> PubChem, NCI Resolver, and RCSB models and ligands all in Jmol and a
> slightly adapted subset of ChemDoodle. No links should cause errors. (Still
> waiting for one little hosting* *tweak at RCSB, which is requiring a bit
> of indirect server action for keyword searches.)
>
> In a Java applet environment, I can load PubChem models with charges (for
> MEP) directly from PubChem using a great new service they are rolling out
> soon. Most happy to beta test that for them! Interesting to compare the
> results with NCI.
>
> Full action requires a couple of files on a server. Which in this case is
> at St. Olaf.
>
> Paul Pillot and I are fast-tracking getting the rest of Jmol into an
> Object JavaScript format. A bit tricky, but one problem will be history: No
> more worry about waiting for the applet to load before sending it scripts.
> We'll just cache them until the applet is ready, then send them off
> automatically. That will be nice!
>
> Bob
>
>
> On Fri, Apr 13, 2012 at 12:03 AM, Robert Hanson wrote:
>
>> OK. Please test!
>>
>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>>
>> -- adds loading of host-local file using
>>
>>   MolGrabberJmol.loadFile(fileName,loadParams)
>>
>> of course, the loadParams business doesn't work with ChemDoodle, but
>> perhaps it will supply reason to add such :)
>>
>> I notice that this does not work for machine-local (hard-drive-based)
>> files in Chrome. I'm guessing that's a security setting.
>>
>> Also, actually, I couldn't get most of these to load into ChemDoodle. The
>> CIF files seem to be unreadable in all cases, and when there is no WebGL,
>> only MOL files are readable, not XYZ, PDB, or CIF.
>>
>> Kevin, now you have something to do! I'm hoping you can check that over
>> and tell me what I'm doing wrong (actually, send me a corrected
>> JmolCD.js!). Something odd in xxxInterpreters, I think. But I don't know
>> what it would be.
>>
>> Bob
>>
>>
>> --
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>>
>>
>> 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
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
> --
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats.
> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
>
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> J. Philip Bays
> Emeritus Professor of Chemistry
> Department of Chemistry and Physics
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu
>
>
>
>
>
>
>
> --
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and 
threat landscape has ch

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Kevin Theisen]

Hi Jeff,

> 1blu takes a long time to load and when it finally loads does not show a 
> cartoon. 

The majority of the delay is probably in the download. Cartoons are for WebGL 
canvases only, so not in the 2D components which some mobile devices will 
default to.

> It shows just the bonds.  :caffeine (PubChem, with map) loads but does not 
> show a surface. 

Surfaces are coming, although only to the WebGL canvases.

>  If the .cif examples are supposed to show anything other than bonds they do 
> not.

We can also show a "Ball and Stick" like representation here. I can also add in 
a unit cell rendering to 2D components. Would that improve the depiction?

Bests,
Kevin





On Apr 24, 2012, at 9:23 AM, Jeff Hansen wrote:

> On my iPod Touch, all load a molecule which I can then rotate.  1blu takes a 
> long time to load and when it finally loads does not show a cartoon.  It 
> shows just the bonds.  :caffeine (PubChem, with map) loads but does not show 
> a surface.  If the .cif examples are supposed to show anything other than 
> bonds they do not.
> 
> 
> ***
> Jeff Hansen
> Department of Chemistry and Biochemistry
> DePauw University
> 602 S. College Ave.
> Greencastle, IN 46135
> jhan...@depauw.edu
> ***
> 
> 
> On Apr 24, 2012, at 12:51 AM, Robert Hanson wrote:
> 
>> Dear Jmol users,
>> 
>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>> 
>> Needs testing on iPads, iPhones, and Android tablet.
>> 
>> I have all file types loading now, I think, including direct tapping into 
>> PubChem, NCI Resolver, and RCSB models and ligands all in Jmol and a 
>> slightly adapted subset of ChemDoodle. No links should cause errors. (Still 
>> waiting for one little hosting tweak at RCSB, which is requiring a bit of 
>> indirect server action for keyword searches.)  
>> 
>> In a Java applet environment, I can load PubChem models with charges (for 
>> MEP) directly from PubChem using a great new service they are rolling out 
>> soon. Most happy to beta test that for them! Interesting to compare the 
>> results with NCI. 
>> 
>> Full action requires a couple of files on a server. Which in this case is at 
>> St. Olaf. 
>> 
>> Paul Pillot and I are fast-tracking getting the rest of Jmol into an Object 
>> JavaScript format. A bit tricky, but one problem will be history: No more 
>> worry about waiting for the applet to load before sending it scripts. We'll 
>> just cache them until the applet is ready, then send them off automatically. 
>> That will be nice!
>> 
>> Bob
>> 
>> 
>> On Fri, Apr 13, 2012 at 12:03 AM, Robert Hanson  wrote:
>> OK. Please test!
>> 
>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>> 
>> -- adds loading of host-local file using
>> 
>>   MolGrabberJmol.loadFile(fileName,loadParams)
>> 
>> of course, the loadParams business doesn't work with ChemDoodle, but perhaps 
>> it will supply reason to add such :)
>> 
>> I notice that this does not work for machine-local (hard-drive-based) files 
>> in Chrome. I'm guessing that's a security setting. 
>> 
>> Also, actually, I couldn't get most of these to load into ChemDoodle. The 
>> CIF files seem to be unreadable in all cases, and when there is no WebGL, 
>> only MOL files are readable, not XYZ, PDB, or CIF. 
>> 
>> Kevin, now you have something to do! I'm hoping you can check that over and 
>> tell me what I'm doing wrong (actually, send me a corrected JmolCD.js!). 
>> Something odd in xxxInterpreters, I think. But I don't know what it would be.
>> 
>> Bob
>> 
>> 
>> -- 
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>> 
>> 
>> 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
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>> 
>> 
>> 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
>> --
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and 
>> threat landscape has changed and how IT managers can respond. Discussions 
>> will include endpoint security, mobile security and the latest in malware 
>> threats. 
>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
> 
> --
> Live Security Virtua

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Jeff Hansen]

On my iPod Touch, all load a molecule which I can then rotate.  1blu takes a 
long time to load and when it finally loads does not show a cartoon.  It shows 
just the bonds.  :caffeine (PubChem, with map) loads but does not show a 
surface.  If the .cif examples are supposed to show anything other than bonds 
they do not.


***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***


On Apr 24, 2012, at 12:51 AM, Robert Hanson wrote:

> Dear Jmol users,
> 
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
> 
> Needs testing on iPads, iPhones, and Android tablet.
> 
> I have all file types loading now, I think, including direct tapping into 
> PubChem, NCI Resolver, and RCSB models and ligands all in Jmol and a slightly 
> adapted subset of ChemDoodle. No links should cause errors. (Still waiting 
> for one little hosting tweak at RCSB, which is requiring a bit of indirect 
> server action for keyword searches.)  
> 
> In a Java applet environment, I can load PubChem models with charges (for 
> MEP) directly from PubChem using a great new service they are rolling out 
> soon. Most happy to beta test that for them! Interesting to compare the 
> results with NCI. 
> 
> Full action requires a couple of files on a server. Which in this case is at 
> St. Olaf. 
> 
> Paul Pillot and I are fast-tracking getting the rest of Jmol into an Object 
> JavaScript format. A bit tricky, but one problem will be history: No more 
> worry about waiting for the applet to load before sending it scripts. We'll 
> just cache them until the applet is ready, then send them off automatically. 
> That will be nice!
> 
> Bob
> 
> 
> On Fri, Apr 13, 2012 at 12:03 AM, Robert Hanson  wrote:
> OK. Please test!
> 
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
> 
> -- adds loading of host-local file using
> 
>   MolGrabberJmol.loadFile(fileName,loadParams)
> 
> of course, the loadParams business doesn't work with ChemDoodle, but perhaps 
> it will supply reason to add such :)
> 
> I notice that this does not work for machine-local (hard-drive-based) files 
> in Chrome. I'm guessing that's a security setting. 
> 
> Also, actually, I couldn't get most of these to load into ChemDoodle. The CIF 
> files seem to be unreadable in all cases, and when there is no WebGL, only 
> MOL files are readable, not XYZ, PDB, or CIF. 
> 
> Kevin, now you have something to do! I'm hoping you can check that over and 
> tell me what I'm doing wrong (actually, send me a corrected JmolCD.js!). 
> Something odd in xxxInterpreters, I think. But I don't know what it would be.
> 
> Bob
> 
> 
> -- 
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
> 
> 
> 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
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
> 
> 
> 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
> --
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and 
> threat landscape has changed and how IT managers can respond. Discussions 
> will include endpoint security, mobile security and the latest in malware 
> threats. 
> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Philip Bays]

Bob:
On my Mac, I am getting some java i/o errors using the signed applet and the 
direct database calls; eg caffeine with map, 2-hexene smiles, aspirin.


On Apr 24, 2012, at 12:51 AM, Robert Hanson wrote:

> Dear Jmol users,
> 
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
> 
> Needs testing on iPads, iPhones, and Android tablet.
> 
> I have all file types loading now, I think, including direct tapping into 
> PubChem, NCI Resolver, and RCSB models and ligands all in Jmol and a slightly 
> adapted subset of ChemDoodle. No links should cause errors. (Still waiting 
> for one little hosting tweak at RCSB, which is requiring a bit of indirect 
> server action for keyword searches.)  
> 
> In a Java applet environment, I can load PubChem models with charges (for 
> MEP) directly from PubChem using a great new service they are rolling out 
> soon. Most happy to beta test that for them! Interesting to compare the 
> results with NCI. 
> 
> Full action requires a couple of files on a server. Which in this case is at 
> St. Olaf. 
> 
> Paul Pillot and I are fast-tracking getting the rest of Jmol into an Object 
> JavaScript format. A bit tricky, but one problem will be history: No more 
> worry about waiting for the applet to load before sending it scripts. We'll 
> just cache them until the applet is ready, then send them off automatically. 
> That will be nice!
> 
> Bob
> 
> 
> On Fri, Apr 13, 2012 at 12:03 AM, Robert Hanson  wrote:
> OK. Please test!
> 
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
> 
> -- adds loading of host-local file using
> 
>   MolGrabberJmol.loadFile(fileName,loadParams)
> 
> of course, the loadParams business doesn't work with ChemDoodle, but perhaps 
> it will supply reason to add such :)
> 
> I notice that this does not work for machine-local (hard-drive-based) files 
> in Chrome. I'm guessing that's a security setting. 
> 
> Also, actually, I couldn't get most of these to load into ChemDoodle. The CIF 
> files seem to be unreadable in all cases, and when there is no WebGL, only 
> MOL files are readable, not XYZ, PDB, or CIF. 
> 
> Kevin, now you have something to do! I'm hoping you can check that over and 
> tell me what I'm doing wrong (actually, send me a corrected JmolCD.js!). 
> Something odd in xxxInterpreters, I think. But I don't know what it would be.
> 
> Bob
> 
> 
> -- 
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
> 
> 
> 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
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
> 
> 
> 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
> --
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and 
> threat landscape has changed and how IT managers can respond. Discussions 
> will include endpoint security, mobile security and the latest in malware 
> threats. 
> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

J. Philip Bays
Emeritus Professor of Chemistry
Department of Chemistry and Physics
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu





--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
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Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Robert Hanson]

Dear Jmol users,

http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm

Needs testing on iPads, iPhones, and Android tablet.

I have all file types loading now, I think, including direct tapping into
PubChem, NCI Resolver, and RCSB models and ligands all in Jmol and a
slightly adapted subset of ChemDoodle. No links should cause errors. (Still
waiting for one little hosting* *tweak at RCSB, which is requiring a bit of
indirect server action for keyword searches.)

In a Java applet environment, I can load PubChem models with charges (for
MEP) directly from PubChem using a great new service they are rolling out
soon. Most happy to beta test that for them! Interesting to compare the
results with NCI.

Full action requires a couple of files on a server. Which in this case is
at St. Olaf.

Paul Pillot and I are fast-tracking getting the rest of Jmol into an Object
JavaScript format. A bit tricky, but one problem will be history: No more
worry about waiting for the applet to load before sending it scripts. We'll
just cache them until the applet is ready, then send them off
automatically. That will be nice!

Bob


On Fri, Apr 13, 2012 at 12:03 AM, Robert Hanson  wrote:

> OK. Please test!
>
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>
> -- adds loading of host-local file using
>
>   MolGrabberJmol.loadFile(fileName,loadParams)
>
> of course, the loadParams business doesn't work with ChemDoodle, but
> perhaps it will supply reason to add such :)
>
> I notice that this does not work for machine-local (hard-drive-based)
> files in Chrome. I'm guessing that's a security setting.
>
> Also, actually, I couldn't get most of these to load into ChemDoodle. The
> CIF files seem to be unreadable in all cases, and when there is no WebGL,
> only MOL files are readable, not XYZ, PDB, or CIF.
>
> Kevin, now you have something to do! I'm hoping you can check that over
> and tell me what I'm doing wrong (actually, send me a corrected
> JmolCD.js!). Something odd in xxxInterpreters, I think. But I don't know
> what it would be.
>
> Bob
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Kevin Theisen]

Hi Bob,

It appears FF4 is mmCIF, which we do not support (at least not yet). I will 
have to do some more study of the CIF format to make sure I understand why 
there are so many variations, but currently, if your file matches the core CIF 
spec, then it will load without issue: http://it.iucr.org/G/

Bests,
Kevin


On Apr 21, 2012, at 12:29 AM, Robert Hanson wrote:

> that's fixed. 
> 
> Looks like Kevin needs to take another look at reading CIF files, though. 
> 
> At http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm?CD the "load ==HEM" 
> link on the right does not work. This is a file of the type 
> 
> http://www.rcsb.org/pdb/files/ligand/FS4.cif
> 
> Bob
> 
> 
> 
> On Fri, Apr 20, 2012 at 10:08 PM, Robert Hanson  wrote:
> Oh, yeah. Not on my PC either - must be something simple
> 
> 
> On Fri, Apr 20, 2012 at 10:08 PM, Robert Hanson  wrote:
> ohoh!!! I'll look at that.
> 
> 
> On Fri, Apr 20, 2012 at 8:19 PM, Philip Bays  wrote:
> Bob:
> 
> For me chemdoodle does not work on either my mac or on my iPod Touch.
> 
> 
> On Apr 20, 2012, at 7:56 PM, Robert Hanson wrote:
> 
>> yes indeedy, both  NCI and PDB allow direct access via AJAX to their 
>> databases. Thank you, guys!
>> 
>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>> 
>> Thus, with Jmol/ChemDoodle there is no need to go to the server except for 
>> an image.
>> 
>> 
>> On Thu, Apr 19, 2012 at 9:31 AM, Otis Rothenberger  
>> wrote:
>> Very nice. I'm a believer. I need to look at the code to see how to fit this 
>> into our Web application.
>> 
>> I should remind users that now that PubChem files can be loaded, MEP 
>> surfaces can also be displayed. It's true that the PubChem SDF's use an 
>> abbreviated approach to partial charges, still the MEP's still have some 
>> classroom utility in my opinion. I assume PubChem's abbreviated partial 
>> charges are rooted in making charge profile searches practical.
>>  
>> Bob added the Jmol reading of these PubChem partial charges in 2010, I think.
>> 
>> Otis
>> 
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>> 
>> 
>> 
>> 
>> On Apr 19, 2012, at 10:13 AM, Robert Hanson wrote:
>> 
>>> More goodies at 
>>> 
>>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>>> 
>>> -- pubChem search
>>> -- keyword lookup at RCSB
>>> -- general way to swap the applet for a block of HTML information if desired
>>> 
>>> Bob
>>> 
>>> 
>>> -- 
>>> Robert M. Hanson
>>> Professor of Chemistry
>>> St. Olaf College
>>> 1520 St. Olaf Ave.
>>> Northfield, MN 55057
>>> http://www.stolaf.edu/people/hansonr
>>> phone: 507-786-3107
>>> 
>>> 
>>> 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
>>> --
>>> For Developers, A Lot Can Happen In A Second.
>>> Boundary is the first to Know...and Tell You.
>>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>> http://p.sf.net/sfu/Boundary-d2dvs2___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>> 
>> 
>> --
>> For Developers, A Lot Can Happen In A Second.
>> Boundary is the first to Know...and Tell You.
>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>> http://p.sf.net/sfu/Boundary-d2dvs2
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>> 
>> 
>> 
>> 
>> -- 
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>> 
>> 
>> 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
>> --
>> For Developers, A Lot Can Happen In A Second.
>> Boundary is the first to Know...and Tell You.
>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>> http://p.sf.net/sfu/Boundary-d2dvs2___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
> 
> J. Philip Bays
> Emeritus Professor of Chemistry
> Department of Chemistry and Physics
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu
> 
> 
> 
> 
> 
> 
> --
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2
> ___

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Philip Bays]

Mostly fixed:-(  The "image only" and "load :tylenol" links do not work.


On Apr 21, 2012, at 12:29 AM, Robert Hanson wrote:

> that's fixed. 
> 
> Looks like Kevin needs to take another look at reading CIF files, though. 
> 
> At http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm?CD the "load ==HEM" 
> link on the right does not work. This is a file of the type 
> 
> http://www.rcsb.org/pdb/files/ligand/FS4.cif
> 
> Bob
> 
> 
> 
> On Fri, Apr 20, 2012 at 10:08 PM, Robert Hanson  wrote:
> Oh, yeah. Not on my PC either - must be something simple
> 
> 
> On Fri, Apr 20, 2012 at 10:08 PM, Robert Hanson  wrote:
> ohoh!!! I'll look at that.
> 
> 
> On Fri, Apr 20, 2012 at 8:19 PM, Philip Bays  wrote:
> Bob:
> 
> For me chemdoodle does not work on either my mac or on my iPod Touch.
> 
> 
> On Apr 20, 2012, at 7:56 PM, Robert Hanson wrote:
> 
>> yes indeedy, both  NCI and PDB allow direct access via AJAX to their 
>> databases. Thank you, guys!
>> 
>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>> 
>> Thus, with Jmol/ChemDoodle there is no need to go to the server except for 
>> an image.
>> 
>> 
>> On Thu, Apr 19, 2012 at 9:31 AM, Otis Rothenberger  
>> wrote:
>> Very nice. I'm a believer. I need to look at the code to see how to fit this 
>> into our Web application.
>> 
>> I should remind users that now that PubChem files can be loaded, MEP 
>> surfaces can also be displayed. It's true that the PubChem SDF's use an 
>> abbreviated approach to partial charges, still the MEP's still have some 
>> classroom utility in my opinion. I assume PubChem's abbreviated partial 
>> charges are rooted in making charge profile searches practical.
>>  
>> Bob added the Jmol reading of these PubChem partial charges in 2010, I think.
>> 
>> Otis
>> 
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>> 
>> 
>> 
>> 
>> On Apr 19, 2012, at 10:13 AM, Robert Hanson wrote:
>> 
>>> More goodies at 
>>> 
>>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>>> 
>>> -- pubChem search
>>> -- keyword lookup at RCSB
>>> -- general way to swap the applet for a block of HTML information if desired
>>> 
>>> Bob
>>> 
>>> 
>>> -- 
>>> Robert M. Hanson
>>> Professor of Chemistry
>>> St. Olaf College
>>> 1520 St. Olaf Ave.
>>> Northfield, MN 55057
>>> http://www.stolaf.edu/people/hansonr
>>> phone: 507-786-3107
>>> 
>>> 
>>> 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
>>> --
>>> For Developers, A Lot Can Happen In A Second.
>>> Boundary is the first to Know...and Tell You.
>>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>> http://p.sf.net/sfu/Boundary-d2dvs2___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>> 
>> 
>> --
>> For Developers, A Lot Can Happen In A Second.
>> Boundary is the first to Know...and Tell You.
>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>> http://p.sf.net/sfu/Boundary-d2dvs2
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>> 
>> 
>> 
>> 
>> -- 
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>> 
>> 
>> 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
>> --
>> For Developers, A Lot Can Happen In A Second.
>> Boundary is the first to Know...and Tell You.
>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>> http://p.sf.net/sfu/Boundary-d2dvs2___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
> 
> J. Philip Bays
> Emeritus Professor of Chemistry
> Department of Chemistry and Physics
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu
> 
> 
> 
> 
> 
> 
> --
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
> 
> 
> 
> 
> -- 
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Robert Hanson]

Right, so did I. See http://www.w3.org/TR/cors/

The Access-Control-Allow-Origin header indicates whether a resource can be
shared based by returning the value of the Origin request header in the
response. ABNF:

Access-Control-Allow-Origin = "Access-Control-Allow-Origin" ":"
origin-list-or-null | "*"


This is a header that the server adds on the way back to the page that
says, "ignore cross-domain issues." RCSB, NCI, and NCBI (almost) have it in
place. So now you can do this in a web page:

jQuery.ajax({
dataType: "text",
type: "GET",
url: fileName,
success: fSuccess
})

and your fSuccess function will get the model data as the first parameter.



On Sat, Apr 21, 2012 at 1:39 AM, Paul Pillot <
paul.pil...@ac-orleans-tours.fr> wrote:

> How does this work technically (JSONP ? other ?) ? I thought it was not
> possible to make ajax calls to other domains without triggering a security
> message (to prevent cross site scripting) ?
> It's very exciting to see this working so well without the signed applet !
> Paul
>
> Le 21 avr. 2012 à 01:56, Robert Hanson a écrit :
>
> yes indeedy, both  NCI and PDB allow direct access via AJAX to their
> databases. Thank you, guys!
>
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>
> Thus, with Jmol/ChemDoodle there is no need to go to the server except for
> an image.
>
>
> On Thu, Apr 19, 2012 at 9:31 AM, Otis Rothenberger 
> wrote:
>
>
>
>
> 
> --
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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
--
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
http://p.sf.net/sfu/Boundary-d2dvs2___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Paul Pillot]

How does this work technically (JSONP ? other ?) ? I thought it was not 
possible to make ajax calls to other domains without triggering a security 
message (to prevent cross site scripting) ?
It's very exciting to see this working so well without the signed applet !
Paul

Le 21 avr. 2012 à 01:56, Robert Hanson a écrit :

> yes indeedy, both  NCI and PDB allow direct access via AJAX to their 
> databases. Thank you, guys!
> 
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
> 
> Thus, with Jmol/ChemDoodle there is no need to go to the server except for an 
> image.
> 
> 
> On Thu, Apr 19, 2012 at 9:31 AM, Otis Rothenberger  
> wrote:
> 
> 

--
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
http://p.sf.net/sfu/Boundary-d2dvs2___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Robert Hanson]

that's fixed.

Looks like Kevin needs to take another look at reading CIF files, though.

At http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm?CD the "load ==HEM"
link on the right does not work. This is a file of the type

http://www.rcsb.org/pdb/files/ligand/FS4.cif

Bob



On Fri, Apr 20, 2012 at 10:08 PM, Robert Hanson  wrote:

> Oh, yeah. Not on my PC either - must be something simple
>
>
> On Fri, Apr 20, 2012 at 10:08 PM, Robert Hanson wrote:
>
>> ohoh!!! I'll look at that.
>>
>>
>> On Fri, Apr 20, 2012 at 8:19 PM, Philip Bays wrote:
>>
>>> Bob:
>>>
>>> For me chemdoodle does not work on either my mac or on my iPod Touch.
>>>
>>>
>>> On Apr 20, 2012, at 7:56 PM, Robert Hanson wrote:
>>>
>>> yes indeedy, both  NCI and PDB allow direct access via AJAX to their
>>> databases. Thank you, guys!
>>>
>>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>>>
>>> Thus, with Jmol/ChemDoodle there is no need to go to the server except
>>> for an image.
>>>
>>>
>>> On Thu, Apr 19, 2012 at 9:31 AM, Otis Rothenberger <
>>> osrot...@chemagic.com> wrote:
>>>
 Very nice. I'm a believer. I need to look at the code to see how to fit
 this into our Web application.

 I should remind users that now that PubChem files can be loaded, MEP
 surfaces can also be displayed. It's true that the PubChem SDF's use an
 abbreviated approach to partial charges, still the MEP's still have some
 classroom utility in my opinion. I assume PubChem's abbreviated partial
 charges are rooted in making charge profile searches practical.

 Bob added the Jmol reading of these PubChem partial charges in 2010, I
 think.

 Otis

 --
 Otis Rothenberger
 o...@chemagic.com
 http://chemagic.com




 On Apr 19, 2012, at 10:13 AM, Robert Hanson wrote:

 More goodies at

 http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm

 -- pubChem search
 -- keyword lookup at RCSB
 -- general way to swap the applet for a block of HTML information if
 desired

 Bob


 --
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107


 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
 --
 For Developers, A Lot Can Happen In A Second.
 Boundary is the first to Know...and Tell You.
 Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!

 http://p.sf.net/sfu/Boundary-d2dvs2___
 Jmol-users mailing list
 Jmol-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-users




 --
 For Developers, A Lot Can Happen In A Second.
 Boundary is the first to Know...and Tell You.
 Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
 http://p.sf.net/sfu/Boundary-d2dvs2
 ___
 Jmol-users mailing list
 Jmol-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-users


>>>
>>>
>>> --
>>> Robert M. Hanson
>>> Professor of Chemistry
>>> St. Olaf College
>>> 1520 St. Olaf Ave.
>>> Northfield, MN 55057
>>> http://www.stolaf.edu/people/hansonr
>>> phone: 507-786-3107
>>>
>>>
>>> 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
>>>
>>> --
>>> For Developers, A Lot Can Happen In A Second.
>>> Boundary is the first to Know...and Tell You.
>>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>>
>>> http://p.sf.net/sfu/Boundary-d2dvs2___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>>  J. Philip Bays
>>> Emeritus Professor of Chemistry
>>> Department of Chemistry and Physics
>>> Saint Mary's College
>>> Notre Dame, IN 46556
>>> pb...@saintmarys.edu
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> --
>>> For Developers, A Lot Can Happen In A Second.
>>> Boundary is the first to Know...and Tell You.
>>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>> http://p.sf.net/sfu/Boundary-d2dvs2
>>> ___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>
>>
>> --
>>

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Robert Hanson]

Oh, yeah. Not on my PC either - must be something simple

On Fri, Apr 20, 2012 at 10:08 PM, Robert Hanson  wrote:

> ohoh!!! I'll look at that.
>
>
> On Fri, Apr 20, 2012 at 8:19 PM, Philip Bays  wrote:
>
>> Bob:
>>
>> For me chemdoodle does not work on either my mac or on my iPod Touch.
>>
>>
>> On Apr 20, 2012, at 7:56 PM, Robert Hanson wrote:
>>
>> yes indeedy, both  NCI and PDB allow direct access via AJAX to their
>> databases. Thank you, guys!
>>
>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>>
>> Thus, with Jmol/ChemDoodle there is no need to go to the server except
>> for an image.
>>
>>
>> On Thu, Apr 19, 2012 at 9:31 AM, Otis Rothenberger > > wrote:
>>
>>> Very nice. I'm a believer. I need to look at the code to see how to fit
>>> this into our Web application.
>>>
>>> I should remind users that now that PubChem files can be loaded, MEP
>>> surfaces can also be displayed. It's true that the PubChem SDF's use an
>>> abbreviated approach to partial charges, still the MEP's still have some
>>> classroom utility in my opinion. I assume PubChem's abbreviated partial
>>> charges are rooted in making charge profile searches practical.
>>>
>>> Bob added the Jmol reading of these PubChem partial charges in 2010, I
>>> think.
>>>
>>> Otis
>>>
>>> --
>>> Otis Rothenberger
>>> o...@chemagic.com
>>> http://chemagic.com
>>>
>>>
>>>
>>>
>>> On Apr 19, 2012, at 10:13 AM, Robert Hanson wrote:
>>>
>>> More goodies at
>>>
>>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>>>
>>> -- pubChem search
>>> -- keyword lookup at RCSB
>>> -- general way to swap the applet for a block of HTML information if
>>> desired
>>>
>>> Bob
>>>
>>>
>>> --
>>> Robert M. Hanson
>>> Professor of Chemistry
>>> St. Olaf College
>>> 1520 St. Olaf Ave.
>>> Northfield, MN 55057
>>> http://www.stolaf.edu/people/hansonr
>>> phone: 507-786-3107
>>>
>>>
>>> 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
>>> --
>>> For Developers, A Lot Can Happen In A Second.
>>> Boundary is the first to Know...and Tell You.
>>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>>
>>> http://p.sf.net/sfu/Boundary-d2dvs2___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>>
>>>
>>> --
>>> For Developers, A Lot Can Happen In A Second.
>>> Boundary is the first to Know...and Tell You.
>>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>> http://p.sf.net/sfu/Boundary-d2dvs2
>>> ___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>
>>
>> --
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>>
>>
>> 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
>>
>> --
>> For Developers, A Lot Can Happen In A Second.
>> Boundary is the first to Know...and Tell You.
>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>
>> http://p.sf.net/sfu/Boundary-d2dvs2___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>>  J. Philip Bays
>> Emeritus Professor of Chemistry
>> Department of Chemistry and Physics
>> Saint Mary's College
>> Notre Dame, IN 46556
>> pb...@saintmarys.edu
>>
>>
>>
>>
>>
>>
>>
>> --
>> For Developers, A Lot Can Happen In A Second.
>> Boundary is the first to Know...and Tell You.
>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>> http://p.sf.net/sfu/Boundary-d2dvs2
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer f

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Robert Hanson]

ohoh!!! I'll look at that.

On Fri, Apr 20, 2012 at 8:19 PM, Philip Bays  wrote:

> Bob:
>
> For me chemdoodle does not work on either my mac or on my iPod Touch.
>
>
> On Apr 20, 2012, at 7:56 PM, Robert Hanson wrote:
>
> yes indeedy, both  NCI and PDB allow direct access via AJAX to their
> databases. Thank you, guys!
>
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>
> Thus, with Jmol/ChemDoodle there is no need to go to the server except for
> an image.
>
>
> On Thu, Apr 19, 2012 at 9:31 AM, Otis Rothenberger 
> wrote:
>
>> Very nice. I'm a believer. I need to look at the code to see how to fit
>> this into our Web application.
>>
>> I should remind users that now that PubChem files can be loaded, MEP
>> surfaces can also be displayed. It's true that the PubChem SDF's use an
>> abbreviated approach to partial charges, still the MEP's still have some
>> classroom utility in my opinion. I assume PubChem's abbreviated partial
>> charges are rooted in making charge profile searches practical.
>>
>> Bob added the Jmol reading of these PubChem partial charges in 2010, I
>> think.
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>>
>>
>>
>>
>> On Apr 19, 2012, at 10:13 AM, Robert Hanson wrote:
>>
>> More goodies at
>>
>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>>
>> -- pubChem search
>> -- keyword lookup at RCSB
>> -- general way to swap the applet for a block of HTML information if
>> desired
>>
>> Bob
>>
>>
>> --
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>>
>>
>> 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
>> --
>> For Developers, A Lot Can Happen In A Second.
>> Boundary is the first to Know...and Tell You.
>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>
>> http://p.sf.net/sfu/Boundary-d2dvs2___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>>
>>
>> --
>> For Developers, A Lot Can Happen In A Second.
>> Boundary is the first to Know...and Tell You.
>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>> http://p.sf.net/sfu/Boundary-d2dvs2
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
>
> --
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>
> http://p.sf.net/sfu/Boundary-d2dvs2___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> J. Philip Bays
> Emeritus Professor of Chemistry
> Department of Chemistry and Physics
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu
>
>
>
>
>
>
>
> --
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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
--
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
http://p.sf.net/sfu/Boundary-d2dvs2___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Philip Bays]

Bob:

For me chemdoodle does not work on either my mac or on my iPod Touch.


On Apr 20, 2012, at 7:56 PM, Robert Hanson wrote:

> yes indeedy, both  NCI and PDB allow direct access via AJAX to their 
> databases. Thank you, guys!
> 
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
> 
> Thus, with Jmol/ChemDoodle there is no need to go to the server except for an 
> image.
> 
> 
> On Thu, Apr 19, 2012 at 9:31 AM, Otis Rothenberger  
> wrote:
> Very nice. I'm a believer. I need to look at the code to see how to fit this 
> into our Web application.
> 
> I should remind users that now that PubChem files can be loaded, MEP surfaces 
> can also be displayed. It's true that the PubChem SDF's use an abbreviated 
> approach to partial charges, still the MEP's still have some classroom 
> utility in my opinion. I assume PubChem's abbreviated partial charges are 
> rooted in making charge profile searches practical.
>  
> Bob added the Jmol reading of these PubChem partial charges in 2010, I think.
> 
> Otis
> 
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
> 
> 
> 
> 
> On Apr 19, 2012, at 10:13 AM, Robert Hanson wrote:
> 
>> More goodies at 
>> 
>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>> 
>> -- pubChem search
>> -- keyword lookup at RCSB
>> -- general way to swap the applet for a block of HTML information if desired
>> 
>> Bob
>> 
>> 
>> -- 
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>> 
>> 
>> 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
>> --
>> For Developers, A Lot Can Happen In A Second.
>> Boundary is the first to Know...and Tell You.
>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>> http://p.sf.net/sfu/Boundary-d2dvs2___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
> 
> 
> --
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
> 
> 
> 
> 
> -- 
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
> 
> 
> 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
> --
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

J. Philip Bays
Emeritus Professor of Chemistry
Department of Chemistry and Physics
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu





--
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
http://p.sf.net/sfu/Boundary-d2dvs2___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Robert Hanson]

yes indeedy, both  NCI and PDB allow direct access via AJAX to their
databases. Thank you, guys!

http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm

Thus, with Jmol/ChemDoodle there is no need to go to the server except for
an image.


On Thu, Apr 19, 2012 at 9:31 AM, Otis Rothenberger wrote:

> Very nice. I'm a believer. I need to look at the code to see how to fit
> this into our Web application.
>
> I should remind users that now that PubChem files can be loaded, MEP
> surfaces can also be displayed. It's true that the PubChem SDF's use an
> abbreviated approach to partial charges, still the MEP's still have some
> classroom utility in my opinion. I assume PubChem's abbreviated partial
> charges are rooted in making charge profile searches practical.
>
> Bob added the Jmol reading of these PubChem partial charges in 2010, I
> think.
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>
>
>
> On Apr 19, 2012, at 10:13 AM, Robert Hanson wrote:
>
> More goodies at
>
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>
> -- pubChem search
> -- keyword lookup at RCSB
> -- general way to swap the applet for a block of HTML information if
> desired
>
> Bob
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
>
> --
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>
> http://p.sf.net/sfu/Boundary-d2dvs2___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> --
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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
--
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
http://p.sf.net/sfu/Boundary-d2dvs2___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Bob Hanson]

So markus says.   Haven't tried that yet. 

Sent from my stupid iphone

On Apr 19, 2012, at 12:58 PM, Otis Rothenberger  wrote:

> Bob,
> 
> I'm not sure because I didn't know you could do that! Do you mean I don't 
> have to use a server readURL script on my server to query Resolver. I can 
> simply query Resolver directly via an AJAX script?
> 
> Otis
> 
> 
> 
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
> 
> 
> 
> 
> On Apr 19, 2012, at 3:14 PM, Bob Hanson wrote:
> 
>> Otis  is PubChem now available via ajax directly, like for NCI?  That is, no 
>> server relay and so no problem with being locked out? As soon as I get a 
>> chance -- traveling all day today -- I will add direct NCI access in 
>> JmolCD.js. I've sent a request for that to RCSB. If we had all three it 
>> would be terrific. 
>> 
>> Sent from my stupid iphone
>> 
>> On Apr 19, 2012, at 7:31 AM, Otis Rothenberger  wrote:
>> 
>>> Very nice. I'm a believer. I need to look at the code to see how to fit 
>>> this into our Web application.
>>> 
>>> I should remind users that now that PubChem files can be loaded, MEP 
>>> surfaces can also be displayed. It's true that the PubChem SDF's use an 
>>> abbreviated approach to partial charges, still the MEP's still have some 
>>> classroom utility in my opinion. I assume PubChem's abbreviated partial 
>>> charges are rooted in making charge profile searches practical.
>>>  
>>> Bob added the Jmol reading of these PubChem partial charges in 2010, I 
>>> think.
>>> 
>>> Otis
>>> 
>>> --
>>> Otis Rothenberger
>>> o...@chemagic.com
>>> http://chemagic.com
>>> 
>>> 
>>> 
>>> 
>>> On Apr 19, 2012, at 10:13 AM, Robert Hanson wrote:
>>> 
 More goodies at 
 
 http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
 
 -- pubChem search
 -- keyword lookup at RCSB
 -- general way to swap the applet for a block of HTML information if 
 desired
 
 Bob
 
 
 -- 
 Robert M. Hanson
 Professor of Chemistry
 St. Olaf College
 1520 St. Olaf Ave.
 Northfield, MN 55057
 http://www.stolaf.edu/people/hansonr
 phone: 507-786-3107
 
 
 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
 --
 For Developers, A Lot Can Happen In A Second.
 Boundary is the first to Know...and Tell You.
 Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
 http://p.sf.net/sfu/Boundary-d2dvs2___
 Jmol-users mailing list
 Jmol-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-users
>>> 
>>> --
>>> For Developers, A Lot Can Happen In A Second.
>>> Boundary is the first to Know...and Tell You.
>>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>> http://p.sf.net/sfu/Boundary-d2dvs2
>>> ___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>> --
>> For Developers, A Lot Can Happen In A Second.
>> Boundary is the first to Know...and Tell You.
>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>> http://p.sf.net/sfu/Boundary-d2dvs2___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
> 
> --
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
--
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
http://p.sf.net/sfu/Boundary-d2dvs2___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Otis Rothenberger]

Bob,

I'm not sure because I didn't know you could do that! Do you mean I don't have 
to use a server readURL script on my server to query Resolver. I can simply 
query Resolver directly via an AJAX script?

Otis



--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com




On Apr 19, 2012, at 3:14 PM, Bob Hanson wrote:

> Otis  is PubChem now available via ajax directly, like for NCI?  That is, no 
> server relay and so no problem with being locked out? As soon as I get a 
> chance -- traveling all day today -- I will add direct NCI access in 
> JmolCD.js. I've sent a request for that to RCSB. If we had all three it would 
> be terrific. 
> 
> Sent from my stupid iphone
> 
> On Apr 19, 2012, at 7:31 AM, Otis Rothenberger  wrote:
> 
>> Very nice. I'm a believer. I need to look at the code to see how to fit this 
>> into our Web application.
>> 
>> I should remind users that now that PubChem files can be loaded, MEP 
>> surfaces can also be displayed. It's true that the PubChem SDF's use an 
>> abbreviated approach to partial charges, still the MEP's still have some 
>> classroom utility in my opinion. I assume PubChem's abbreviated partial 
>> charges are rooted in making charge profile searches practical.
>>  
>> Bob added the Jmol reading of these PubChem partial charges in 2010, I think.
>> 
>> Otis
>> 
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>> 
>> 
>> 
>> 
>> On Apr 19, 2012, at 10:13 AM, Robert Hanson wrote:
>> 
>>> More goodies at 
>>> 
>>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>>> 
>>> -- pubChem search
>>> -- keyword lookup at RCSB
>>> -- general way to swap the applet for a block of HTML information if desired
>>> 
>>> Bob
>>> 
>>> 
>>> -- 
>>> Robert M. Hanson
>>> Professor of Chemistry
>>> St. Olaf College
>>> 1520 St. Olaf Ave.
>>> Northfield, MN 55057
>>> http://www.stolaf.edu/people/hansonr
>>> phone: 507-786-3107
>>> 
>>> 
>>> 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
>>> --
>>> For Developers, A Lot Can Happen In A Second.
>>> Boundary is the first to Know...and Tell You.
>>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>> http://p.sf.net/sfu/Boundary-d2dvs2___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>> 
>> --
>> For Developers, A Lot Can Happen In A Second.
>> Boundary is the first to Know...and Tell You.
>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>> http://p.sf.net/sfu/Boundary-d2dvs2
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
> --
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

--
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
http://p.sf.net/sfu/Boundary-d2dvs2___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Bob Hanson]

Otis  is PubChem now available via ajax directly, like for NCI?  That is, no 
server relay and so no problem with being locked out? As soon as I get a chance 
-- traveling all day today -- I will add direct NCI access in JmolCD.js. I've 
sent a request for that to RCSB. If we had all three it would be terrific. 

Sent from my stupid iphone

On Apr 19, 2012, at 7:31 AM, Otis Rothenberger  wrote:

> Very nice. I'm a believer. I need to look at the code to see how to fit this 
> into our Web application.
> 
> I should remind users that now that PubChem files can be loaded, MEP surfaces 
> can also be displayed. It's true that the PubChem SDF's use an abbreviated 
> approach to partial charges, still the MEP's still have some classroom 
> utility in my opinion. I assume PubChem's abbreviated partial charges are 
> rooted in making charge profile searches practical.
>  
> Bob added the Jmol reading of these PubChem partial charges in 2010, I think.
> 
> Otis
> 
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
> 
> 
> 
> 
> On Apr 19, 2012, at 10:13 AM, Robert Hanson wrote:
> 
>> More goodies at 
>> 
>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>> 
>> -- pubChem search
>> -- keyword lookup at RCSB
>> -- general way to swap the applet for a block of HTML information if desired
>> 
>> Bob
>> 
>> 
>> -- 
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>> 
>> 
>> 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
>> --
>> For Developers, A Lot Can Happen In A Second.
>> Boundary is the first to Know...and Tell You.
>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>> http://p.sf.net/sfu/Boundary-d2dvs2___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
> 
> --
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2
> ___
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> https://lists.sourceforge.net/lists/listinfo/jmol-users
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Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Otis Rothenberger]

Very nice. I'm a believer. I need to look at the code to see how to fit this 
into our Web application.

I should remind users that now that PubChem files can be loaded, MEP surfaces 
can also be displayed. It's true that the PubChem SDF's use an abbreviated 
approach to partial charges, still the MEP's still have some classroom utility 
in my opinion. I assume PubChem's abbreviated partial charges are rooted in 
making charge profile searches practical.
 
Bob added the Jmol reading of these PubChem partial charges in 2010, I think.

Otis

--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com




On Apr 19, 2012, at 10:13 AM, Robert Hanson wrote:

> More goodies at 
> 
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
> 
> -- pubChem search
> -- keyword lookup at RCSB
> -- general way to swap the applet for a block of HTML information if desired
> 
> Bob
> 
> 
> -- 
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
> 
> 
> 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
> --
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

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Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Robert Hanson]

More goodies at

http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm

-- pubChem search
-- keyword lookup at RCSB
-- general way to swap the applet for a block of HTML information if desired

Bob


-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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
--
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
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Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Robert Hanson]

Paul, I expect we will merge. So please use the format I'm using as much as
possible.


Jmol.functionName() = function {}

We want to dispense with

_findApplet  pretty much and assume that in most cases we have the applet
object already.

For example,

JmolApplet()

should work, but it should also return a "Jmol.Applet" instance.


Bob

On Tue, Apr 17, 2012 at 8:33 AM, Paul Pillot <
paul.pil...@ac-orleans-tours.fr> wrote:

> Bob,
> I am still working on a rewrite of Jmol.js
> It takes time, but my efforts are going in the same way as the library you
> made.
> Hope I could make it available soon.
>
> Paul
>
> Le 17 avr. 2012 à 14:11, Robert Hanson a écrit :
>
>
>
> 2012/4/17 Angel Herráez 
>
>> > Specifically, http://chemapps.stolaf.edu/jmol/chemdoodle/JmolCD.js is
>> > a library of extensions to ChemDoodle. What it actually does is to
>> > create a high-level object called "Jmol" (conveniently!) that loads
>> > applets in a new way. I think it is our new "Jmol object" JavaScript.
>> > And I suggest we make it THE development platform for the applet.
>>
>> This sounds like an exciting advance, and I'm just so sorry that I
>> cannot follow it more closely now.
>> My suggestion is that this change in Jmol.js dealing with applet
>> objects is quite radical, and maybe justifies a change in major
>> version number. That is, close down 12.4 with the old method and
>> start 12.5 when the new Jmol.js starts to be developed.
>> That would help sort out problems by making more apparent to users
>> that a new system has been adopted (even though the users might not
>> really notice the change since all is run "behind the curtains" by
>> Jmol.js)
>>
>>
> I think that's a great idea. Won't happen until June or July, but we can
> aim for that.
>
>
>
>
> --
> Better than sec? Nothing is better than sec when it comes to
> monitoring Big Data applications. Try Boundary one-second
> resolution app monitoring today. Free.
> http://p.sf.net/sfu/Boundary-dev2dev
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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
--
Better than sec? Nothing is better than sec when it comes to
monitoring Big Data applications. Try Boundary one-second 
resolution app monitoring today. Free.
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Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Jaime Prilusky]

I'm counting on that. Please let me know if you need any help.
Jaim

On Apr 17, 2012, at 4:50 PM, Nicolas Vervelle wrote:

Hi,

I haven't really followed this discussion.
Can it be used for the MediaWiki extension ?

Nico

On Tue, Apr 17, 2012 at 3:33 PM, Paul Pillot 
mailto:paul.pil...@ac-orleans-tours.fr>> wrote:
Bob,
I am still working on a rewrite of Jmol.js
It takes time, but my efforts are going in the same way as the library you made.
Hope I could make it available soon.

Paul

Le 17 avr. 2012 à 14:11, Robert Hanson a écrit :



2012/4/17 Angel Herráez mailto:angel.herr...@uah.es>>
> Specifically, http://chemapps.stolaf.edu/jmol/chemdoodle/JmolCD.js is
> a library of extensions to ChemDoodle. What it actually does is to
> create a high-level object called "Jmol" (conveniently!) that loads
> applets in a new way. I think it is our new "Jmol object" JavaScript.
> And I suggest we make it THE development platform for the applet.

This sounds like an exciting advance, and I'm just so sorry that I
cannot follow it more closely now.
My suggestion is that this change in Jmol.js dealing with applet
objects is quite radical, and maybe justifies a change in major
version number. That is, close down 12.4 with the old method and
start 12.5 when the new Jmol.js starts to be developed.
That would help sort out problems by making more apparent to users
that a new system has been adopted (even though the users might not
really notice the change since all is run "behind the curtains" by
Jmol.js)


I think that's a great idea. Won't happen until June or July, but we can aim 
for that.


--
Better than sec? Nothing is better than sec when it comes to
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Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Nicolas Vervelle]

Hi,

I haven't really followed this discussion.
Can it be used for the MediaWiki extension ?

Nico

On Tue, Apr 17, 2012 at 3:33 PM, Paul Pillot <
paul.pil...@ac-orleans-tours.fr> wrote:

> Bob,
> I am still working on a rewrite of Jmol.js
> It takes time, but my efforts are going in the same way as the library you
> made.
> Hope I could make it available soon.
>
> Paul
>
> Le 17 avr. 2012 à 14:11, Robert Hanson a écrit :
>
>
>
> 2012/4/17 Angel Herráez 
>
>> > Specifically, http://chemapps.stolaf.edu/jmol/chemdoodle/JmolCD.js is
>> > a library of extensions to ChemDoodle. What it actually does is to
>> > create a high-level object called "Jmol" (conveniently!) that loads
>> > applets in a new way. I think it is our new "Jmol object" JavaScript.
>> > And I suggest we make it THE development platform for the applet.
>>
>> This sounds like an exciting advance, and I'm just so sorry that I
>> cannot follow it more closely now.
>> My suggestion is that this change in Jmol.js dealing with applet
>> objects is quite radical, and maybe justifies a change in major
>> version number. That is, close down 12.4 with the old method and
>> start 12.5 when the new Jmol.js starts to be developed.
>> That would help sort out problems by making more apparent to users
>> that a new system has been adopted (even though the users might not
>> really notice the change since all is run "behind the curtains" by
>> Jmol.js)
>>
>>
> I think that's a great idea. Won't happen until June or July, but we can
> aim for that.
>
>
>
>
> --
> Better than sec? Nothing is better than sec when it comes to
> monitoring Big Data applications. Try Boundary one-second
> resolution app monitoring today. Free.
> http://p.sf.net/sfu/Boundary-dev2dev
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
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Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Paul Pillot]

Bob,
I am still working on a rewrite of Jmol.js
It takes time, but my efforts are going in the same way as the library you made.
Hope I could make it available soon.

Paul

Le 17 avr. 2012 à 14:11, Robert Hanson a écrit :

> 
> 
> 2012/4/17 Angel Herráez 
> > Specifically, http://chemapps.stolaf.edu/jmol/chemdoodle/JmolCD.js is
> > a library of extensions to ChemDoodle. What it actually does is to
> > create a high-level object called "Jmol" (conveniently!) that loads
> > applets in a new way. I think it is our new "Jmol object" JavaScript.
> > And I suggest we make it THE development platform for the applet.
> 
> This sounds like an exciting advance, and I'm just so sorry that I
> cannot follow it more closely now.
> My suggestion is that this change in Jmol.js dealing with applet
> objects is quite radical, and maybe justifies a change in major
> version number. That is, close down 12.4 with the old method and
> start 12.5 when the new Jmol.js starts to be developed.
> That would help sort out problems by making more apparent to users
> that a new system has been adopted (even though the users might not
> really notice the change since all is run "behind the curtains" by
> Jmol.js)
> 
> 
> I think that's a great idea. Won't happen until June or July, but we can aim 
> for that. 
>  
--
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Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Robert Hanson]

2012/4/17 Angel Herráez 

> > Specifically, http://chemapps.stolaf.edu/jmol/chemdoodle/JmolCD.js is
> > a library of extensions to ChemDoodle. What it actually does is to
> > create a high-level object called "Jmol" (conveniently!) that loads
> > applets in a new way. I think it is our new "Jmol object" JavaScript.
> > And I suggest we make it THE development platform for the applet.
>
> This sounds like an exciting advance, and I'm just so sorry that I
> cannot follow it more closely now.
> My suggestion is that this change in Jmol.js dealing with applet
> objects is quite radical, and maybe justifies a change in major
> version number. That is, close down 12.4 with the old method and
> start 12.5 when the new Jmol.js starts to be developed.
> That would help sort out problems by making more apparent to users
> that a new system has been adopted (even though the users might not
> really notice the change since all is run "behind the curtains" by
> Jmol.js)
>
>
I think that's a great idea. Won't happen until June or July, but we can
aim for that.


>
>
> > It's really got some nice features, like being able to go to a
> > server-side JmolData.jar
>
> Can you elaborate on what are the requirements for the server?
>
>
>
PHP. Files are in the appletweb directory on SourceForge.

Bob


-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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
--
Better than sec? Nothing is better than sec when it comes to
monitoring Big Data applications. Try Boundary one-second 
resolution app monitoring today. Free.
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Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Angel Herráez]

> Specifically, http://chemapps.stolaf.edu/jmol/chemdoodle/JmolCD.js is 
> a library of extensions to ChemDoodle. What it actually does is to 
> create a high-level object called "Jmol" (conveniently!) that loads 
> applets in a new way. I think it is our new "Jmol object" JavaScript. 
> And I suggest we make it THE development platform for the applet. 

This sounds like an exciting advance, and I'm just so sorry that I 
cannot follow it more closely now.
My suggestion is that this change in Jmol.js dealing with applet 
objects is quite radical, and maybe justifies a change in major 
version number. That is, close down 12.4 with the old method and 
start 12.5 when the new Jmol.js starts to be developed.
That would help sort out problems by making more apparent to users 
that a new system has been adopted (even though the users might not 
really notice the change since all is run "behind the curtains" by 
Jmol.js)



> It's really got some nice features, like being able to go to a 
> server-side JmolData.jar 

Can you ellaborate on what are the requirements for the server?



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Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Robert Hanson]

Kevin has fixed the problems with CIF files (mostly). Thank you, Kevin!

I think this is a pretty good start to a solution to a very difficult
problem. If you take a look at

  http://chemapps.stolaf.edu/jmol/chemdoodle

and its contained files, you will see some interesting ones. Specifically,
http://chemapps.stolaf.edu/jmol/chemdoodle/JmolCD.js is a library of
extensions to ChemDoodle. What it actually does is to create a high-level
object called "Jmol" (conveniently!) that loads applets in a new way. I
think it is our new "Jmol object" JavaScript. And I suggest we make it THE
development platform for the applet. It's really got some nice features,
like being able to go to a server-side JmolData.jar if Java or applets are
not enabled on a device to get just an image, or work just like we have
now, if you want that. It does require an additional 250K JavaScript
download, but if you are willing to live with that, I think it has a lot to
offer. This library is used by
http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm  Take a look behind
the scenes there, and you will see this:

  var Info = {
id: "molgrabber1",
width: 300,
height: 300,
debug: true,
addSelectionOptions: true,
serverURL: "http://chemapps.stolaf.edu/jmol/jmolcd2.php";,
defaultModel: "morphine",
useChemDoodleOnly: useChemDoodleOnly,
useJmolOnly: useJmolOnly,
useWebGlIfAvailable: useWebGlIfAvailable,
useImageOnly: useImageOnly,
jmolJarPath: ".",
jmolJarFile: (useSignedApplet ? "JmolAppletSigned.jar" :
"JmolApplet.jar"),
jmolIsSigned: useSignedApplet,
jmolReadyFunctionName: "jmol_isReady"
}


and then, later:

molgrabber = Jmol.getMolGrabber(Info)

That's all there is to it! This creates a Jmol object called "molgrabber"
that can act like the applet, but also do all sorts of other interesting
things. As this progresses, I'll add all the standard applet code to that,
and eventually, I think, Jmol.js will no longer be necessary, though right
now it is. For example, right now you can use

  molgrabber.script("background white")

or whatever.

Mind you, ChemDoodle has no high-level scripting language, and it's not set
up to change an image on the fly, so that would only work if you have just
the standard Jmol applet there. But in any case, it's a start. Here's a new
capability of the UNSIGNED applet:

molgrabber.search("$tylenol")

That retrieves the NCI "tylenol" model.

molgrabber.search("=1crn")

Does what you think. -- retrieves a model from the PDB database, even for
the unsigned applet.


So check it out!


Bob


-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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
--
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
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Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Robert Hanson]

Yes, there's something about that model and several others that the
ChemDoodle CIF interpreter doesn't like. Kevin Theisen is looking into it.

On Fri, Apr 13, 2012 at 11:17 AM, Jeff Hansen  wrote:

> That is correct Bob.  Just press Enter in Safari and it loads the
> molecule.  I did have problems with the load 
> sebi0105c.ccdc.cif
>  link.  It worked via Jmol but not ChemDoodle.  Just gave a blank box.
>  All on my MacBook Pro using Safari.  Haven't tried any other configuration.
>
>
> ***
> Jeff Hansen
> Department of Chemistry and Biochemistry
> DePauw University
> 602 S. College Ave.
> Greencastle, IN 46135
> jhan...@depauw.edu
> ***
>
>
> On Apr 13, 2012, at 10:43 AM, Robert Hanson wrote:
>
> Phil -- the OK prompt is just some debugging I left in so that Kevin could
> quickly see what sort of files we were dealing with that were causing
> problems in ChemDoodle. Nothing more than that. I think it's any time
> ChemDoodle is loading a model in its 2D mode. Can't you just press ENTER
> and have that Safari box disappear? I would have thought the OK button had
> the focus at that point, even if you can't see it. Well, anyway -- you're
> probably done playing. Other Mac users with computers that do not have
> WebGL beware!
>
> Bob
>
> On Fri, Apr 13, 2012 at 5:19 AM, Philip Bays  wrote:
>
>> Bob:
>>
>> I like what you are doing here.  I realize that I am looking at only
>> test2, but I am playing like a student -- randomly clicking links:-)  I am
>> out of town and only have my MacBook pro with me.  I note in Firefox that
>> when you are in the chemdoodle mode and you try to load a file that
>> chemdoodle cannot read, you get a listing of the file with an "OK" button
>> at the bottom to dismiss the pop-up.   However, in Safari, that pop-up is
>> so long, and with no way to get to the bottom, you cannot get to that
>> button.   You can quit Safari, but the popup remains (and in fact Safari
>> does not quit, though the model display screen does.)   You have to do a
>> force quit to get it to go away.
>>
>> The chemdoodle approach works on my old iPod touch though for those files
>> that it can read:-)
>>
>> Phil
>>
>> On Apr 13, 2012, at 1:03 AM, Robert Hanson wrote:
>>
>> OK. Please test!
>>
>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>>
>> -- adds loading of host-local file using
>>
>>   MolGrabberJmol.loadFile(fileName,loadParams)
>>
>> of course, the loadParams business doesn't work with ChemDoodle, but
>> perhaps it will supply reason to add such :)
>>
>> I notice that this does not work for machine-local (hard-drive-based)
>> files in Chrome. I'm guessing that's a security setting.
>>
>> Also, actually, I couldn't get most of these to load into ChemDoodle. The
>> CIF files seem to be unreadable in all cases, and when there is no WebGL,
>> only MOL files are readable, not XYZ, PDB, or CIF.
>>
>> Kevin, now you have something to do! I'm hoping you can check that over
>> and tell me what I'm doing wrong (actually, send me a corrected
>> JmolCD.js!). Something odd in xxxInterpreters, I think. But I don't know
>> what it would be.
>>
>> Bob
>>
>>
>> --
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>>
>>
>> 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
>>
>> --
>> For Developers, A Lot Can Happen In A Second.
>> Boundary is the first to Know...and Tell You.
>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>>
>> http://p.sf.net/sfu/Boundary-d2dvs2___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>> J. Philip Bays
>> Emeritus Professor of Chemistry
>> Department of Chemistry and Physics
>> Saint Mary's College
>> Notre Dame, IN 46556
>> pb...@saintmarys.edu
>>
>>
>>
>>
>>
>>
>>
>> --
>> For Developers, A Lot Can Happen In A Second.
>> Boundary is the first to Know...and Tell You.
>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>> http://p.sf.net/sfu/Boundary-d2dvs2
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
>
>
>
> --
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.ne

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Jeff Hansen]

That is correct Bob.  Just press Enter in Safari and it loads the molecule.  I 
did have problems with the load sebi0105c.ccdc.cif link.  It worked via Jmol 
but not ChemDoodle.  Just gave a blank box.  All on my MacBook Pro using 
Safari.  Haven't tried any other configuration.


***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***


On Apr 13, 2012, at 10:43 AM, Robert Hanson wrote:

> Phil -- the OK prompt is just some debugging I left in so that Kevin could 
> quickly see what sort of files we were dealing with that were causing 
> problems in ChemDoodle. Nothing more than that. I think it's any time 
> ChemDoodle is loading a model in its 2D mode. Can't you just press ENTER and 
> have that Safari box disappear? I would have thought the OK button had the 
> focus at that point, even if you can't see it. Well, anyway -- you're 
> probably done playing. Other Mac users with computers that do not have WebGL 
> beware!
> 
> Bob
> 
> On Fri, Apr 13, 2012 at 5:19 AM, Philip Bays  wrote:
> Bob:
> 
> I like what you are doing here.  I realize that I am looking at only test2, 
> but I am playing like a student -- randomly clicking links:-)  I am out of 
> town and only have my MacBook pro with me.  I note in Firefox that when you 
> are in the chemdoodle mode and you try to load a file that chemdoodle cannot 
> read, you get a listing of the file with an "OK" button at the bottom to 
> dismiss the pop-up.   However, in Safari, that pop-up is so long, and with no 
> way to get to the bottom, you cannot get to that button.   You can quit 
> Safari, but the popup remains (and in fact Safari does not quit, though the 
> model display screen does.)   You have to do a force quit to get it to go 
> away.
> 
> The chemdoodle approach works on my old iPod touch though for those files 
> that it can read:-)
> 
> Phil
> 
> On Apr 13, 2012, at 1:03 AM, Robert Hanson wrote:
> 
>> OK. Please test!
>> 
>> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>> 
>> -- adds loading of host-local file using
>> 
>>   MolGrabberJmol.loadFile(fileName,loadParams)
>> 
>> of course, the loadParams business doesn't work with ChemDoodle, but perhaps 
>> it will supply reason to add such :)
>> 
>> I notice that this does not work for machine-local (hard-drive-based) files 
>> in Chrome. I'm guessing that's a security setting. 
>> 
>> Also, actually, I couldn't get most of these to load into ChemDoodle. The 
>> CIF files seem to be unreadable in all cases, and when there is no WebGL, 
>> only MOL files are readable, not XYZ, PDB, or CIF. 
>> 
>> Kevin, now you have something to do! I'm hoping you can check that over and 
>> tell me what I'm doing wrong (actually, send me a corrected JmolCD.js!). 
>> Something odd in xxxInterpreters, I think. But I don't know what it would be.
>> 
>> Bob
>> 
>> 
>> -- 
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>> 
>> 
>> 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
>> --
>> For Developers, A Lot Can Happen In A Second.
>> Boundary is the first to Know...and Tell You.
>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>> http://p.sf.net/sfu/Boundary-d2dvs2___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
> 
> J. Philip Bays
> Emeritus Professor of Chemistry
> Department of Chemistry and Physics
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu
> 
> 
> 
> 
> 
> 
> --
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
> 
> 
> 
> 

--
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
http://p.sf.net/sfu/Boundary-d2dvs2___
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Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Robert Hanson]

Phil -- the OK prompt is just some debugging I left in so that Kevin could
quickly see what sort of files we were dealing with that were causing
problems in ChemDoodle. Nothing more than that. I think it's any time
ChemDoodle is loading a model in its 2D mode. Can't you just press ENTER
and have that Safari box disappear? I would have thought the OK button had
the focus at that point, even if you can't see it. Well, anyway -- you're
probably done playing. Other Mac users with computers that do not have
WebGL beware!

Bob

On Fri, Apr 13, 2012 at 5:19 AM, Philip Bays  wrote:

> Bob:
>
> I like what you are doing here.  I realize that I am looking at only
> test2, but I am playing like a student -- randomly clicking links:-)  I am
> out of town and only have my MacBook pro with me.  I note in Firefox that
> when you are in the chemdoodle mode and you try to load a file that
> chemdoodle cannot read, you get a listing of the file with an "OK" button
> at the bottom to dismiss the pop-up.   However, in Safari, that pop-up is
> so long, and with no way to get to the bottom, you cannot get to that
> button.   You can quit Safari, but the popup remains (and in fact Safari
> does not quit, though the model display screen does.)   You have to do a
> force quit to get it to go away.
>
> The chemdoodle approach works on my old iPod touch though for those files
> that it can read:-)
>
> Phil
>
> On Apr 13, 2012, at 1:03 AM, Robert Hanson wrote:
>
> OK. Please test!
>
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>
> -- adds loading of host-local file using
>
>   MolGrabberJmol.loadFile(fileName,loadParams)
>
> of course, the loadParams business doesn't work with ChemDoodle, but
> perhaps it will supply reason to add such :)
>
> I notice that this does not work for machine-local (hard-drive-based)
> files in Chrome. I'm guessing that's a security setting.
>
> Also, actually, I couldn't get most of these to load into ChemDoodle. The
> CIF files seem to be unreadable in all cases, and when there is no WebGL,
> only MOL files are readable, not XYZ, PDB, or CIF.
>
> Kevin, now you have something to do! I'm hoping you can check that over
> and tell me what I'm doing wrong (actually, send me a corrected
> JmolCD.js!). Something odd in xxxInterpreters, I think. But I don't know
> what it would be.
>
> Bob
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
>
> --
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>
> http://p.sf.net/sfu/Boundary-d2dvs2___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> J. Philip Bays
> Emeritus Professor of Chemistry
> Department of Chemistry and Physics
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu
>
>
>
>
>
>
>
> --
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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
--
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
http://p.sf.net/sfu/Boundary-d2dvs2___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Robert Hanson]

They are all there on that site, Kevin. Just remove "test2.htm" and you can
see what's in that directory.

On Fri, Apr 13, 2012 at 6:40 AM, Kevin Theisen  wrote:

> Hi Bob,
>
> Can you send me a zip of the files you are having trouble with, I will
> check them out. I think it may have to do with how the line delimiters are
> handled.
>
> -Kevin
>
>
>
> On Apr 13, 2012, at 1:03 AM, Robert Hanson wrote:
>
> OK. Please test!
>
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>
> -- adds loading of host-local file using
>
>   MolGrabberJmol.loadFile(fileName,loadParams)
>
> of course, the loadParams business doesn't work with ChemDoodle, but
> perhaps it will supply reason to add such :)
>
> I notice that this does not work for machine-local (hard-drive-based)
> files in Chrome. I'm guessing that's a security setting.
>
> Also, actually, I couldn't get most of these to load into ChemDoodle. The
> CIF files seem to be unreadable in all cases, and when there is no WebGL,
> only MOL files are readable, not XYZ, PDB, or CIF.
>
> Kevin, now you have something to do! I'm hoping you can check that over
> and tell me what I'm doing wrong (actually, send me a corrected
> JmolCD.js!). Something odd in xxxInterpreters, I think. But I don't know
> what it would be.
>
> Bob
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
>
> --
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>
> http://p.sf.net/sfu/Boundary-d2dvs2___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> --
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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
--
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
http://p.sf.net/sfu/Boundary-d2dvs2___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Kevin Theisen]

Hi Bob,

Can you send me a zip of the files you are having trouble with, I will check 
them out. I think it may have to do with how the line delimiters are handled.

-Kevin



On Apr 13, 2012, at 1:03 AM, Robert Hanson wrote:

> OK. Please test!
> 
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
> 
> -- adds loading of host-local file using
> 
>   MolGrabberJmol.loadFile(fileName,loadParams)
> 
> of course, the loadParams business doesn't work with ChemDoodle, but perhaps 
> it will supply reason to add such :)
> 
> I notice that this does not work for machine-local (hard-drive-based) files 
> in Chrome. I'm guessing that's a security setting. 
> 
> Also, actually, I couldn't get most of these to load into ChemDoodle. The CIF 
> files seem to be unreadable in all cases, and when there is no WebGL, only 
> MOL files are readable, not XYZ, PDB, or CIF. 
> 
> Kevin, now you have something to do! I'm hoping you can check that over and 
> tell me what I'm doing wrong (actually, send me a corrected JmolCD.js!). 
> Something odd in xxxInterpreters, I think. But I don't know what it would be.
> 
> Bob
> 
> 
> -- 
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
> 
> 
> 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
> --
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

--
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
http://p.sf.net/sfu/Boundary-d2dvs2___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Philip Bays]

Bob:

I like what you are doing here.  I realize that I am looking at only test2, but 
I am playing like a student -- randomly clicking links:-)  I am out of town and 
only have my MacBook pro with me.  I note in Firefox that when you are in the 
chemdoodle mode and you try to load a file that chemdoodle cannot read, you get 
a listing of the file with an "OK" button at the bottom to dismiss the pop-up.  
 However, in Safari, that pop-up is so long, and with no way to get to the 
bottom, you cannot get to that button.   You can quit Safari, but the popup 
remains (and in fact Safari does not quit, though the model display screen 
does.)   You have to do a force quit to get it to go away.

The chemdoodle approach works on my old iPod touch though for those files that 
it can read:-)

Phil

On Apr 13, 2012, at 1:03 AM, Robert Hanson wrote:

> OK. Please test!
> 
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
> 
> -- adds loading of host-local file using
> 
>   MolGrabberJmol.loadFile(fileName,loadParams)
> 
> of course, the loadParams business doesn't work with ChemDoodle, but perhaps 
> it will supply reason to add such :)
> 
> I notice that this does not work for machine-local (hard-drive-based) files 
> in Chrome. I'm guessing that's a security setting. 
> 
> Also, actually, I couldn't get most of these to load into ChemDoodle. The CIF 
> files seem to be unreadable in all cases, and when there is no WebGL, only 
> MOL files are readable, not XYZ, PDB, or CIF. 
> 
> Kevin, now you have something to do! I'm hoping you can check that over and 
> tell me what I'm doing wrong (actually, send me a corrected JmolCD.js!). 
> Something odd in xxxInterpreters, I think. But I don't know what it would be.
> 
> Bob
> 
> 
> -- 
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
> 
> 
> 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
> --
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

J. Philip Bays
Emeritus Professor of Chemistry
Department of Chemistry and Physics
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu





--
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
http://p.sf.net/sfu/Boundary-d2dvs2___
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Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Angel Herráez]

This is amazing, Bob
Your keep us astonished once and again!

One small comment:
the "image only" link works, but having the Jmol frank in the image 
is a bit misleading; I just went and tried to rotate it :). Maybe not 
include the frank? Of course, having it is advertising, which may be 
good.

Or maybe 

frank off;
set echo 100% 0%;
echo image created by Jmol;



--
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
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___
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Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Jaime Prilusky]

This is really something!!
It looks so smooth and simple :-)
Well done!!

On Apr 13, 2012, at 8:03 AM, Robert Hanson wrote:

OK. Please test!

http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm

-- adds loading of host-local file using

  MolGrabberJmol.loadFile(fileName,loadParams)

of course, the loadParams business doesn't work with ChemDoodle, but perhaps it 
will supply reason to add such :)

I notice that this does not work for machine-local (hard-drive-based) files in 
Chrome. I'm guessing that's a security setting.

Also, actually, I couldn't get most of these to load into ChemDoodle. The CIF 
files seem to be unreadable in all cases, and when there is no WebGL, only MOL 
files are readable, not XYZ, PDB, or CIF.

Kevin, now you have something to do! I'm hoping you can check that over and 
tell me what I'm doing wrong (actually, send me a corrected JmolCD.js!). 
Something odd in xxxInterpreters, I think. But I don't know what it would be.

Bob


--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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
--
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
http://p.sf.net/sfu/Boundary-d2dvs2___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

--
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
http://p.sf.net/sfu/Boundary-d2dvs2___
Jmol-users mailing list
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Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Egon Willighagen]

On Fri, Apr 13, 2012 at 7:03 AM, Robert Hanson  wrote:
> OK. Please test!
>
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm

Very nice!

Egon


-- 
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

--
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
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___
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Re: [Jmol-users] Jmol/ChemDoodle -- test2

[Robert Hanson]

OK. Please test!

http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm

-- adds loading of host-local file using

  MolGrabberJmol.loadFile(fileName,loadParams)

of course, the loadParams business doesn't work with ChemDoodle, but
perhaps it will supply reason to add such :)

I notice that this does not work for machine-local (hard-drive-based) files
in Chrome. I'm guessing that's a security setting.

Also, actually, I couldn't get most of these to load into ChemDoodle. The
CIF files seem to be unreadable in all cases, and when there is no WebGL,
only MOL files are readable, not XYZ, PDB, or CIF.

Kevin, now you have something to do! I'm hoping you can check that over and
tell me what I'm doing wrong (actually, send me a corrected JmolCD.js!).
Something odd in xxxInterpreters, I think. But I don't know what it would
be.

Bob


-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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
--
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
http://p.sf.net/sfu/Boundary-d2dvs2___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users