Re: [Jmol-users] Jmol/ChemDoodle -- test2
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 osrot...@chemagic.com 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
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
osrot...@chemagic.comwrote:
--
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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--
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
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Re: [Jmol-users] Jmol/ChemDoodle -- test2
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 hans...@stolaf.edu wrote: Oh, yeah. Not on my PC either - must be something simple On Fri, Apr 20, 2012 at 10:08 PM, Robert Hanson hans...@stolaf.edu wrote: ohoh!!! I'll look at that. On Fri, Apr 20, 2012 at 8:19 PM, Philip Bays pb...@saintmarys.edu 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 -- 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,
Re: [Jmol-users] Jmol/ChemDoodle -- test2
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 hans...@stolaf.edu wrote: Oh, yeah. Not on my PC either - must be something simple On Fri, Apr 20, 2012 at 10:08 PM, Robert Hanson hans...@stolaf.edu wrote: ohoh!!! I'll look at that. On Fri, Apr 20, 2012 at 8:19 PM, Philip Bays pb...@saintmarys.edu 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 -- Robert M. Hanson Professor of
[Jmol-users] Bye Bye mmCIF?
Maybe we don't need to invest too much on mmCIF support, and concentrate on the upcoming PWF (wwPDB Working Format). This might be the new format that (based on an undisclosed source), PDB is seeking to get the crystallographic community approval on. When, how and if this will happen is unknown to me. Jaim On Apr 21, 2012, at 3:41 PM, Kevin Theisen wrote: 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 -- 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
