Re: [Jmol-users] JSmol Lite and PDB files?
If I set the src: (or script: load ...) field in the Info variable to load anything other than a MOL file, there is nothing displayed: www.permafrost.ch/jsmol/eis-lite.htm (code from lite4.htm) The normal Jmol.getAppletHtml works fine, though: www.permafrost.ch/jsmol/eis.htm Sorry if I lack some deeper insights into JSmol, I should be glad if you can point me to some other source of information than wiki.jmol.org Martin -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol Lite and PDB files?
Hi Martin You need to read carefully the instructions. You are trying the lightweight object, with getTMApplet, but that does not use JSmol.min.js but the special JSmol.lite.js and not all Info parameters are supported and even if src was supported, it must be a script of commands, not a filename to load http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Lightweight_JSmol http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Info#Lightweight_versi on -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol Lite and PDB files?
Also, you won't be able to read a binary file (.gz) with JSmol.lite.nojq.js. It is VERY light On Tue, Mar 18, 2014 at 10:59 AM, tinus updates tinusupda...@gmail.comwrote: If I set the src: (or script: load ...) field in the Info variable to load anything other than a MOL file, there is nothing displayed: www.permafrost.ch/jsmol/eis-lite.htm (code from lite4.htm) The normal Jmol.getAppletHtml works fine, though: www.permafrost.ch/jsmol/eis.htm Sorry if I lack some deeper insights into JSmol, I should be glad if you can point me to some other source of information than wiki.jmol.org Martin -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol Lite and PDB files?
proto._parse = function(data) {
// just MOL data for now
this._parseSDF(data);
}
On Tue, Mar 18, 2014 at 10:59 AM, tinus updates tinusupda...@gmail.comwrote:
If I set the src: (or script: load ...) field in the Info variable to
load anything other than a MOL file, there is nothing displayed:
www.permafrost.ch/jsmol/eis-lite.htm
(code from lite4.htm)
The normal Jmol.getAppletHtml works fine, though:
www.permafrost.ch/jsmol/eis.htm
Sorry if I lack some deeper insights into JSmol, I should be glad if you
can point me to some other source of information than wiki.jmol.org
Martin
--
Learn Graph Databases - Download FREE O'Reilly Book
Graph Databases is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/13534_NeoTech
___
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Learn Graph Databases - Download FREE O'Reilly Book
Graph Databases is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/13534_NeoTech___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol Lite and PDB files?
Thank you all! I have understood that Jmol.getTMApplet uses JSmol.lite.js or JSmol.lite.nojq.js. So I adapted the lite4.htm file provided in the distribution. The other liteX.htm files did not work out of the box, so I left them aside. Robert, I found your quoted code in js/JSmol.full.lite.js and js/JSmol.full.lite.nojq.js and js/JSmolTM.js, but not in JSmol.lite.js. Now I'm somewhat confused on which JSmolXXX.js I should use best for viewing PDB on iPads, and if JSmol.lite(.nojq).js does (as the other files) support just MOL at the time. The xyz.gz file at www.permafrost.ch/jsmol/eis-lite.htm was a left-over from testing, it is now replaced with the correct sz/ice.pdb. I wonder by the way if a bigger molecule or structure is displayed clearly enough with the limited rendering. -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol Lite and PDB files?
Martin, replaced with the correct sz/ice.pdb. Please try src: load sz/ice.pdb, instead of src: sz/ice.pdb, I wonder by the way if a bigger molecule or structure is displayed clearly enough with the limited rendering. Bigger is not the issue (althugh i may respond slowly). Limited rendering means only Ball and Stick is available -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol Lite and PDB files?
On Tue, Mar 18, 2014 at 2:48 PM, tinus updates tinusupda...@gmail.comwrote: Thank you all! I have understood that Jmol.getTMApplet uses JSmol.lite.js or JSmol.lite.nojq.js. So I adapted the lite4.htm file provided in the distribution. The other liteX.htm files did not work out of the box, so I left them aside. yes, I just spotted that bug. It has to do with reading files from PubChem. Robert, I found your quoted code in js/JSmol.full.lite.js and js/JSmol.full.lite.nojq.js and js/JSmolTM.js, but not in JSmol.lite.js. Now I'm somewhat confused on which JSmolXXX.js I should use best for viewing PDB on iPads, and if JSmol.lite(.nojq).js does (as the other files) support just MOL at the time. JSmol.full.lite.nojq.js is just the uncompressed version of JSmol.lite.nojq.js -- no need to use that except for debugging. Same for JSmol.full.lite.js and JSmol.lite.js, and JSmol.full.js and JSmol.min.js. JSmol.lite.js is light, but also contains jQuery, which you need. So if you are not already using jQuery, use that. The nojq.js version is for developers who need to use or want to use their own version of jQuery -- usually in larger sites such as RCSB. That one is super-light (51K). The xyz.gz file at www.permafrost.ch/jsmol/eis-lite.htm was a left-over from testing, it is now replaced with the correct sz/ice.pdb. I wonder by the way if a bigger molecule or structure is displayed clearly enough with the limited rendering. Once again, you must use MOL file format for JSmol-Lite. Just read that file into any other version of Jmol and then use select * write eis.mol to create the MOL file version. You are under 1000 atoms, so that should be fine. Bob -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] JSmol Lite and PDB files?
Hi, I want to show some structures to my students on iPad 2. Somehow I can only get small MOL files to display, no PDB files. Is there a list of supported file formats? The normal JSmol works just fine, but is slow on iPad. Thanks! Martin -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol Lite and PDB files?
On Mon, Mar 17, 2014 at 4:11 PM, tinus updates tinusupda...@gmail.comwrote: Hi, I want to show some structures to my students on iPad 2. Somehow I can only get small MOL files to display, no PDB files. Is there a list of supported file formats? The normal JSmol works just fine, but is slow on iPad. Thanks! PDB files should be fine; no specific list of file formats, as all in Jmol are supported. iPad will be slow; normal meaning what? Martin -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] JSmol lite
I'm wondering if we should try to produce a really trimmed-down lite version of Jmol -- a very very minimal core set of functionality that could have better load performance on mobile devices for very basic tasks. Maybe just wireframe spacefill ballssticks no text no math (just simple Rasmol-like script commands) just XYZ/MOL file reading (basically a ChemDoodle-HTML5-only-like level of capability) What would be a reasonable goal for code size? Suggestions? (I think I could make it to automatically load additional functionality as needed.) Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol lite
Bob, I feel like cherry picking functionality to include would present difficulties to users; e.g. I thought JSmol could do x, but it can't! This is a wild idea, but could the entire command-running apparatus be decoupled from display and mouse actions, with significant savings in code size? I'm imagining something like a kiosk mode, without the machinery of scripting behind it. I understand this may not be possible; just wanted to throw it out there. On Wednesday, January 30, 2013, Robert Hanson wrote: I'm wondering if we should try to produce a really trimmed-down lite version of Jmol -- a very very minimal core set of functionality that could have better load performance on mobile devices for very basic tasks. Maybe just wireframe spacefill ballssticks no text no math (just simple Rasmol-like script commands) just XYZ/MOL file reading (basically a ChemDoodle-HTML5-only-like level of capability) What would be a reasonable goal for code size? Suggestions? (I think I could make it to automatically load additional functionality as needed.) Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- --- Michael Evans Organic Chemistry Graduate Student, Moore Group University of Illinois, Urbana-Champaign -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol lite
Bob, The ability to load minimal with the possibility of expanding as needed would be wonderful! Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Jan 30, 2013, at 1:23 PM, Robert Hanson wrote: I'm wondering if we should try to produce a really trimmed-down lite version of Jmol -- a very very minimal core set of functionality that could have better load performance on mobile devices for very basic tasks. Maybe just wireframe spacefill ballssticks no text no math (just simple Rasmol-like script commands) just XYZ/MOL file reading (basically a ChemDoodle-HTML5-only-like level of capability) What would be a reasonable goal for code size? Suggestions? (I think I could make it to automatically load additional functionality as needed.) Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol lite
Agreed, Otis. I realized after reading your message that a version of JSmol that worked that way would be highly desirable, provided the process of loading files as needed is acceptable from a user experience perspective. Cheers, Mike --- Michael Evans Organic Chemistry Graduate Student, Moore Group University of Illinois, Urbana-Champaign On Wed, Jan 30, 2013 at 12:54 PM, Otis Rothenberger osrot...@chemagic.comwrote: Michael, I understand your concern, but I'm think about page application development. If I understand Bob correctly, then functionality would be loaded from server as needed. These loads would be controlled by the page application developer so that it's hidden from users. If that's what Bob is suggesting, I think it would be great. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Jan 30, 2013, at 1:33 PM, Michael Evans wrote: Bob, I feel like cherry picking functionality to include would present difficulties to users; e.g. I thought JSmol could do x, but it can't! This is a wild idea, but could the entire command-running apparatus be decoupled from display and mouse actions, with significant savings in code size? I'm imagining something like a kiosk mode, without the machinery of scripting behind it. I understand this may not be possible; just wanted to throw it out there. On Wednesday, January 30, 2013, Robert Hanson wrote: I'm wondering if we should try to produce a really trimmed-down lite version of Jmol -- a very very minimal core set of functionality that could have better load performance on mobile devices for very basic tasks. Maybe just wireframe spacefill ballssticks no text no math (just simple Rasmol-like script commands) just XYZ/MOL file reading (basically a ChemDoodle-HTML5-only-like level of capability) What would be a reasonable goal for code size? Suggestions? (I think I could make it to automatically load additional functionality as needed.) Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- --- Michael Evans Organic Chemistry Graduate Student, Moore Group University of Illinois, Urbana-Champaign -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol lite
A fast, minimal JSmol, able to load additional features on demand, will be great. However, I think this will have little impact on model loading and management speed. Is this correct? Jaim On Jan 30, 2013, at 8:23 PM, Robert Hanson wrote: I'm wondering if we should try to produce a really trimmed-down lite version of Jmol -- a very very minimal core set of functionality that could have better load performance on mobile devices for very basic tasks. Maybe just wireframe spacefill ballssticks no text no math (just simple Rasmol-like script commands) just XYZ/MOL file reading (basically a ChemDoodle-HTML5-only-like level of capability) What would be a reasonable goal for code size? Suggestions? (I think I could make it to automatically load additional functionality as needed.) Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol lite
Minimified and Gzipped, Jsmol is a 700-800kB download. I am not sure that reducing the download is the way to go in order to improve user experience on mobile phones. I've seen JSmol once on an Iphone and it was really slow. Too slow to call it interactive. Maybe targeting at the graphic performance would be a better goal. Paul Le 30 janv. 2013 à 19:59, Michael Evans a écrit : Agreed, Otis. I realized after reading your message that a version of JSmol that worked that way would be highly desirable, provided the process of loading files as needed is acceptable from a user experience perspective. Cheers, Mike --- Michael Evans Organic Chemistry Graduate Student, Moore Group University of Illinois, Urbana-Champaign On Wed, Jan 30, 2013 at 12:54 PM, Otis Rothenberger osrot...@chemagic.com wrote: Michael, I understand your concern, but I'm think about page application development. If I understand Bob correctly, then functionality would be loaded from server as needed. These loads would be controlled by the page application developer so that it's hidden from users. If that's what Bob is suggesting, I think it would be great. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Jan 30, 2013, at 1:33 PM, Michael Evans wrote: Bob, I feel like cherry picking functionality to include would present difficulties to users; e.g. I thought JSmol could do x, but it can't! This is a wild idea, but could the entire command-running apparatus be decoupled from display and mouse actions, with significant savings in code size? I'm imagining something like a kiosk mode, without the machinery of scripting behind it. I understand this may not be possible; just wanted to throw it out there. On Wednesday, January 30, 2013, Robert Hanson wrote: I'm wondering if we should try to produce a really trimmed-down lite version of Jmol -- a very very minimal core set of functionality that could have better load performance on mobile devices for very basic tasks. Maybe just wireframe spacefill ballssticks no text no math (just simple Rasmol-like script commands) just XYZ/MOL file reading (basically a ChemDoodle-HTML5-only-like level of capability) What would be a reasonable goal for code size? Suggestions? (I think I could make it to automatically load additional functionality as needed.) Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- --- Michael Evans Organic Chemistry Graduate Student, Moore Group University of Illinois, Urbana-Champaign -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
