Re: [Jmol-users] Protein Loading

[Philip Bays]

You should not have looked at that page:-(   It has not been updated in a long 
time and needs some work, but it also uses a much older version of jsmol — 
12/14/13.  It also works for me to drag and drop onto that.  But simply 
replacing it with the new version throws a bunch of javascript errors on 
loading.   Will look at what that is all about tomorrow— maybe.

Phil


> On Apr 1, 2016, at 6:31 PM, Robert Hanson  wrote:
> 
> Drag-drop can't utilize jsmol.php, because it is not a "file" per se, just a 
> bunch of bytes. But try it in your installation at 
> http://sites.saintmarys.edu/~pbays/   -- 
> worked for me there
> 
> Bob
> 
> ​
> --
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

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


--
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Protein Loading

[Robert Hanson]

Drag-drop can't utilize jsmol.php, because it is not a "file" per se, just
a bunch of bytes. But try it in your installation at
http://sites.saintmarys.edu/~pbays/  -- worked for me there

Bob

​
--
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Protein Loading

[Angel Herráez]

Hi Phil

> OK. It does not work with my implementation on any of the browsers on the 
> mac, but it does with 
> your jsmol.htm file. So it's me:-(

gzipped files must go via jsmol.php at least for some browsers. With local 
pages and files I usually have problems loading locally (since php is not 
possible locally). It could be related to this.
Have you set properly the "server path" (to jsmol.php)? That would affect for  
pages from web server.


> structure is type of secondary structure -- different types of helix, 
> sheet, etc.

Yes. Documented in the web, http://jmol.sourceforge.net/jscolors/


> group is just 1->n within each chain.

You can also think of it as residue number (proteins and nucleic acids), 
although hetero groups will also have a number.
Color by group is a rainbow (see webpage above)
There is both "color group" and "color monomer" which behave different in 
some models (absolute or relative rainbow)


--
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Protein Loading

[Philip Bays]

OK.  It does not work with my implementation on any of the browsers on the mac, 
but it does with your jsmol.htm file.   So it’s me:-(


> On Apr 1, 2016, at 4:24 PM, Robert Hanson  wrote:
> 
> 
> 
> On Fri, Apr 1, 2016 at 2:52 PM, Philip Bays  > wrote:
> I have a file entitled 5e6e.pdb.gz that I downloaded this week. Using 
> previous versions of jsmol.min, this file would load via drag-and-drop or 
> using the local-file load mechanism. In the latest version, jsmol version 
> (03.31) I get a "file not recognized" error.  I can download the structure 
> directly from RCSB.
> 
> with Firefox/Windows and Chrome/Windows I had no problem drag-dropping into 
> JSmol. 
> Is this perhaps browser/platform dependent?
> 
>  
> 
> A definition question: In the various sample test files involving 
> macromolecules that I have looked at, Bob uses the terms “structure” and 
> “groups" as a color and display choices.   I am not sure what I am looking at 
> in each case.  I thought it might be 4° structure, but now I am not sure.
> 
> 
> structure is type of secondary structure -- different types of helix, sheet, 
> etc.
> 
> group is just 1->n within each chain.
> 
>  
> Phil
> 
> Philip Bays
> Emeritus Professor of Chemistry
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu 
> 
> 
> 
> --
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140 
> 
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net 
> https://lists.sourceforge.net/lists/listinfo/jmol-users 
> 
> 
> 
> 
> -- 
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr 
> 
> 
> If nature does not answer first what we want,
> it is better to take what answer we get. 
> 
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
> 
> --
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

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


--
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Protein Loading

[Robert Hanson]

On Fri, Apr 1, 2016 at 2:52 PM, Philip Bays  wrote:

> I have a file entitled 5e6e.pdb.gz that I downloaded this week. Using
> previous versions of jsmol.min, this file would load via drag-and-drop or
> using the local-file load mechanism. In the latest version, jsmol version
> (03.31) I get a "file not recognized" error.  I can download the structure
> directly from RCSB.
>

with Firefox/Windows and Chrome/Windows I had no problem drag-dropping into
JSmol.
Is this perhaps browser/platform dependent?



>
> A definition question: In the various sample test files involving
> macromolecules that I have looked at, Bob uses the terms “structure” and
> “groups" as a color and display choices.   I am not sure what I am looking
> at in each case.  I thought it might be 4° structure, but now I am not sure.
>
>
structure is type of secondary structure -- different types of helix,
sheet, etc.

group is just 1->n within each chain.



> Phil
>
> Philip Bays
> Emeritus Professor of Chemistry
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu
>
>
>
>
> --
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] Protein Loading

[Philip Bays]

I have a file entitled 5e6e.pdb.gz that I downloaded this week. Using previous 
versions of jsmol.min, this file would load via drag-and-drop or using the 
local-file load mechanism. In the latest version, jsmol version (03.31) I get a 
"file not recognized" error.  I can download the structure directly from RCSB.

A definition question: In the various sample test files involving 
macromolecules that I have looked at, Bob uses the terms “structure” and 
“groups" as a color and display choices.   I am not sure what I am looking at 
in each case.  I thought it might be 4° structure, but now I am not sure.

Phil

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



--
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users