Re: [Jmol-users] Placing Jmol image in same web page

[Robert Hanson]

On Wed, Sep 10, 2008 at 9:33 AM, Steven R. Spilatro
<[EMAIL PROTECTED]>wrote:

> Thanks to everyone for the feedback on the 'Placing Jmol image in
> same web page' which I've updated.
> http://www.marietta.edu/~spilatrs/MnQuiry/JmolDemo/jmolImgCopy.html
> 'Output size' now shows a default (Lesson of the Night: do not put
> radio buttons in a  if you want to set the checked
> property).


nah. huh? must be something else. Of course you can put a checkbox in a
table and have it checked


> Bob, I played around with jmolGetPropertyAsJavaObject("image"), but
> no luck yet.
>

;)


>
> Steve
>
> Dr. Steven R. Spilatro
> Department of Biology and Environmental Science
> Marietta College
>
>
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-- 
Robert M. Hanson
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
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Re: [Jmol-users] identifying proteins in mol2 files

[Robert Hanson]

We could set up the mol2 reader to do this. BUT I have to be convinced first
that it's a real standard. What programs write these? Is it just totally
arbitrary what these IDs are? Are the names standard? Try some more unusual
structures, like DNA, RNA, nonstandard amino acids, 1BLU with its FeS4
sites. Hemoglobin.

On Wed, Sep 10, 2008 at 8:51 AM, Angel Herraez <[EMAIL PROTECTED]> wrote:

> Dear Frieda
>
> I've never tried that. From the doc
> http://www.tripos.com/data/support/mol2.pdf
> it seems that atoms can have IDs and residue IDs; they quote an
> example:
> 1 CA -0.149 0.299 0.000 C.3 1 ALA1 0.000
> BACKBONE|DICT|DIRECT
> 1 CA -0.149 0.299 0.000 C.3
> [...] the atom is named CA and is [...] It belongs to the
> substructure with ID 1 which is named ALA1.
>
> So, Jmol should be able to interpret that, but maybe the file reader
> has not been set for that.
> As far as I know, the "protein" is determined based on bonding and
> key atom names (N, CA, C) within the same residue.
> Similarly for residue names.
>
> A quick test with a pdb file read into Accelrys DS Viewer 1.7 and
> saved into mol2 shows that the atom IDs are read in Jmol (example:
> select *.CA works), but not recognized as protein. "select ala"
> doesn't work either.
> So maybe it's just the residue ID part that is not being interpreted.
> Notably, that goes after the coordinates, rather than before them as
> in pdb.
>
>
>
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-- 
Robert M. Hanson
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
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Re: [Jmol-users] identifying proteins in mol2 files

[Reichsman Frieda]

Hi Angel,

Thanks - your results are identical with my own--I thought perhaps  
Jmol could interpret the structure as protein but found it didn't. I  
wanted to be sure that that was the intended behavior of Jmol, not a  
flaw in the mol2 formating. Now I am satisfied on that point.

So Bob, would that be possible then, for Jmol's file reader to be able  
to read a mol2 file containing residue names and appropriate atom  
names, as protein? I don't know what else would need to be taken into  
consideration so I'm not sure if this is even a reasonable request.

Frieda

On Sep 10, 2008, at 9:51 AM, Angel Herraez wrote:

> Dear Frieda
>
> I've never tried that. From the doc
> http://www.tripos.com/data/support/mol2.pdf
> it seems that atoms can have IDs and residue IDs; they quote an
> example:
> 1 CA -0.149 0.299 0.000 C.3 1 ALA1 0.000
> BACKBONE|DICT|DIRECT
> 1 CA -0.149 0.299 0.000 C.3
> [...] the atom is named CA and is [...] It belongs to the
> substructure with ID 1 which is named ALA1.
>
> So, Jmol should be able to interpret that, but maybe the file reader
> has not been set for that.

>
> As far as I know, the "protein" is determined based on bonding and
> key atom names (N, CA, C) within the same residue.
> Similarly for residue names.
>
> A quick test with a pdb file read into Accelrys DS Viewer 1.7 and
> saved into mol2 shows that the atom IDs are read in Jmol (example:
> select *.CA works), but not recognized as protein. "select ala"
> doesn't work either.
>
> So maybe it's just the residue ID part that is not being interpreted.
> Notably, that goes after the coordinates, rather than before them as
> in pdb.


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[Jmol-users] Placing Jmol image in same web page

[Steven R. Spilatro]

Thanks to everyone for the feedback on the 'Placing Jmol image in 
same web page' which I've updated.
http://www.marietta.edu/~spilatrs/MnQuiry/JmolDemo/jmolImgCopy.html
'Output size' now shows a default (Lesson of the Night: do not put 
radio buttons in a  if you want to set the checked 
property).  Rolf, I'm not sure what's going on in Linux, but I had 
noticed that the output size settings have browser-dependent effects 
on the image in the Iframe and does not change the size of the copied 
or saved image. I have added a note about this.
Bob, I played around with jmolGetPropertyAsJavaObject("image"), but 
no luck yet.

Steve

Dr. Steven R. Spilatro
Department of Biology and Environmental Science
Marietta College


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Re: [Jmol-users] identifying proteins in mol2 files

[Angel Herraez]

Dear Frieda

I've never tried that. From the doc
http://www.tripos.com/data/support/mol2.pdf
it seems that atoms can have IDs and residue IDs; they quote an 
example:
1 CA -0.149 0.299 0.000 C.3 1 ALA1 0.000
BACKBONE|DICT|DIRECT
1 CA -0.149 0.299 0.000 C.3
[...] the atom is named CA and is [...] It belongs to the
substructure with ID 1 which is named ALA1. 

So, Jmol should be able to interpret that, but maybe the file reader 
has not been set for that.
As far as I know, the "protein" is determined based on bonding and 
key atom names (N, CA, C) within the same residue.
Similarly for residue names.

A quick test with a pdb file read into Accelrys DS Viewer 1.7 and 
saved into mol2 shows that the atom IDs are read in Jmol (example: 
select *.CA works), but not recognized as protein. "select ala" 
doesn't work either.
So maybe it's just the residue ID part that is not being interpreted. 
Notably, that goes after the coordinates, rather than before them as 
in pdb.



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Re: [Jmol-users] identifying proteins in mol2 files

[Reichsman Frieda]

Some mol2 files contain amino acid residue names (preceded by the res  
number) at character 60 or 61, like this:


1  N  17.0470  14.0990   3.6250 N.3   1 THR 
0.0677
2  CA 16.9670  12.7840   4.3380 C.3   1 THR 
0.8095
3  C  15.6850  12.7550   5.1330 C.2   1 THR 
0.4469
4  O  15.2680  13.8250   5.5940 O.2   1 THR
-0.2562
5  CB 18.1700  12.7030   5.3370 C.3   1 THR 
0.8346
6  OG119.3340  12.8290   4.4630 O.2   1 THR
-0.1477
7  CG218.1500  11.5460   6.3040 C.3   1 THR 
0.2847


So I thought perhaps there would be a way to recognize the structure  
with residue names as protein.

Frieda


On Sep 10, 2008, at 9:37 AM, Robert Hanson wrote:

no. not that I know of. Only PDB and CIF support for that. Is there  
some sort of MOL2 designation that would suggest otherwise?


On Wed, Sep 10, 2008 at 8:22 AM, Reichsman Frieda  
<[EMAIL PROTECTED]> wrote:

Hi Bob et al.,

If a mol2 file is correctly formated, should Jmol be able to recognize
"protein" (as in 'select protein') and residue names?

Thanks,
Frieda

//

Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
413-253-2405

//


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--
Robert M. Hanson
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
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Re: [Jmol-users] identifying proteins in mol2 files

[Robert Hanson]

no. not that I know of. Only PDB and CIF support for that. Is there some
sort of MOL2 designation that would suggest otherwise?

On Wed, Sep 10, 2008 at 8:22 AM, Reichsman Frieda <[EMAIL PROTECTED]> wrote:

> Hi Bob et al.,
>
> If a mol2 file is correctly formated, should Jmol be able to recognize
> "protein" (as in 'select protein') and residue names?
>
> Thanks,
> Frieda
>
> //
>
> Frieda Reichsman, PhD
> Molecules in Motion
> Interactive Molecular Structures
> http://www.moleculesinmotion.com
> 413-253-2405
>
> //
>
>
> -
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> ___
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>



-- 
Robert M. Hanson
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
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[Jmol-users] identifying proteins in mol2 files

[Reichsman Frieda]

Hi Bob et al.,

If a mol2 file is correctly formated, should Jmol be able to recognize  
"protein" (as in 'select protein') and residue names?

Thanks,
Frieda

//

Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
413-253-2405

//


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Re: [Jmol-users] Jmol Tutorial-Authoring Template Released

[Reichsman Frieda]

Forgot to mention, this is the best link for a demo of JTAT:
http://www.bioinformatics.org/jmol-tutorials/jtat/jtatdemo/contents/contents.htm

Frieda
//

Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
413-253-2405

//




On Sep 10, 2008, at 6:27 AM, Angel Herraez wrote:

> El 10 Sep 2008 a las 5:13, Robert Hanson escribió:
>> http://www.umass.edu/molvis/bme3d/materials/jmoltuts/antibody/ 
>> contents
>> /contents.htm
>> Jmol Version 11.3.13 2007-08-28 16:07
>>
>> really?
>
> I'm quite sure that tutorial was written some time ago, and does not
> use Eric's newest JTAT. So it's probably so, really.
>
>
> -
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Re: [Jmol-users] Jmol Tutorial-Authoring Template Released

[Reichsman Frieda]

On Sep 10, 2008, at 6:27 AM, Angel Herraez wrote:


El 10 Sep 2008 a las 5:13, Robert Hanson escribió:
http://www.umass.edu/molvis/bme3d/materials/jmoltuts/antibody/ 
contents

/contents.htm
Jmol Version 11.3.13 2007-08-28 16:07

really?


I'm quite sure that tutorial was written some time ago, and does not
use Eric's newest JTAT. So it's probably so, really.


Thanks for pointing this out Bob. Yes, Angel is correct. The  
particular tutorial you've cited (Antibody) was finished well before  
JTAT was ready for use by others as a tutorial authoring tool. At that  
time, 11.3.13 was a current Jmol release.


This is in contrast to the latest release of JTAT, a shell into which  
a tutorial can be built, and which has the current or nearly current  
Jmol. Here is a link to the "empty shell" -- no molecule loaded --  
which has Jmol 11.6.RC12.

http://www.bioinformatics.org/jmol-tutorials/jtat/template/contents/contents.htm
This is what someone would download to start using JTAT to build a  
tutorial: Download JTAT


We can of course update the Jmol version in previous JTATs, but  
obviously have not done that in this case (yet).


Best,
Frieda


//

Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
413-253-2405

//


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Re: [Jmol-users] Placing Jmol image in same web page

[Rolf Huehne]

Steven R. Spilatro wrote:
> Hi everyone,
> I've created a demo page for placing images of 
> the Jmol model into the same web page, drawing 
> upon some ideas and code from Angel Herráez and 
> Dean Edwards.  For compliant browsers, the 
> base64-encoded Jmol image is simply directly to 
> an image element; for non-base64 compliant 
> browsers, the decoded image is targeted to an 
> Iframe. I've tested in several browsers (but not 
> Chrome); while the image can be copied and pasted 
> from either type of element; I find that a saved 
> file from the Iframe does not open in Photoshop. .
> 
> I welcome comments and feedback. The page is at:
> http://www.marietta.edu/~spilatrs/MnQuiry/JmolDemo/jmolImgCopy.html
> 

 Test System 
Browser: Firefox 2.0.0.16
 Java  : 1.4.2_18
 OS: Linux, OpenSuSE 10.2
-

When I first tried it with Firefox 2 on Linux I got the image (with
"image" checked). Because the image looked distorted I wanted to look at
the properties using the context menu but Firefox crashed.

After restarting the browser the image creation (with "image" checked)
didn't work and I got the following Javascript error messages:

  jmolWaitScript is not a function
  applet.getPropertyAsString is not a function

After reloading the page it worked again (no new error messages, only
after "shift reload" later).
The properties dialog worked this time and showed "400x300".
When I saved it and opened it with a graphics program it was not
distorted and as size was shown "435x471".
So either it is not clear enough what "Output Size" is supposed to mean
or it is not working as expected.

The "Iframe" method also worked (no distorted image).

Regards,
Rolf

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Re: [Jmol-users] Jmol Tutorial-Authoring Template Released

[Angel Herraez]

El 10 Sep 2008 a las 5:13, Robert Hanson escribió:
> http://www.umass.edu/molvis/bme3d/materials/jmoltuts/antibody/contents
> /contents.htm
> Jmol Version 11.3.13 2007-08-28 16:07
> 
> really?

I'm quite sure that tutorial was written some time ago, and does not 
use Eric's newest JTAT. So it's probably so, really.


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Re: [Jmol-users] Jmol Tutorial-Authoring Template Released

[Robert Hanson]

http://www.umass.edu/molvis/bme3d/materials/jmoltuts/antibody/contents/contents.htm
Jmol Version 11.3.13  2007-08-28 16:07

really?

Bob

On Mon, Sep 8, 2008 at 10:15 PM, Eric Martz <[EMAIL PROTECTED]>wrote:

> At long last, I have completed a version of the Jmol
> Tutorial-Authoring Template (JTAT) that I believe to be adequately
> documented, and fully functional
> (http://bioinformatics.org/jmol-tutorials). Improvements since I last
> put up a pre-release version (July 2008):
>
>  - Documentation on how to use the template, color key functions,
> etc. to author a tutorial has been completed.
>
>  - A new chapter on DRuMS Color Schemes has been added to the JTAT
> Demonostration Tutorial.
>
>  - The chapter on Animations and Movies in the JTAT Demonstration
> Tutorial has been clarified.
>
>  - Functions are provided to easily generate standard color keys,
> and scripts are provided to apply the standard color schemes to
> molecular views. A Quick Reference page for color HTML is provided.
>
>  - Support for checkboxes that modify the molecular view. Example:
> View 1 in the Demo Tutorial chapter on Color Schemes.
>
>  - After centering an atom by clicking on it, the next time "Center
> Clicked" is checked, a new button appears for re-centering the entire
> molecule.
>
>  - The links (at the bottom of every page in a tutorial) for further
> exploration of the molecules in the tutorial now support links to
> FirstGlance in Jmol that display modified or customized PDB files
> included in the tutorial, as well as the usual published PDB codes.
>
>  - Jmol applet has been updated to the current version (11.6.RC12).
>
> Of course, the entire template and website is downloadable in a
> single file, jtat.zip.
>
> Caveat: I will be away from email until after September 20. Any
> questions, feedback, or things that I botched up will have to wait
> till after I get back.
>
> -Eric
>
> /* - - - - - - - - - - - - - - - - - - - - - - - - - - -
> Eric Martz, Professor Emeritus, Dept Microbiology
> U Mass, Amherst -- http://www.umass.edu/molvis/martz
>
> Top Five 3D MolVis Technologies http://Top5.MolviZ.Org
> 3D Wiki with Scene-Authoring Tools http://Proteopedia.Org
> Biochem 3D Education Resources http://MolviZ.org
> See 3D Molecules, Install Nothing! - http://firstglance.jmol.org
> Protein Explorer - 3D Visualization: http://proteinexplorer.org
> Workshops: http://workshops.proteinexplorer.org
> World Index of Molecular Visualization Resources: http://molvisindex.org
> ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
> Atlas of Macromolecules: http://atlas.proteinexplorer.org
> PDB Lite Macromolecule Finder: http://pdblite.org
> Molecular Visualization EMail List (molvis-list):
>   http://bioinformatics.org/mailman/listinfo/molvis-list
> - - - - - - - - - - - - - - - - - - - - - - - - - - - */
>
>
> -
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-- 
Robert M. Hanson
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
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