[Jmol-users] http://www.bbc.co.uk/news/technology-35427685

[Rzepa, Henry S]

This  BBC article suggests the gradual end of  Java applet support, with Oracle 
suggesting using " plug-in free Java Web Start technology”.

I have no problems with  using JSmol for all the new sites I have created these 
last 3 years or so, but am wondering about all the legacy sites  I have left 
over the years pre-dating 2013  and the easiest way to keep them running.  
Mapping to  the JSmol invocations is not automatic.

Any suggestions please? 
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Re: [Jmol-users] http://www.bbc.co.uk/news/technology-35427685

[Angel Herráez]

Dear Henry,

I agree this is a prickly issue.

>From my limited experience with Java Web Start, my opinion is that it is not 
practical at all. You must wait for a lengthy download, then it will open, it 
leaves whoever knowns which and how many files in your computer, next 
day you use that page you must start again. I see it as only adequate for 
professional, regular use of some piece of software. General users will just 
quit.
Nothing to do with the swift experience of Jmol/Java in a webpage and even 
with JSmol pages. 

In my view, Oracle has been digging its own grave re. Java.


Regarding conversion of old sites, this is my experience:

- If the sites have a simple code for inserting the Jmols, the Jmol2.js adapter 
library will probably take care of the update with minimal effort.
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Conversion_using_th
e_Jmol2.js_.27adapter.27_library

- Another problem may be change in behaviour of a few JmolScript 
commands along versions (not to do with the move to JSmol), but that only 
shows up when you have sophisticated scripts.

- Pages using frames are hard, if not impossible, to adapt using Jmol2.js and 
the old syntax. I tried and I gave up, rewriting my pages to avoid the frames 
and use the new JSmol.js ways. Fortunately, since most groups of my pages 
were using centralised, common javascript files to insert and manage the 
Jmols, the task was much lighter than expected. 

- You still need to review that all buttons, scripts etc. work properly. It may 
or 
not be easy, depending on the complexity of your pages+scripting


>  Mapping to  the JSmol invocations is not automatic.

I agree, it's not wholly, but read above.


> Any suggestions please? 

I am always available for being hired ;-)  
both monetary and academic reward are acceptable


Hope all is well with you. Too long since we last met!
Cheers,
A.


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Re: [Jmol-users] Minset

[Robert Hanson]

Yes. I just used this:

isosurface minset 1000 "=1blu" mesh nofill

and it worked great to remove the water density.
​
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Re: [Jmol-users] red-blue splotches on EP isosurfaces

[Robert Hanson]

Can you be more specific? Exact script? better: PNGJ file sent to
hans...@stolaf.edu

On Thu, Jan 28, 2016 at 7:20 PM, John Keller  wrote:

> Hi  All,
>
> What causes red/blue splotches on EP isosurfaces? Is there any sure way to
> avoid them in jmol?
>
> John
>
>
>
> *
>
> John W. Keller, Ph.D.
>
> Professor of Chemistry Emeritus
>
> Department of Chemistry & Biochemistry
>
> Division of Research, College of Natural
>
>  Science & Mathematics
>
> University of Alaska Fairbanks
>
> jwkel...@alaska.edu
>
> *
>
>
>
>
>
> Sent from Mail  for
> Windows 10
>
>
>
>
> --
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>
>


-- 
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
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Re: [Jmol-users] new DSSR

[Robert Hanson]

On Thu, Jan 28, 2016 at 1:08 PM, Pshemak Maslak  wrote:

>
> The new DSSR has base pairs and nucleotide indexed by numbers,  For
> example (the 9th base-pair):
>
> auxiliaryinfo.models[1].dssr.pairs[9].bp"A-T"
>


x=_M.dssr.pairs.getProperty("SELECT nt* where bp='T-A' or bp='A-T'")
select within(@x)

_M is the auxiliaryInfo for the current model.

Note that x is an array of associative arrays:

[...  {
"nt1"  :  "|1|D|DT|12"
"nt2"  :  "|1|E|DA|27"
   }
  {
"nt1"  :  "|1|D|DT|15"
"nt2"  :  "|1|E|DA|24"
   }
...]

Jmol finds those "unit ids" in there. Better is to use  ( ) around the nt*:

x=_M.dssr.pairs.getProperty("SELECT (nt*) where bp='T-A' or bp='A-T'")

This creates a clean array of those unit ids:

$ x=_M.dssr.pairs.getProperty("SELECT (nt*) where bp='T-A' or bp='A-T'")
$ print x
|1|E|DT|34
|1|D|DA|5
|1|E|DT|31
|1|D|DA|8
|1|E|DT|29
|1|D|DA|10
|1|E|DA|27
|1|D|DT|12
|1|E|DA|24
|1|D|DT|15



> auxiliaryinfo.models[1].dssr.pairs[9].nt1"|1|D|A|10"

auxiliaryinfo.models[1].dssr.pairs[9].nt2"|1|E|T|29"
>



x = _M.dssr.pairs[9]
select within(@x)

x = _M.dssr.pairs[9].nt1
select within(@x)

x = _M.dssr.pairs[9].nt2
select within(@x)


>
> What is the proper syntax to select any one of these"
>
> Thanks,
>
> PM
>
>
>
>
>
> --
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> 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
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[Jmol-users] new DSSR

[Pshemak Maslak]

The new DSSR has base pairs and nucleotide indexed by numbers,  For 
example (the 9th base-pair):

auxiliaryinfo.models[1].dssr.pairs[9].bp"A-T"
auxiliaryinfo.models[1].dssr.pairs[9].nt1"|1|D|A|10"
auxiliaryinfo.models[1].dssr.pairs[9].nt2"|1|E|T|29"

What is the proper syntax to select any one of these"

Thanks,

PM




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[Jmol-users] Fwd: Re: new DSSR

[Pshemak Maslak]

Thanks Rolf!

PM

Forwarded per Rolf's request

On 01/28/2016 07:08 PM, Pshemak Maslak wrote:
>
> The new DSSR has base pairs and nucleotide indexed by numbers,  For
> example (the 9th base-pair):
>
> auxiliaryinfo.models[1].dssr.pairs[9].bp"A-T"
> auxiliaryinfo.models[1].dssr.pairs[9].nt1"|1|D|A|10"
> auxiliaryinfo.models[1].dssr.pairs[9].nt2"|1|E|T|29"
>
> What is the proper syntax to select any one of these"
>
 From the example I showed in the previous thread regarding the DSSR
change I would suspect that the first base would be residue "A" number
"10" from chain "D". And I would suspect the "1" being the model number.
But because it wasn't included in the former residue selection
expression I am not really sure.

The syntax for the selection expression is the same as before:
   select [A]10:D
   select [T]29:E

Or if you would add the (suspected) model number it would look like this:
   select [A]10:D/1
   select [T]29:E/1

You can split the 'nt1' and 'nt2' strings by "|" into an array and then
build the selection expression as a string:

- Jmol commands --
nt1 = auxiliaryinfo.models[1].dssr.pairs[9].nt1.split("|");
nt2 = auxiliaryinfo.models[1].dssr.pairs[9].nt2.split("|");

res_nt1 = "[" + nt1[4] + "]" + nt1[5] + ":" + nt1[3] + "/" + nt1[2];
res_nt2 = "[" + nt2[4] + "]" + nt2[5] + ":" + nt2[3] + "/" + nt2[2];

select @res_nt1;
select @res_nt2;
--

I currently cannot post to the 'jmol-users' list because my recent email
address change wasn't confirmed there yet. Please forward my answer to
the list so that others can also see it.

Regards,
Rolf
-- 

Rolf Huehne
Postdoc

Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany

Phone:   +49 3641 65 6205
Fax: +49 3641 65 6210
E-Mail:  rolf.hue...@leibniz-fli.de
Website: http://www.leibniz-fli.de

   Scientific Director: Prof. Dr. K. Lenhard Rudolph
Head of Administration: Dr. Daniele Barthel
Chairman of Board of Trustees: Burkhard Zinner

VAT No: DE 153 925 464
Register of Associations: No. 230296, Amtsgericht Jena
Tax Number: 162/141/08228




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[Jmol-users] Electron Density Maps Made Easy

[Eric Martz]

If you ever need a non-technical explanation of electron density maps 
and their relationships to temperature (B value), these pages may be 
quite useful:

http://bioinformatics.org/molvis/edm

I use them in the workshops I teach on protein structure.

In 2010, with Bob's help, I made these two pages about electron density 
maps. One shows the relationship between electron density (shown as a 
"cloud" of data points, each with a density value) and the usual map, 
which is an isomesh at one sigma. The second shows how the map looks 
around a region with low temperature (B value) vs. one of high 
temperature, in a 2.0 Angstrom resolution protein.

Until now these have been using the old unsigned Jmol Java applet, but 
yesterday I easily got them running in JSmol! I'm pleasantly surprised 
at the performance.

Because they are data intensive they load and rotate faster and smoother 
in Firefox (or Safari).
http://bioinformatics.org/firstglance/fgij/notes.htm#browsers

-Eric

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[Jmol-users] Split: Websites Using Jmol

[Eric Martz]

At http://wiki.jmol.org

the page /Websites Using Jmol/ was very large (text >32K) and cumbersome 
to edit.


I have split it into two pages of about equal length, A-L and M-Z.

I also inserted blank lines between letters of the alphabet to make 
these pages more readable.


While doing so, the entries with chemeddl.org links were wrongly 
rejected as blacklisted or spam by the wiki system. I was forced to give 
those URL's in plain text rather than as links.


The main page
http://wiki.jmol.org/index.php/Websites_Using_Jmol
now has links to the two sub-pages.

I hope this was a beneficial and agreeable change.

Sincerely, Eric

--
Eric Martz, Professor Emeritus, Dept Microbiology
University of Massachusetts, Amherst MA US
Martz.MolviZ.Org 
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[Jmol-users] red-blue splotches on EP isosurfaces

[John Keller]

Hi  All,
What causes red/blue splotches on EP isosurfaces? Is there any sure way to 
avoid them in jmol?
John

*
John W. Keller, Ph.D.
Professor of Chemistry Emeritus
Department of Chemistry & Biochemistry
Division of Research, College of Natural 
 Science & Mathematics 
University of Alaska Fairbanks
jwkel...@alaska.edu
*


Sent from Mail for Windows 10

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Re: [Jmol-users] isosurface mesh resolution question

[Robert Hanson]

Frieda,

You cannot set the resolution of an isosurface that comes from a volume
data file such as that using the RESOLUTION option. What you can do is use
the DOWNSAMPLE option. What this does is to skip points in the grid. The
RESOLUTION option is only for isosurfaces that are generated de novo by
Jmol -- vdw, sasurface, molecular, solvent.

Bob


On Thu, Jan 28, 2016 at 8:39 PM, Frieda Reichsman  wrote:

> Hi Bob,
>
> Using the following command:
>
> isosurface id ~m40 rmsd 2.0 sign red [x00dd00] within 1.5 {ret}
> "250u-2m-0.40.ccp4" resolution 5.0 mesh nofill;
>
> and trying to the resolution of the mesh to a finer level, I find no
> change in resolution from the default. I’ve tried placing “resolution 5.0”
> in a variety of different locations within the command, to no effect.
>
> Also - will red become the negative rmsd in the way I’ve set it up? Hard
> to tell from the documentation.
>
> Thanks,
> Frieda
>
>
>
> //
>
> Frieda Reichsman, PhD
> Molecules in Motion
> Interactive Molecular Structures
> http://www.moleculesinmotion.com
> USA
> 00 +1 413-320-7449
>
> //
>
>
>
>
>
>
>
>
> --
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>


-- 
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
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[Jmol-users] isosurface mesh resolution question

[Frieda Reichsman]

Hi Bob,

Using the following command:

isosurface id ~m40 rmsd 2.0 sign red [x00dd00] within 1.5 {ret} 
"250u-2m-0.40.ccp4" resolution 5.0 mesh nofill;

and trying to the resolution of the mesh to a finer level, I find no change in 
resolution from the default. I’ve tried placing “resolution 5.0” in a variety 
of different locations within the command, to no effect.

Also - will red become the negative rmsd in the way I’ve set it up? Hard to 
tell from the documentation.

Thanks,
Frieda



//

Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
USA
00 +1 413-320-7449

//






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[Jmol-users] Minset

[Frieda Reichsman]

Hi Bob,

I’m trying to get rid of scraps or shards of surface and tried the “minset” 
modifier in my isosurface command. Is minset applicable here?

isosurface MINSET 10 id ~m40 rmsd 2.0 sign red [x00dd00] within 2.5 {ret} 
insideout "250u-2m-0.40.ccp4”;

Thanks,
Frieda


//

Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
USA
00 +1 413-320-7449

//






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