Re: [Jmol-users] bugs?

[Robert Hanson]

OK, that's useful information. Please see if you have the same problem with
synchronization here:

http://chemapps.stolaf.edu/jmol/jsmol/sync4.htm

(Oh, except the St. Olaf web server just went down) Maybe try another site
with that.

My guess is that those pages are not loading smoothly. You can help that
along using

Jmol.setAppletSync = function(applets, commands, isJmolJSV) {
Jmol._syncedApplets = applets;   // an array of appletIDs
Jmol._syncedCommands = commands; // an array of commands; one or
more may be null
Jmol._syncedReady = {};
Jmol._isJmolJSVSync = isJmolJSV;
}

Issuing this ahead of time guarantees that they will load in the exact
order specified in the arrays, one after the other, with no commands issued
until all are loaded. Something  like this:

Jmol.setAppletSync(["jmolApplet1", "jmolApplet2"], ["", ""])






On Wed, Dec 30, 2015 at 3:13 PM, Spinney, Richard <
rspin...@chemistry.ohio-state.edu> wrote:

>
>
>
> I also have a number of pages that used “ESP mapped total electron density
> surfaces. They are JVXL files (version 2.2) generated using the Jmol
> application. The isosurfaces appear but the color mapping is missing, they
> appear in a single chromic orange color.
>
>
please send me that file so I can see what you are talking about.


>
>
> I also noticed that the “lcaocartoon scale 1.0 CAP unitcell "cpk"” command to 
> created “packed” unit cells seems to have a bug. Atoms that are half in the 
> unit cell have a flat surface on the cell wall, but atoms at the corner of 
> the unit cell are missing 2 or 3 of the flat surfaces along the unit cell 
> walls.
>
>
>

found it -- those are the atoms on edges, which require two cuts. That was
tricky!



> Thanks, Rick
>
>
>
> Dr. Richard Spinney
>
> Department of Chemistry & Biochemistry
>
> The Ohio State University
>
> 120A Celeste Laboratory
>
> 120 West 18th Ave
>
> Columbus, Ohio 43210
>
>
>
> Email: rspin...@chemistry.ohio-state.edu
>
> Phone:(614) 247 - 6847
>
> Fax:  (614) 292 - 1685
>
>
>
>
> --
>
> ___
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> 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
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Re: [Jmol-users] Jmol on Maven Central

[Nicolas Vervelle]

Hi Mark,

I'm probably the one who deployed the old version a long time ago (or Bob,
not sure).
I'm currently way too busy on various matters to keep doing releases for
Jmol.

I think having a volunteer to deal with releases on Maven central would be
very helpful. Anyone interested ?
There are some ant scripts in Jmol source code to deploy there, but they
haven't been used in a very long time.
So, first thing would be to check if they still work correctly (probably by
testing snapshots releases), and then try to find which SVN revision should
be deployed as a given version.

Nico



On Wed, Dec 30, 2015 at 5:06 PM, Mark Williamson  wrote:

> Dear Jmol users,
>
> I see that there is a version of Jmol on Maven central:
>
> http://search.maven.org/#search|ga|1|jmol
>
> However the latest version here is around 13. I was wondering if the
> person who deployed this is on this list and if it would be possible for
> that person to deploy a more recent (say 14) version of Jmol?
>
> Thanks,
>
> Mark
>
>
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[Jmol-users] Chrome bug? JU.Point3fi.set2

[Eric Martz]

Dear Bob,

Proteopedia is attempting to use 14.4.1_2015.12.23

The following error occurs in Chrome, but not in Firefox.
This occurs on all pages, e.g. this random PDB entry
http://proteopedia.org/w/1ao5

This error does not occur when loading the same 1ao5 at
http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm

TypeError: JU.Point3fi.set2 is not a function try/catch path:
0 function (b,d)
  args[0]=TypeError: JU.Point3fi.set2 is not a function
  args[1]=function (){a.instantialize(this,arguments)}
1 J.render.RepaintManager.render(a,b,d,c)
  args[0]=[J.g3d.Graphics3D object]
  args[1]=[JM.ModelSet object]

etc

Thanks, Eric

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Re: [Jmol-users] Chrome bug? JU.Point3fi.set2

[Robert Hanson]

This is not reproducible for me. It is most likely some sort of browser
caching issue. Hopefully not more than that. I will wait to hear more.
​
Bob
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