[Jmol-users] SMARTS question

[Eric Martz]

This selects the aromatic ring carbons of Phe and Tyr:

rings6 = {*}.find("SMARTS","c1c1", true)

It does not select the 6-atom ring of Trp.

This selects the ring of His:

ringsh = {*}.find("SMARTS","c1cncn1", true)

How do I select the 5 and 6 atom rings of Trp?

Thanks, Eric


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Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

[Eric Martz]

Hi, Henry,

In addition to Internet Explorer 11* (still included in Windows 10 as 
far as I know), several minor browsers that still supported Java when 
last I checked in March 2017 are listed here:


http://proteopedia.org/w/Installing_and_enabling_Java#Browsers_That_Support_Java

* See

http://proteopedia.org/w/Installing_and_enabling_Java#Accessing_Internet_Explorer_in_Windows_10

-Eric

On 6/8/17 6:29 AM, Rzepa, Henry S wrote:

I have had a look at Safari preview 32.  In the preferences/security tab, the 
current production safari has settings for

1. Allow WebGL
2. Allow Internet Plugins,  and in this latter one can configure to allow  Java.

In Safari 32, both of these are now gone.   With  High Sierra developer preview 
about to be released into  beta, may bring confirmation that  Safari too has 
now not merely been deprecated but disallowed.

If correct, this means that Jmol.jar can only now run in application mode, and 
not as a browser plugin.

Still,  Apple promise that the new Safari will be  “faster”, although  I 
suspect it has some way to go to be as fast as compiled Java.


I wonder what the missing  WebGL means? It never really took off did it!

Henry


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Re: [Jmol-users] Jmol Anniversaries?

[Eric Martz]

Hi Henry,

I have a paragraph of Jmol history in footnote 1 here:

http://proteopedia.org/w/Jmol

Which leads to early history by searching for "jmol" at openscience.org:

http://openscience.org/?s=jmol

Much of Jmol's command language was invented by Roger Sayle when he 
created RasMol. Tim Maffet used Roger's public domain source code when 
he created the browser plug-in MDL Chime, which was the best 
within-browser solution from 1996 until Jmol superceded it ca. 2006. 
Thus, Chime included most of RasMol's command language. Michael "Miguel" 
Howard, who I believe first adapted Jmol to display macromolecules, 
incorporated the RasMol/Chime command language into Jmol, facilitating 
the transitions of RasMol and Chime users to Jmol. Of course Jmol's 
command language is now vastly larger and more powerful and complex than 
the languages of RasMol & Chime. But the original RasMol language is 
still a core subset.


Although far from complete, quite a bit of pre-Jmol history is here, 
including physical models and early computer graphics:


http://History.MolviZ.Org

-Eric

On 6/7/17 2:28 AM, Rzepa, Henry S wrote:

Does anyone know the various anniversary dates?

1. Jmol (was it really only released in 2001?  I thought it came about 
just a year or so after  Java itself was released in 1996?)

2. JSmol (2014?)
3. Bob’s own entry after Miguel handed on (??)

Is there a hall of fame, going back perchance to  Xmol (which started 
the bandwagon, + Rasmol as a separate fork?) and key 
timelines/contributors? The Jmol Wikipedia page is not that strong on 
the history).


Henry Rzepa, http://orcid.org/-0002-8635-8390

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Re: [Jmol-users] labeling residue by position relative to observer

[Eric Martz]

Dear Luciano,

Wow! That is amazing! It worked easily for me (MacBook Pro).

For people who haven't tried it: Go the link below. It asks permission 
to use your camera. Follow simple instructions to calibrate (takes less 
than one minute). Then whatever part of the molecule you look at rotates 
to the front! By tracking your eye movements!


-Eric


On 5/16/17 2:59 AM, Luciano Abriata wrote:
And Eric, regarding the anecdote, actually I wanted to do this for 
something similar. With help from Angel I coupled an eye gazer that 
uses the webcam to track the user's eyes. Then, whatever part of the 
molecule you look at comes to the front (and now its frontmost 
residues get labeled). It doesn't work very well due to the low 
"resolution" of the eye gazer, but with good light on your face you 
can see the effect coming up!


https://lucianoabriata.altervista.org/jsinscience/jsmolwebgazer/jsmolwebgazer.html



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Re: [Jmol-users] labeling residue by position relative to observer

[Eric Martz]

Dear Luciano,

Below is a script that selects the frontmost atom as the molecule is 
rotated by the mouse. It defines a set of 4 atoms, and whichever becomes 
frontmost is selected. This script can be adapted to run any arbitrary 
script triggered by one of a specified set of atoms becoming frontmost 
due to rotation of the molecule with the mouse. Thus, it could be 
adapted to label the frontmost atom.


The script defines a set of 4 atoms in atomlist. Every 100 milliseconds, 
it runs checkOrient(), which re-determines which of the 4 atoms is 
frontmost, and selects it. The selection is visible because 
selectionHalos is on.


Copy the script below and paste it into the Jmol console, or paste it 
into a plain text file, and drop that file into Jmol. As you rotate the 
molecule with the mouse, the frontmost atom is highlighted with a yellow 
halo. It does not seem to work if the molecule is spinning.


In April, 2012, we had the pleasure of a visit by Bob Hanson at our 
campus (UMass, Amherst). Craig Martin's Molecular Playground (website is 
currently unresponsive, but http://molecularplayground.org) was a major 
topic of discussion. Karsten Theis asked Bob if, when a person rotates 
the projected molecule by waving their arm, a script could be triggered 
to show more detail about whatever is in front. Within one day, Bob came 
up with orient.spt (below). Here is a photo commemorating this meeting: 
http://proteopedia.org/w/Proteopedia:Scrapbook#Molecular_Playground_Team 
-- as far as I know, this method has not yet been incorporated into 
Molecular Playground modules, or any other uses.


--

// orient.spt -- tracks the orientation of four points
// This script by Robert Hanson, April, 2012 for Karsten Theis, Eric 
Martz, Craig Martin.
// The frontmost of the 4 atoms specified in atomlist is selected every 
0.1 sec.
// This script can be adapted to run any arbitrary script when a 
specified atom

// becomes the frontmost of a specified set of atoms.

load DATA "mol"
C:/jmol-dev/bobtest/mmff94_dative.mol2
__Jmol-12_04301213583D 1   1.0 0.0 0
Jmol version 12.3.24_dev  2012-04-27 23:05 EXTRACT: ({0:24})
 25 26  0  0  0  0  1 V2000
  -8.19190  -2.59960  15.52080 N   0  0  0  0  0  0
  -7.34730  -2.94810  16.47440 C   0  0  0  0  0  0
  -7.02800  -2.03140  17.44970 N   0  0  0  0  0  0
  -6.80300  -4.16350  16.55330 N   0  0  0  0  0  0
  -7.15100  -5.04140  15.59320 C   0  0  0  0  0  0
  -6.48610  -6.26490  15.62980 N   0  0  0  0  0  0
  -8.03730  -4.74600  14.54960 C   0  0  0  0  0  0
  -8.39880  -5.63640  13.58900 N   0  0  0  0  0  0
  -9.27230  -5.22870  12.63230 C   0  0  0  0  0  0
  -9.64070  -6.23510  11.58280 C   0  0  0  0  0  0
  -9.79140  -3.93470  12.64140 C   0  0  0  0  0  0
 -10.75920  -3.46050  11.59680 C   0  0  0  0  0  0
  -9.44170  -3.03720  13.60530 N   0  0  0  0  0  0
  -8.56300  -3.44580  14.55720 C   0  0  0  0  0  0
  -8.61250  -1.68180  15.51700 H   0  0  0  0  0  0
  -6.87870  -1.06530  17.18790 H   0  0  0  0  0  0
  -6.29240  -2.39870  18.05420 H   0  0  0  0  0  0
  -5.95280  -6.40360  16.48240 H   0  0  0  0  0  0
  -7.05940  -7.06120  15.35990 H   0  0  0  0  0  0
 -10.71720  -6.43030  11.60180 H   0  0  0  0  0  0
  -9.12410  -7.18450  11.75870 H   0  0  0  0  0  0
  -9.35260  -5.87520  10.59050 H   0  0  0  0  0  0
 -11.04610  -2.41970  11.78010 H   0  0  0  0  0  0
 -11.66930  -4.06770  11.61530 H   0  0  0  0  0  0
 -10.30480  -3.51330  10.60280 H   0  0  0  0  0  0
  1 15  1  0  0  0
  1 14  2  0  0  0
  1  2  1  0  0  0
  2  4  2  0  0  0
  2  3  1  0  0  0
  3 17  1  0  0  0
  3 16  1  0  0  0
  4  5  1  0  0  0
  5  7  2  0  0  0
  5  6  1  0  0  0
  6 19  1  0  0  0
  6 18  1  0  0  0
  7 14  1  0  0  0
  7  8  1  0  0  0
  8  9  2  0  0  0
  9 11  1  0  0  0
  9 10  1  0  0  0
 10 22  1  0  0  0
 10 21  1  0  0  0
 10 20  1  0  0  0
 11 13  2  0  0  0
 11 12  1  0  0  0
 12 25  1  0  0  0
 12 24  1  0  0  0
 12 23  1  0  0  0
 13 14  1  0  0  0
M  END
END "mol"

atomlist = ["C10","C12","N3","N6"]



function checkOrient() {
ptcenter = {*}.xyz
q = quaternion()// current rotation
asort = []
for (var i = 1; i <= atomlist.length; i++) {
var a = atomlist[i]
var pt = {atomName=a}.xyz - ptcenter
asort[i] = [a, (q%pt).z]
}
asort = asort.sort(2)
var frontAtom = (asort[0])[1]
select {atomName=frontatom}
}

selectionHalos on
# run checkOrient() every 100 milliseconds.
timeout "t1" -100 "checkOrient()"


-Eric

Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- Martz.MolviZ.Org <http://Martz.MolviZ.Org>

 * Top Five 3D MolVis Tools: Top5.MolviZ.Org <http://top5.MolviZ.Org>
 * FirstGlance: 3D Molecules in /Nature/: FirstGlance.Jmol.Org
   <http://firstglance.jmol.Org>
 * Protein 3D Structure Wiki: Proteoped

Re: [Jmol-users] ...still problems with the extended display...

[Eric Martz]

Did you try moving the console to where you want it, then clicking Quit 
(or Close) from Jmol's pull-down File menu? On a Mac, this saves the 
window positions so the next time you start Jmol, they are remembered. 
In contrast, other methods of quitting (Jmol menu in the menubar, Quit; 
Cmd-Q) do NOT save the window positions. Not sure about Windows 7.


On 5/9/17 6:03 AM, MS wrote:
Sorry, just to add the my previous email is that the problem of the 
console window not appearing after I switch back to a single display 
still persists... I tried everything, unplugging and uninstalling the 
other monitor, moving the jmol window from a monitor to another, but 
nothing, as soon as I close jmol and restart it, the console window 
goes to the wrong monitor...

Any suggestions will be welcomed.

Thanks,


Marco


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Re: [Jmol-users] Secondary structure does not match DSSP

[Eric Martz]

Dear Nicholas,

Angel is correct. By default, Jmol shows the secondary structure that 
the authors specified in the PDB file with HELIX, SHEET and TURN 
records. You will notice that often, authors do not specify TURN records 
so there are no blue turns initially. After you calculate structure, and 
color structure, turns are colored blue, and the ends of strands and 
helices may be different than before.


Also, Jmol distinguishes three kinds of helices, and gives them distinct 
colors:


 * Alpha 3.6(13)
 * 3.0(10)
 * Pi 4.4(16)

Each kind is illustrated here in JSmol:
http://proteopedia.org/w/Helices_in_Proteins

See also http://proteopedia.org/w/Secondary_structure

-Eric


On 4/23/17 4:56 AM, Angel Herráez wrote:

Hi Nicholas


However, if I issue the command $calculate structure and then redisplay, the 
structure
is then shown with a ribbon consistent with DSSP, running from 365 to 373. Can 
anyone
tell me why Jmol doesn't display this stretch according to DSSP in the first 
place?

I am not certain, but it is likely that when you load a file Jmol will use the
secondary structure declared in the PDB file, and not the DSSP result unless
you invoke this later (using calculate).

As far as I can interpret, the pdb file says beta strands for
Tyr350---Trp356
Cys370---Pro373

so  365-368  are not a beta strand





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Re: [Jmol-users] Java support in browsers

[Eric Martz]

Correction:

On 4/6/17 5:58 PM, Eric Martz wrote:
> Windows 10:  Firefox ESR, Pale Moon, Seamonkey, Maxthon (but see 
> caution about data sent to China by Maxthon at above link). I can't 
> test Waterfox because I don't have 64-bit Windows.
The correction is that Firefox ESR in Windows runs both the Jmol_S Java 
applet and JSmol from local files.

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Re: [Jmol-users] Java support in browsers

[Eric Martz]

Thanks, Henry! I did not know about unchecking "Run in safe mode" 
(hidden unless you hold down the option key). After doing that, I can 
run Jmol_S Java applet from local files (FirstGlance in Jmol) in Safari, 
which is convenient for testing while developing.


We list browsers that still support Java here:
http://proteopedia.org/w/Installing_and_enabling_Java#Browsers_That_Support_Java

Those that will run Jmol_S Java applet from local files are:
OS X: Waterfox, Seamonkey, Safari (fussy to configure, see above).
  Firefox ESR (see above link) maybe -- my system is unreliable for 
testing this for idiosyncratic reasons.


Windows 10:  Pale Moon, Seamonkey, Maxthon (but see caution about data 
sent to China by Maxthon at above link). I can't test Waterfox or 
Firefox ESR because I don't have 64-bit Windows.


All browsers that will run Jmol_S/Java applet from local files will also 
run JSmol from local files, with the exception of Maxthon.


Best regards, Eric


On 4/6/17 9:38 AM, Rzepa, Henry S wrote:

Apologies if my post-tracking is not up to scratch.  I have been silently 
grappling with  Java security policies on my own routine browser  Safari.  This 
browser, including the  “Safari technology preview”, the latest version of 
which was released only yesterday, still support the  browser plugin  API.

Each host does have to be individually enabled, and more than that  it has to 
be set to run in  “safe mode” if Java requires read/write access from local 
user directories. But having done that it is still supported, even in the 
future-looking technology preview version. I have documented it here for our 
own local use:https://wiki.ch.ic.ac.uk/wiki/index.php?title=It:jmol



On 29 Mar 2017, at 20:59, Angel Herráez  wrote:

(I'm following another thread started by David Hibbitts but this is a different
topic, so I changed the subject)

David,
May I ask what is the information you have regarding future support of Java
by Waterfox?


On 29 Mar 2017 at 15:14, David Hibbitts wrote:

It's hard to know how much any of us should invest in these java-specific 
issues given the aggressive nature of browsers toward javascript --
but my website really serves my research group, not the general public, and 
there I can certainly get the users to install Waterfox+JAVA.

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Re: [Jmol-users] rotate best? DOCUMENTATION

[Eric Martz]

Right! I did not have all atoms selected. I suggest a change "best 
orientation for viewing" to "best orientation for viewing the selected 
atoms". And change "the model's containing box" to "the containing box 
of the selected atoms". It never occurred to me to select all first. 
Also I had difficulty understanding "thinnest along the line of site". 
(It should be "line of sight"). I suggest "thinnest front to back".


Jean-Baptiste: do "select all" before you "rotate best".

Bob: Thanks!

-Eric

On 10/28/16 12:59 PM, Robert Hanson wrote:



On Fri, Oct 28, 2016 at 11:09 AM, Eric Martz 
<ema...@microbio.umass.edu <mailto:ema...@microbio.umass.edu>> wrote:


1. When I apply "rotate best" to 1d66, I expect the distance from the
frontmost to backmost atoms to be minimized, and the distance from the
leftmost to rightmost atoms to be maximized. Neither appears to
happen.
Do I misunderstand the goal?


works for me. What are you seeing? Do you have all the atoms selected?

" Rotates the model to a calculated "best" orientation for
viewing, such
that the model's containing box is thinnest along the line of site
(z),
and widest horizontally (x)."


That should read -- such that the box containing /the selected atoms/

When I apply "rotate best" to 3hyd (a linear peptide), the top to
bottom
distance seems to be minimized and the left to right maximized,
with the
front to back intermediate.

If "rotate best" is working properly, could someone please explain
it to me?

2. Are there any other commands that automatically rotate the model to
an optimal orientation? It appears to me that "moveto
front|top|bottom|left|right|back" relates to the initial (reset)
orientation, not to any "optimal" orientation.


Just that  one.

Thanks, Eric



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[Jmol-users] rotate best?

[Eric Martz]

1. When I apply "rotate best" to 1d66, I expect the distance from the 
frontmost to backmost atoms to be minimized, and the distance from the 
leftmost to rightmost atoms to be maximized. Neither appears to happen. 
Do I misunderstand the goal?

" Rotates the model to a calculated "best" orientation for viewing, such 
that the model's containing box is thinnest along the line of site (z), 
and widest horizontally (x)."

When I apply "rotate best" to 3hyd (a linear peptide), the top to bottom 
distance seems to be minimized and the left to right maximized, with the 
front to back intermediate.

If "rotate best" is working properly, could someone please explain it to me?

2. Are there any other commands that automatically rotate the model to 
an optimal orientation? It appears to me that "moveto 
front|top|bottom|left|right|back" relates to the initial (reset) 
orientation, not to any "optimal" orientation.

Thanks, Eric


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[Jmol-users] Protein sequence alignment display/analysis: MSAReveal.Org

[Eric Martz]

Apologies for this off-topic message which involves Jmol only 
tangentially, but will hopefully be of interest to some Jmol users.


Recently I wanted to view some FASTA format protein sequence alignments 
and was not able to find free software that made me happy. So I made


MSAReveal.Org (free, open source)

 * Paste in protein sequences or alignments in FASTA format.
 * Genus and species, gene names, and UniProt IDs are extracted from
   the headers and tabulated. UniProt IDs are linked to UniProt.
 * Checkboxes control coloring of amino acids/groups.
 * Touching an amino acid reports its 3-letter abbreviation and
   sequence number in a tooltip. You don’t have to memorize all 20
   one-letter amino acid codes.
 * The sequence listing can be horizontally scrolled, or wrapped at a
   specified number of amino acids.
 * A sequence numbering offset can be specified with “start=N” in the
   header of each sequence. A negative number enables numbering to
   start at 1 for the mature protein, after a negatively numbered
   signal sequence.
 * A consensus is reported with the frequencies of amino acids in each
   column.
 * Statistics are tabulated including lengths (excluding gaps),
   percentages identity, percentages in gaps, percentages charged,
   percentages aromatic, net charge at neutral pH, etc. etc..
 * Minimum, average, and maximum are given for each column in Statistics.
 * The Statistics Table can be sorted on any column.
 * A search mechanism finds and highlights sequence fragments/motifs
   regardless of gaps. It accepts multiple amino acid possibilities at
   a given position.
 * Search hits are listed with links so you can jump to any hit instantly.
 * Numerous irregularities or warnings are reported, including the
   ambiguous codes B, J, O, U, X, Z and illegal characters, which can
   be located easily with the search mechanism.
 * A description of each alignment, added to the first header, will be
   displayed.
 * A description of each sequence, added to its header, will be
   displayed when its taxon is touched.
 * A Protein Data Bank ID, when added to the header (e.g. “PDB=2ace”)
   will be tabulated and linked to display the 3D model in
   FirstGlance.Jmol.Org.

A more detailed overview with snapshots:
http://bioinformatics.org/msareveal/help.html#overview

Demonstration and test alignments are built in. Instructions are 
provided for downloading sequences from UniProt, and aligning them with 
free, easy, quick Jalview (using MAFFT, TCOFFEE, MUSCLE, etc.). Displays 
any FASTA alignments, e.g. from the ConSurf Server.  MSAReveal.Org works 
in all popular browsers, Windows or OS X. Tested up to a total of one 
million amino acids, and with alignments containing hundreds of sequences.


Sincerely, Eric

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Re: [Jmol-users] Java Applet Mouse problems in Firefox on MacOS 10.11.6

[Eric Martz]

Tested on OS 10.10.5 Yosemite, Java 1.8.0_101:

Jmol.jar: wheel zoom and 2 of the 3 mouse translation modes work. I 
can't get double click of wheel and drag to work but it might relate to 
some configuration of the wheel click on my system. Rolf said the mouse 
gestures work in the application. So I confirm this.


JSmol in Firefox 49.0: Same results as in the application. Rolf said all 
3 mouse gestures work in Firefox JSmol. I confirm two of them and the 
wheel zoom.


Eric


On 9/23/16 1:52 PM, Robert Hanson wrote:

1) What is the case in Jmol.jar (Java only, not browser)?
2) What is the case with JSmol (HTML5, not Java)?

This will help settle the issue of where the problem is coming from.



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Re: [Jmol-users] Java Applet Mouse problems in Firefox on MacOS 10.11.6

[Eric Martz]

Dear Rolf,

I confirm the failure of translation by mouse (all 3 methods) in Firefox 
with Java, and the failure of wheel zoom in Firefox or Safari (but yes 
translation is working in Safari+Java).


However, I tested in OS 10.10.5 *Yosemite*, with Java 1.8.0_*101*, 
Firefox 49.0, Safari *10.0*.


Zoom by Shift-Drag: works in Safari, NOT in Firefox.

Zoom by drag at right edge of Jmol_S window: works in both Firefox and 
Safari.


Let us sadly remember that Oracle has announced plans to deprecate the 
Java browser plugin in 1.9, and to discontinue the plugin at a future 
date. Also Firefox plans to discontinue Java browser plugin by the end 
of this year. See links at 
http://proteopedia.org/w/Installing_and_enabling_Java (Firefox link 
under "Alternatives").


I have been reluctant to upgrade from Yosemite to El Capitan.

On my main workstation, the Java plugin broke about a year ago for 
unknown reasons, during an upgrade of Java. Since then I have been 
unable to get Java to work in Firefox or Safari on that workstation 
(2014 MacBook Pro). I tried uninstalling and reinstalling Firefox and 
Java. Also I upgrade Java regularly. The Jmol application works, but not 
the plugin. Any suggestions welcome as this is quite frustrating! My 
tests above were on a 2013 Mac Mini.


Best regards, Eric

On 9/23/16 10:52 AM, Rolf Huehne wrote:

Hi all,

I recently upgraded the operating system of my MacBook from 'Mavericks'
to 'El Capitan' (10.11.6). This included also to upgrade Oracle Java to
1.8.0_102 and Firefox to 49.0.

In Firefox it is now impossible on my system to translate the model in
Jmol (14.6.3_2016.09.18, also earlier versions) with the mouse by any of
the mouse gestures described in the mouse manual
(http://wiki.jmol.org/index.php/MouseManual):
a) Shift + double-click and drag the main button
b) double-click and drag the middle button
c) Ctrl + drag the secondary button

It also doesn't work any more to bind 'translate' directly to dragging
of the middle button.

In Safari 9.1.2 all three mouse gestures still work. And in JSmol
(Javascript) they also work in Firefox.

In the Jmol application the mouse gestures also work.

In addition, the mouse wheel doesn't work for zooming in Jmol both in
Firefox and Safari. Instead the window is scrolled down. It also doesn't
help to click first into the applet window before using the mouse wheel.
But this already happened with Mavericks.

Kind regards,
Rolf

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Re: [Jmol-users] Java Applet Mouse problems in Firefox on MacOS 10.11.6

[Eric Martz]

Correction to my previous message:

On the Mac Mini I have NOT upgraded Java to 101. Those test results were 
with Java 1.8.0_*91*.


-Eric

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[Jmol-users] Crash attempting a compare

[Eric Martz]

Dear Bob,

I did an alignment using compare between two PDB files and it worked 
perfectly.

I attempted a very similar one and Jmol (July 11) freezes.

Easy to reproduce:

https://www.dropbox.com/s/q71q3vfdszyru9c/myosin_morph_Eric.zip?dl=0

Run the Jmol.jar in that folder (as file references are local).

Drop in align12.spt. All good and beautiful!

Drop in align01.spt. Freeze.

The only difference is the 2 PDB files employed.

Thanks, Eric


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[Jmol-users] show 1-letter sequence?

[Eric Martz]

How do I show the one-letter amino acid sequence? (without the sequence 
numbers, e.g. ready for a BLAST search)

I see 'show sequence' which reports 3-letter amino acid codes with 
sequence number.

I looked at 'getProperty' but did not spot what I need.

Thanks, Eric


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[Jmol-users] Write 2 PDB models?

[Eric Martz]

If I load 2 models, then "frame all; select all;", I expect that "write 
PDB" will write both models. Instead, the PDB file has MODEL/ENDMDL 
records for 2 models, but the first model contains no coordinates. Is 
this a bug or a feature?

load =3hyd
load append =4qxx
frame all

select all

write "test.pdb"


Thanks, Eric


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Re: [Jmol-users] Rename chain?

[Eric Martz]

Interesting idea, Angel. But part of my purpose is to be able to create 
crystal symmetry PDB files that can be handled by FirstGlance as it is. 
It assumes that each chain has a different name and many of its tools 
are coded under that assumption.

With all the other power in Jmol, it seems reasonable to me that chains 
could be renamed.


On 6/22/16 6:19 PM, Angel Herráez wrote:
> Eric,
>
> You could use variables that you assign and then select by those
>
> e.g.
> chainA = {chain=A and 1.1}
> chainB = {chain=B and 1.1}
> chainC = {chain=C and 1.1}
> chainG = {chain=A and 2.1}
> chainH = {chain=B and 2.1}
> chainI = {chain=C and 2.1}
>
> then
> select chainG
>
>
>
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Re: [Jmol-users] Rename chain?

[Eric Martz]

Dear Bob,

Like Angel, I'm a little unsure what your reply means.

Is there no way to change the chain name assigned to specified atoms?

If not, I think it would be very useful.

-Eric


On 6/22/16 12:37 PM, Robert Hanson wrote:

Yes, sorry,  that's a failure to throw an error. Fixed.



On Sun, Jun 19, 2016 at 8:43 PM, Eric Martz <ema...@microbio.umass.edu 
<mailto:ema...@microbio.umass.edu>> wrote:


How do I change the name of a chain from e.g. A to B?

For example, I load chain A, then load append the same chain A, then
translate selected 2.1.

I would rather refer to the translated chain as chain=B than (chain=A
and 2.1). (This is a simple example but the actual case I have in mind
has two copies of six chains. Also the existing code in FirstGlance
knows about chain names but is limited to model 1.)

In the atom properties table, chain is not assignable.

{chain=a and 2.1}.chain = g # or "g"

does not generate an error, but afterwards, "select chain=g" gets zero
atoms.

Thanks, -Eric



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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] Rename chain?

[Eric Martz]

How do I change the name of a chain from e.g. A to B?

For example, I load chain A, then load append the same chain A, then 
translate selected 2.1.

I would rather refer to the translated chain as chain=B than (chain=A 
and 2.1). (This is a simple example but the actual case I have in mind 
has two copies of six chains. Also the existing code in FirstGlance 
knows about chain names but is limited to model 1.)

In the atom properties table, chain is not assignable.

{chain=a and 2.1}.chain = g # or "g"

does not generate an error, but afterwards, "select chain=g" gets zero 
atoms.

Thanks, -Eric


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Re: [Jmol-users] updating SpectralZoo pages

[Eric Martz]

New versions of JSmol are supposed to be backwards compatible. There are 
very few intentional changes that require changes in the JSmol command 
scripts, generally quite minor.


It would be good to "set debugscript on" and see where the errors occur.

If you are still stumped, copy the error reports into an email and maybe 
someone on this list will have a suggestion.


If you have loops in your JSmol commands (for or while), I think some 
older syntaxes may not work. Check the manual.


http://chemapps.stolaf.edu/jmol/docs/

Good luck! -Eric


On 6/9/16 3:30 PM, Jennifer L. Muzyka wrote:
We recently got a new server to host the SpectralZoo 
(http://chemserv.centre.edu/muzyka/spectralzoo), with new versions of 
PHP and MySQL.  Some of my SpectralZoo scripts broke, so I thought it 
might be time to upgrade the Jmol (actually JSmol) that I’m using on 
the site.  I see even more errors, and I’m stumped about how to solve 
them.  It looks like I was previously using a version of Jmol from 
11/2013.  Can someone point me to something to read to help me sort 
out the changes so that I can manage the troubleshooting?  (Clearly I 
have been away from programming for too long…..)  I would appreciate 
any advice you can offer or articles you can point me towards.  Thanks.

Jennifer








Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu 
http://web.centre.edu/muzyka
http://organicers.org

859-238-5413
fax 859-236-7925








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[Jmol-users] A little history

[Eric Martz]

ire learning and 
remembering command language. Then users can concentrate on the 
molecules, rather than the software.


Granted, developing such resources takes a great deal of time. Hopefully 
you can find some gems for organic chemistry in the wiki list Websites 
Using Jmol <http://wiki.jmol.org/index.php/Websites_Using_Jmol>.


-Eric

On 6/1/16 8:38 PM, John Keller wrote:


Hi Eric,

 Thanks for the links.  I have a lot of experience with elementary 
level Jmol (Windows versions) for teaching applications in organic and 
general chemistry. Jmol can be intimidating, especially since it seems 
to be under continual development with changing features and commands 
that work in some versions and not in others (such as “bondorder”). 
However, the average computer-savvy, Mac-using chemistry teacher 
should be able to use a subset of commands to illustrate small 
molecules in various ways for themselves, and for their students.


I am giving a workshop on Web Based Molecular Modeling at the 
American Chemical Society Northwest Regional meeting (NORM2016) in 
about a month. The main emphasis will be on how to use WebMO, Jmol and 
other free or low cost resources in teaching HS and college general 
chemistry. I will mention your excellent sites in the context of 
bio-molecule visualization.


After I sent my email to the list, I did find a page where someone 
described how to create a OS X package that will install just like a 
something from the App Store. I just bought an older Mac so I will be 
able to speak the Apple lingo with teachers at this workshop!


John Keller

University of Alaska Fairbanks

Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for 
Windows 10


*From: *Eric Martz <mailto:ema...@microbio.umass.edu>
*Sent: *Wednesday, June 1, 2016 1:25 PM
*To: *jmol-users@lists.sourceforge.net 
<mailto:jmol-users@lists.sourceforge.net>

*Subject: *Re: [Jmol-users] Jmol for mac installation

Dear John,

Jmol, by itself, is challenging to use for most purposes. It has an 
extensive command language with thousands of commands and 
permutations. Therefore many people, myself included, have created 
explanations or tutorials that show molecules using Jmol, but are much 
easier to use, with built-in help that is lacking in Jmol per se.


Examples are

  * http://biomodel.uah.es/en/model3 (Carbohydrates, Lipids, Vitamins,
Proteins, Nucleic Acids)
  * http://MolviZ.Org (DNA, hemoglobin, antibody, water, lactose
repressor, collagen, etc.)
  * http://Proteopedia.Org has many articles with interactive molecule
in Jmol. Use the search slot, or browse lists at:
  * http://proteopedia.org/w/High_school_teachers%27_resources
  * 
http://proteopedia.org/w/Teaching_Scenes%2C_Tutorials%2C_and_Educators'_Pages

<http://proteopedia.org/w/Teaching_Scenes%2C_Tutorials%2C_and_Educators%27_Pages>

For general exploration of any macromolecule, I believe 
http://FirstGlance.Jmol.Org is easiest (disclosure of possible bias: I 
wrote the user interface) but it is designed for research or 
specialized study. If you want to give students access to specific 
molecules not available in existing tutorials, you can make your own 
web page with links that show the molecule in FirstGlance, or your own 
page in Proteopedia.Org.


To answer your question:

Jmol is not, as far as I know, available in the Apple Store. You 
download it free from http://Jmol.org.


Jmol is available as a stand-alone application (Jmol.jar). It has 
almost no built-in help. To do more than see the initial view of a 
molecule, you need to use the menu (complicated, no help) or learn the 
commands. Yes, you can drop it onto the Mac Dock (on the right end).


The resources I listed above, designed for students and educators, all 
work in a web browser, using the plug-in form of Jmol (JSmol or the 
Java applet). For those, all you need is a bookmark or link. Nothing 
needs to be installed, except Java which is not necessary for most 
purposes.


Please don't hesitate to ask if we can help.

-Eric

On 6/1/16 3:41 PM, John Keller wrote:

Hi All,

I don't see Jmol in the Apple App Store. Is there an easy way for
a Mac user, such as a high school teacher, to install Jmol on
their OS X machine? Hopefully this would place the Jmol icon on
the toolbar too.

John Keller





Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- Martz.MolviZ.Org <http://Martz.MolviZ.Org>

 * Top Five 3D MolVis Tools: Top5.MolviZ.Org <http://top5.MolviZ.Org>
 * FirstGlance: 3D Molecules in /Nature/: FirstGlance.Jmol.Org
   <http://firstglance.jmol.Org>
 * Protein 3D Structure Wiki: Proteopedia.Org <http://proteopedia.Org>
 * Education: Biochem in 3D at MolviZ.Org <http://MolviZ.Org>
 * Find Functional Patches in Proteins: ConSurf <http://consurf.tau.ac.il>
 * Atlas of Macromolecules: Atlas.MolviZ.Org <http://atlas.MolviZ.Org>
 * Interactive M

Re: [Jmol-users] Jmol for mac installation

[Eric Martz]

Dear John,

Jmol, by itself, is challenging to use for most purposes. It has an 
extensive command language with thousands of commands and permutations. 
Therefore many people, myself included, have created explanations or 
tutorials that show molecules using Jmol, but are much easier to use, 
with built-in help that is lacking in Jmol per se.


Examples are

 * http://biomodel.uah.es/en/model3 (Carbohydrates, Lipids, Vitamins,
   Proteins, Nucleic Acids)
 * http://MolviZ.Org (DNA, hemoglobin, antibody, water, lactose
   repressor, collagen, etc.)
 * http://Proteopedia.Org has many articles with interactive molecule
   in Jmol. Use the search slot, or browse lists at:
 * http://proteopedia.org/w/High_school_teachers%27_resources
 * http://proteopedia.org/w/Teaching_Scenes%2C_Tutorials%2C_and_Educators'_Pages

For general exploration of any macromolecule, I believe 
http://FirstGlance.Jmol.Org is easiest (disclosure of possible bias: I 
wrote the user interface) but it is designed for research or specialized 
study. If you want to give students access to specific molecules not 
available in existing tutorials, you can make your own web page with 
links that show the molecule in FirstGlance, or your own page in 
Proteopedia.Org.


To answer your question:

Jmol is not, as far as I know, available in the Apple Store. You 
download it free from http://Jmol.org.


Jmol is available as a stand-alone application (Jmol.jar). It has almost 
no built-in help. To do more than see the initial view of a molecule, 
you need to use the menu (complicated, no help) or learn the commands. 
Yes, you can drop it onto the Mac Dock (on the right end).


The resources I listed above, designed for students and educators, all 
work in a web browser, using the plug-in form of Jmol (JSmol or the Java 
applet). For those, all you need is a bookmark or link. Nothing needs to 
be installed, except Java which is not necessary for most purposes.


Please don't hesitate to ask if we can help.

-Eric

On 6/1/16 3:41 PM, John Keller wrote:

Hi All,
I don't see Jmol in the Apple App Store. Is there an easy way for a 
Mac user, such as a high school teacher, to install Jmol on their OS X 
machine? Hopefully this would place the Jmol icon on the toolbar too.

John Keller




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[Jmol-users] Animations from FirstGlance in Jmol

[Eric Martz]

I have just released a new version of FirstGlance in Jmol 
 with the ability to save static images or 
presentation-ready multi-GIF animations. I have tried to make a 
user-friendly interface that can save these in just a few clicks, with 
optimal defaults. I welcome feedback from anyone who tries it out.


You can see some example animations in

 * Google Slides
   

   or
 * Downloadable Powerpoint
   

   (both sets of slides have the same content)

In order to simplify things, FirstGlance uses 'canned' rendering and 
color schemes. It does not have tools for customizing the rendering and 
colors. Customization in JSmol can be done most easily with the /Scene 
Authoring Tools /built into Proteopedia.Org (see its Video Guide 
). Once 
you customize a molecular scene in Proteopedia, it is immediately 
available to share with anyone anywhere.


Any scene in Proteopedia (or on any Jmol web page) can be saved as a 
presentation animation. You just open the Jmol Console, write a PNGJ 
file, drop that into FirstGlance, and proceed to use the Save Animation 
tool in FirstGlance. (If you know how to use the 'capture' command in 
Jmol, you don't need to use FirstGlance, of course.) See Instructions 
.


Thanks to Bob Hanson for the amazing 'capture' command, which even more 
amazingly saves files to your local disk from JSmol or Jmol_S in a web 
browser. Thanks to Angel Herraez for help along the way, and to everyone 
in the Jmol team!


-Eric

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Re: [Jmol-users] Hide unitcell text?

[Eric Martz]

Thank you Angel! That works!

-Eric


On 5/30/16 5:52 AM, Angel Herráez wrote:
> Dear Eric
> I think it's this:
>
> set displayCellParameters false
>
>
>
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[Jmol-users] Hide unitcell text?

[Eric Martz]

I use

load "" {555 555 1} range -7.0;

to show crystal contacts. That command automatically displays unit cell 
parameters and space group as text in the upper left corner of Jmol. It 
looks like an echo but

set echo off

does not hide it. I would appreciate some way to hide/display that text. 
This is not high priority but would be nice. Ideally it could be a named 
echo enabling something like

set echo unitcellparameters hidden

Thanks, Eric


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Re: [Jmol-users] capture hermitelevel full quality

[Eric Martz]

That works! Thanks Bob and Angel!


On 5/27/16 1:39 AM, Robert Hanson wrote:

sure enough -- I forgot about that:

int val1 = vwr.getHermiteLevel();
val1 = (val1 <= 0 ? -val1 : vwr.getInMotion(true) ? 0 : val1);

Thus, hermite level is set to 0 only if the value is positive and the 
model is in motion. But during spinning (which includes capture) we have;


  public int getHermiteLevel() {
return (tm.spinOn ? 0 : g.hermiteLevel);
  }

changing that to:

  public int getHermiteLevel() {
return (tm.spinOn  && g.hermiteLevel > 0 ? 0 : g.hermiteLevel);
  }

​does the trick. Thank's Angel!

Have released that as Jmol 14.6.0_2016.05.26, though it might also 
read Jmol 14.6.0_2016.05.24 -- so I guess that is being overwritten. 
But it does have this fix in it.


*Download Jmol-14.6.0_2016.05.24-binary.zip (66.4 MB) 




*


Bob



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Re: [Jmol-users] capture hermitelevel full quality

[Eric Martz]

Dear Angel,

No I was NOT aware of the minus trick for hermitelevel. Indeed, that 
preserves full quality during mouse rotation, but not during capture.

Bob: perhaps all that is needed then is to extend the minus hermitelevel 
trick to the capture command.

Thanks Angel!

-Eric


On 5/26/16 2:19 PM, Angel Herráez wrote:
> Dear Eric
>
>> Currently, rendering is simplified (even at platformSpeed 10) during
>> rotation.
> Are you aware that using negative values in hermitelevel does NOT simplify
> the rendering during mouse rotation? I wonder if that's also the case for
> automated rotation like in capture
>
>
>
>
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[Jmol-users] capture hermitelevel full quality

[Eric Martz]

Dear Bob,

I would like to request a new setting that enables multi-GIFs captured 
for presentations to show the full beauty of non-zero hermitelevels, 
antialiased.

Currently, rendering is simplified (even at platformSpeed 10) during 
rotation. This is good. But when using "capture", speed is much less 
important than getting the best quality animation for a presentation.

Please see this example:
https://docs.google.com/presentation/d/1AJwD1Sb05nSUsGt9KSAhMIoMR0HptS1ntwTjZDayMRw/edit?usp=sharing

Perhaps not simplifying should simply be the default (and the only 
option) for "capture"?

-Eric

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Re: [Jmol-users] hermiteLevel vs. cartoon bug

[Eric Martz]

Thank you Bob. The May 24 version seems to work as desired regarding 
hermitelevel.


Also in comparing, I noticed that with hermitelevel on in the May 17 
version, at high zoom, JSmol essentially freezes when you try to rotate. 
The May 24 version rotates at reasonable speed, even with antialiasing on.


Eric

On 5/24/16 10:21 PM, Robert Hanson wrote:
anyway, I think it's fixed. It wasn't totally coming out of 
hermiteLevel 4 when the level was set to 0.



​


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Re: [Jmol-users] jmolScriptWait() vs. symmetry loading

[Eric Martz]

OK thanks for the heads up!


On 5/24/16 9:27 PM, Robert Hanson wrote:
Eric, I do see that it takes an oddly long time to load a file using 
scriptWait (5 seconds instead of instantaneously). I don't know what 
that is about, but it suggests you should not use scriptWait for 
loading a file, if possible.



Bob
​


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[Jmol-users] jmolScriptWait() vs. symmetry loading

[Eric Martz]

This is merely FYI:

When sent with jmolScript*Wait*(), the following commands work in 
JSmol/HTML5 but not in Jmol_S/Java:


load "" {555 555 1} range -7.0; # loads asymmetric unit plus crystal contacts 
within 7.0 Angstroms

load "" {1 1 1}; # loads unit cell

They work fine in Jmol_S/Java when sent with jmolScript().

When sent with jmolScriptWait(), the result is:

script ERROR: java.security.AccessControlException: access denied 
("java.net.SocketPermission" "www.pdb.org:80" "connect,resolve")


 load "" { 1 1 1 }
or
 load "" { 555 555 1 } range -7.0

-Eric
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[Jmol-users] Unit cell, axes bug/feature?

[Eric Martz]

Dear Bob,

In JSmol December 23 2015 (and earlier) the following commands do NOT 
display the unit cell nor axes:

load "" {555 555 1} range -7.0;

load "" {1 1 1};

In JSmol May 17, 2016 these commands display the unit cell and axes.

Is this an intentional change?

Its easy enough to turn the unit cell/axes off if it is intentional.

Thanks, Eric


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Re: [Jmol-users] Jmol_S crash by set picking center in FirstGlance only

[Eric Martz]

Dear Bob,

Thanks for pointing me to investigate pickCallBack.

The problem was that clicking an atom in "set picking center" mode was 
sending, via pickCallBack, an otherwise innocuous script via 
jmolScript*Wait*().


This crashed the Java applet but created no problem for JSmol/HTML5.

Once I coded to use jmolScript() (no Wait) while in "set picking center" 
mode, the problem was solved.


jmolScriptWait() did solve another problem earlier, and generally seems 
to me a good idea, so I use it by default for all scripts in 
FirstGlance, with certain exceptions (such as zoomto and now "set 
picking center").


Whew! Thanks again!

Eric

On 5/23/16 12:09 AM, Robert Hanson wrote:
Check your callback function. Perhaps it is hanging in that. I think 
it is jmolPickCallback


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[Jmol-users] hermiteLevel vs. cartoon bug

[Eric Martz]

Dear Bob,

I think there is a bug regarding hermiteLevel vs. cartoon.

In the May 17 (or Feb 18) application:

print hermitelevel # reports default zero

load =4qxx

cartoon only # now I see a "rope" as expected

set hermitelevel 4 # rope turns to flat rendering with elbows when rotated

set hermitelevel 0 # flat rendering with elbows even when stationary

trace only # rope is back and remains solid when rotated

cartoon only # unwanted flat elbows are back even when stationary

-Eric


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[Jmol-users] platformSpeed DOCUMENTATION

[Eric Martz]

I am confused about platformSpeed.

1. Documentation says maximum value is 8, but default value is 10 since 
earlier than last December.

2. Does JSmol do any automatic detection of the platform and set 
platformspeed to lower values on e.g. mobile devices?

Bob, could you please update the docs? Thanks,

Eric


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Re: [Jmol-users] measure label flapping

[Eric Martz]

Switching positions is fine. But in the neighborhood of the switch, it 
flaps back and forth. Not a biggie, but would be distracting in a 
multi-gif from capture.



On 5/23/16 12:01 AM, Robert Hanson wrote:
just the way it is, I think. It has to switch positions so as to be 
aligned properly.


On Sun, May 22, 2016 at 2:53 PM, Eric Martz <ema...@microbio.umass.edu 
<mailto:ema...@microbio.umass.edu>> wrote:


The flapping of labels on angle measures also occurs in Jmol April 22
and December 23.

It would be especially annoying in a captured spin or rocking
multi-gif.


On 5/22/16 3:48 PM, Eric Martz wrote:
> In Jmol May 17, the labels on angles "flap" during rotation.
>
> I did not compare with earlier versions of Jmol.
>
> Demo: At http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
>
> (Is there a way to specify an earlier Jmol version here?)
>
> With caffeine in the reset position
>
> measure 14 5 2
>
> now turn on spinning and watch the 41.1 degree angle label. At
certain
> angles of rotation, it "flaps" back and forth.
>
> Minor but annoying.
>
> -Eric
>
>
>

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it is better to take what answer we get.

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[Jmol-users] Jmol_S crash by set picking center in FirstGlance only

[Eric Martz]

Dear Bob,

I have run out of ideas for debugging the following problem. Perhaps you 
can help?


After I start FirstGlance using Java

http://bioinformatics.org/firstglance/fgij/fg.htm?mol=1d66

if I open the Jmol Console and enter

*set picking center*

and then *c**lick on an atom*, Jmol_S freezes/crashes.

This happens in Windows 7/Firefox and also in OS X/Safari.

This happens with Jmol_S May 17, April 21, and December 23 (in FirstGlance).

There is no error message with set debugscript on, nor in the Java console.

This bug does *not* happen in JSmol/HTML5 mode.

This bug does *not* happen in the Jmol application.

I cannot reproduce this using

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

Even when I drop the FirstGlance initial state into stolaf:Jmol_S (via 
state script or pngj) and then set picking center in the Console, click 
on atom, there is no problem.


I notice that, after entering "set picking center" but before clicking 
an atom, and saving a state script or pngj, the saved files do NOT set 
picking to center. "Show picking" reports picking="identify". Nor do I 
find any mention of picking or center in the state script commands. This 
may be a bug in state scripts, but it is not the freezing/crashing bug I 
am trying to isolate.


Any help would be much appreciated!

Thanks, Eric

P.S. The public version of FirstGlance linked above uses Jmol from 
_December 23_. There is a private under-development version of 
FirstGlance using Jmol _May 17_ at


http://bioinformatics.org/firstglance/fgi*x*/fg.htm?mol=1d66

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Re: [Jmol-users] measure label flapping

[Eric Martz]

The flapping of labels on angle measures also occurs in Jmol April 22 
and December 23.

It would be especially annoying in a captured spin or rocking multi-gif.


On 5/22/16 3:48 PM, Eric Martz wrote:
> In Jmol May 17, the labels on angles "flap" during rotation.
>
> I did not compare with earlier versions of Jmol.
>
> Demo: At http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
>
> (Is there a way to specify an earlier Jmol version here?)
>
> With caffeine in the reset position
>
> measure 14 5 2
>
> now turn on spinning and watch the 41.1 degree angle label. At certain
> angles of rotation, it "flaps" back and forth.
>
> Minor but annoying.
>
> -Eric
>
>
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[Jmol-users] measure label flapping

[Eric Martz]

In Jmol May 17, the labels on angles "flap" during rotation.

I did not compare with earlier versions of Jmol.

Demo: At http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm

(Is there a way to specify an earlier Jmol version here?)

With caffeine in the reset position

measure 14 5 2

now turn on spinning and watch the 41.1 degree angle label. At certain 
angles of rotation, it "flaps" back and forth.

Minor but annoying.

-Eric


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Re: [Jmol-users] JmolApplet.jar

[Eric Martz]

Dear Bob,

1. Is JmolApplet.jar the /unsigned/ applet? I don't mind dropping 
that from the distribution.


2. JSmol/HTML5 is truly a life-saver! Bless you Bob and the other team 
members for JSmol! For most entries in the PDB, it is perfectly 
satisfactory and it is the default in FirstGlance.Jmol.Org.


Nevertheless, I consider JmolAppletSigned.jar to be essential. It is 
essential for NMR ensembles and large models. It gives much smoother 
rotation and faster operation for just about everything. 
FirstGlance.Jmol.Org has a checkbox and a preference setting (cookie) 
and a query parameter option to use Java.


I am close to releasing a new version of FirstGlance that includes a 
button to save a rocking or rotating animation (using 'capture'). In the 
default HTML5 mode, with high quality on (antialiasdisplay), it can take 
several minutes (even more on older computers or mobile devices) to 
generate the multi-GIF file. Generation is more than ten-times faster 
using the signed Java applet.


I will be quite upset if/when Oracle actually stops providing a Java 
browser plugin, at which time no Java applet will work, see the pink box at


http://proteopedia.org/w/Installing_and_enabling_Java

Best regards, Eric


On 5/18/16 1:04 AM, Robert Hanson wrote:

Two questions:

1. What would you think of dropping JmolApplet.jar from the 
distribution?

2. How about JmolAppletSigned.jar?

Could these, perhaps be in a separate zip for download, perhaps 
JmolAppletJava.zip?


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[Jmol-users] DOCUMENTATION set echo

[Eric Martz]

Dear Bob,

Under "set echo"

section "scaling"

Is a red link to "set fontScaling true" but the link incorrectly goes to 
"#setmisc".

It should go to "#setlabels".

Thanks, Eric


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[Jmol-users] Message/print echo text?

[Eric Martz]

Is there a way to message or print (or show) the text currently 
displayed at a named echo position?


For example, something like

   set echo top left

   echo "1d66"

   message echo top

but that message command doesn't work and I haven't found a method.

Of course I can keep what I echo in a variable and use that, but before 
I code it that way, I wondered if there is a more direct method.


Thanks, Eric

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[Jmol-users] request: slabByAtom false for "slab set"

[Eric Martz]

Dear Bob,

"slab set" will be very useful to convey to novices what "slab on" is doing.

It would be more useful if the cut face would remain flat (cutting 
through some atoms) rather than removing cut atoms, leaving only 
spherical atoms inside the cut plane.

That is, could "set slabByAtom false" be made to apply to "slab set", 
please?

Thanks, Eric

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[Jmol-users] capture resets slab :(

[Eric Martz]

"capture" appears to reset slab. This is frustrating since I was 
anticipating a marvelous animation showing the internal cavity of a 
proteasome (rocking).

Tested with Valentine's Day Jmol app.

load =1d66
slab 50
slab on
slab set
capture "x.gif" rock 45

-Eric


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[Jmol-users] slab vs. visible?

[Eric Martz]

$ load =1d66
select all # FIRST SELECT
slab 50
depth 50
slab on
slab set
depth set
select visible # SECOND SELECT
TRANSCRIPTION/DNA 06-MAR-92   1D66
DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX
found biomolecule 1: D, E, A, B
1D66

1762 atoms selected
1762 atoms selected # I was hoping for far fewer!
$
-
1. Test was with the Valentine's Day Jmol app.

2. I was hoping that atoms rendered invisible by slab would not be 
selected with "select visible". But the invisible atoms are selected. 
*Can this be fixed?*


I wanted to make the slab-visible atoms opaque and the slab-invisible 
atoms translucent. (Is there another way to do this?)


3. I just "discovered" slab set and depth set, which make the *slab of 
visible atoms rotate together with the slab planes* (the slab planes 
rotate too!). This is FANTASTIC! I have wanted this for years, but 
didn't realize (or forgot, quite likely) it was implemented, and so easy 
to use! It will be so useful in explaining to novices what slab is doing.


4. When the above commands are entered one by one manually, the result 
is correct. When the above commands are pasted into the application 
console as a single script, the *slab 50 fails* to work. Only depth 50 
works. This would seem to be a bug.


-Eric
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[Jmol-users] cyclic peptide trace?

[Eric Martz]

1hvz is a cyclic 18 amino acid peptide with a peptide bond between 
residues 1 and 18. JSmol shows a break in the cartoon/trace/backbone 
between 1 and 18, but in wireframe, shows the peptide bond. Is the break 
in cartoon/trace/backbone a bug or a feature? -Eric



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Re: [Jmol-users] Mouse-slabbing in JSmol on Mac

[Eric Martz]

In FirstGlance, I changed the key binding for dragging the entire slab 
with this Jmol command:


bind "ALT+SHIFT+LEFT+drag" _slabAndDepth;

The help panel that appears when you depress the Slab button in 
FirstGlance includes


*"Drag the slab*: hold down ALT and SHIFT, then click and drag up and down."

-Eric

On 1/31/16 3:12 PM, Frieda Reichsman wrote:

Hi All,

On the Jmol Wiki mouse manual page 
, Ctrl+Shift activates 
mouse slabbing (after the 'slab on' command is issued). It works for 
me in the Java application, but is JSmol, it doesn't. As suggested on 
the wiki, I tried pressing the mouse button first, then the Ctrl Shift 
keys, then drag, but this produces only rotation.


Anyone know how to get this to work on Mac?

Frieda


//

Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
USA

//








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[Jmol-users] make isomesh lines closer?

[Eric Martz]

The script below generates isomeshes that look like this:


Is there some way to make the lines in the isomesh closer together (more 
lines per Angstrom), or the sizes of triangles/squares in solid surfaces 
smaller? (This is what we thought 'resolution' might have done.)


BEGIN SCRIPT

zap
background black

load =1s8j

select ret
wireframe only
wireframe 0.22
hide not selected
center ret
zoom 450

# GENERATE ISOSURFACE FROM CCP4 MAP 

isosurface s1 minset 20 rmsd 2.0 sign pink lightgreen within 2.5 {ret} 
insideout "1s8j_diff.mFo-DFc.ccp4.gz" mesh nofill;


END OF SCRIPT

If you want to try the above script, you can download the ccp4.gz 
difference electron density map here:

https://www.dropbox.com/s/dt7wmuyjdr6fgh6/1s8j_diff.mFo-DFc.ccp4.gz?dl=0

-Eric (& Frieda)

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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

--
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University of Massachusetts, Amherst MA US
Martz.MolviZ.Org <http://Martz.MolviZ.Org>
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[Jmol-users] DOCUMENTATION capture

[Eric Martz]

Bob, please correct this

 capture "filename" ROCK degrees axis

to this

 capture "filename" ROCK *axis degrees

*Thanks, Eric*
*
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[Jmol-users] write x.png: frank gone

[Eric Martz]

The command

write x.png

saves the image but when saved from a browser, the orange JSmol and red 
Jmol_S franks are not in the image. Is there a setting to permit the 
frank to remain in the image?

When saved from the application, the gray "Jmol" frank remains in the image.

(I have tested JSmol releases from Dec 23, Jan 9, Jan 15).

I would like the frank to remain in the image by default so that images 
saved from FirstGlance and shown in presentations will advertise Jmol.

Thanks, Eric

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Re: [Jmol-users] Average of two XYZ coordinate sets?

[Eric Martz]

Thank you Rolf! Wow, I thought it would be much simpler! Something like

z = {x, y}.average
or
z = average({x}, {y})

I was sure I was missing something simple.
I would never have figured this out without your help!
-Eric

On 1/16/16 8:31 PM, Rolf Huehne wrote:
> Am 17.01.16 um 00:23 schrieb Eric Martz:
>> x = {gly6:a}.xyz
>> y = {asp13:a}.xyz
>>
>> How do I get one set of XYZ coordinates that is the average of x and y?
>>
> The following provides the individual averages of the x,y and z
> coordinates as a new coordinate set:
>
>  Example 
> load =1deh;
> x={1:A}.xyz;
> y={2:A}.xyz;
> ax = [x.x,y.x].average;
> ay = [x.y,y.y].average;
> az = [x.z,y.z].average;
> a = point(ax ay az);
> show x;
> show y;
> show a;
>
>  Example output -
> x = {16.2048337 12.8088332 2.9686667}
> y = {14.445142857142857 10.353857142857143 0.37728571428571434}
> a = {15.324988095238098 11.581345238095238 1.6729761904761906}
> -
>
> Eric, is that what you want?
>
> Regards,
> Rolf
>
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[Jmol-users] Average of two XYZ coordinate sets?

[Eric Martz]

x = {gly6:a}.xyz
y = {asp13:a}.xyz

How do I get one set of XYZ coordinates that is the average of x and y?

Thanks, Eric

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[Jmol-users] Future of write, capture from browser?

[Eric Martz]

Dear Bob and Jmol development team,

You have made no comment to the contrary, so unless I hear otherwise I 
am going to proceed developing code for FirstGlance that assumes there 
is no plan to block 'write' and 'capture' operations in JSmol/HTML5 or 
Jmol_S/Java.

Currently they do work (in some but not all browser/OS combinations).

This will enable buttons in FirstGlance to save images or animations of 
the current molecular view. I think that will be quite exciting, despite 
the generation of animations in JSmol/HTML5 being slow. People will be 
willing to wait.

-Eric

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Re: [Jmol-users] Saving files from JSmol

[Eric Martz]

Dear Bob,

I have updated the JSmol in my graphics saving test
http://bioinformatics.org/firstglance/fgix/
to your January 9 update.

When using *Java*: clicking "Save Image or Animation for Powerpoint" and 
then the button "Save Image":


I believe that the Jmol java applet is generating this 'canceled' 
message. It comes back via messagecallback.


script ERROR: canceled

 <<

Re: [Jmol-users] how to parse JSON data within Jmol

[Eric Martz]

Dear Angel (and everyone),

For years I have wanted a way to find out (in javascript or in JSmol) 
the number of atoms (or molecular weight) of a PDB entry before 
attempting to load it into JSmol. But I have not known how to do this.

If you know, please send me a sample of the code.

When the size exceeds a threshold, I would load only alpha carbons.

Already, for JSmol, I load only model 1 (in FirstGlance). Luckily this 
works when there is only one model; and it prevents JSmol from freezing 
with NMR ensembles of multiple models. But I do not know how to 
determine the number of models in an entry before attempting to load it.

Regards, Eric

On 1/12/16 1:10 PM, Angel Herráez wrote:
> Excellent!
>
> Thanks a lot, Rolf
>
>


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Re: [Jmol-users] how to parse JSON data within Jmol

[Eric Martz]

Thanks, Otis,

But I need to know BEFORE I load the model(s).
I envision this as being a two-step process.
Given a PDB code, first query to find out the weight or number of atoms 
and number of models.
Then decide how to load:
-all atoms, all models?
-all atoms, model 1 only?
-alpha carbons and nucleic phosphorus atoms only?
-(for extremely large models) every third alpha carbon?

And the decision would depend on whether using JSmol or Jmol_S.
See e.g.
http://proteopedia.org/wiki/index.php/Jmol/Visualizing_large_molecules 
(written in 2011, needs updating).

-Eric

On 1/13/16 1:44 PM, Otis Rothenberger wrote:
> Eric,
>
> alert(Jmol.evaluateVar(jmolApplet0, "{*}.size”))
>
> should do the trick.
>
> Otis
> --
> Otis Rothenberger
> o...@chemagic.org
> http://chemagic.org
>
>> On Jan 13, 2016, at 1:37 PM, Eric Martz <ema...@microbio.umass.edu> wrote:
>>
>> Dear Angel (and everyone),
>>
>> For years I have wanted a way to find out (in javascript or in JSmol)
>> the number of atoms (or molecular weight) of a PDB entry before
>> attempting to load it into JSmol. But I have not known how to do this.
>>
>> If you know, please send me a sample of the code.
>>
>> When the size exceeds a threshold, I would load only alpha carbons.
>>
>> Already, for JSmol, I load only model 1 (in FirstGlance). Luckily this
>> works when there is only one model; and it prevents JSmol from freezing
>> with NMR ensembles of multiple models. But I do not know how to
>> determine the number of models in an entry before attempting to load it.
>>
>> Regards, Eric
>>
>> On 1/12/16 1:10 PM, Angel Herráez wrote:
>>> Excellent!
>>>
>>> Thanks a lot, Rolf
>>>
>>>
>>
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Re: [Jmol-users] how to parse JSON data within Jmol

[Eric Martz]

That looks wonderful, Rolf.
I'll let you know after I try it.
Thanks so much!!
-Eric

On 1/13/16 2:28 PM, Rolf Huehne wrote:
> On 01/13/2016 08:22 PM, Rolf Huehne wrote:
>> On 01/13/2016 07:37 PM, Eric Martz wrote:
>>> Dear Angel (and everyone),
>>>
>>> For years I have wanted a way to find out (in javascript or in JSmol)
>>> the number of atoms (or molecular weight) of a PDB entry before
>>> attempting to load it into JSmol. But I have not known how to do this.
>>>
>>> If you know, please send me a sample of the code.
>>>
>>> When the size exceeds a threshold, I would load only alpha carbons.
>>>
>> Eric, as you might have expected, you could do it by using the PDBE API
>> that Angel used within his question.
>>
>> The following function needs as a parameter the PDB code (lower-case!)
>> and would return the combined molecular weight of all molecules.
>> It will only work for asymmetric units. (If you would build up a
>> biological unit within Jmol more information would be needed.)
>>
>> --- Jmol function --
>> function getPdbEntryWeight(pdbId) {
>>  var weight = 0;
>>
>>  if (pdbId != "") {
>>var queryUrl = "http://www.ebi.ac.uk/pdbe/api/pdb/entry/molecules/;
>> + pdbId;
>>var info = eval(load(queryUrl));
>>
>>if (info.type == "hash") {
>>  for (var entity in info[pdbId]) {
>>var currentWeight =  entity..weight;
>>if (currentWeight != "") {
>>  weight = weight + currentWeight;
>>}
>>  }
>>}
>>  }
>>
>>  return weight;
>> }
>>
>> - Example code ---
>> weight = getPdbEntry("1deh");
>> print weight;
>>
>> --Example output -
>> 40749.875
>> --
>>
> Sorry, I forgot the 'Weight' in the example function call':
>
> weight = getPdbEntryWeight("1deh");
>
> Regards,
> Rolf
>


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Re: [Jmol-users] Saving files from JSmol

[Eric Martz]

Dear Bob,

Here is where you can test saving images or animations from a form 
button in FirstGlance:


http://bioinformatics.org/firstglance/fgix/

You can start it with JSmol or Jmol_S (see checkbox "use Java").

Click on the orange link below the molecule "Save Image or Animation for 
Powerpoint".


Saving images (png) from *JSmol* works fine in all browsers except MS Edge.

Saving images (png) from *Jmol_S* causes Jmol to report "ERROR: 
*canceled*". Is this intentional?


Attempting to save an animation from *JSmol* when the script is sent 
with jmolScript() generates TypeError: params.get() is null. However the 
saved file does contain the animation!


You can see my commands here at the bottom of this file:
http://bioinformatics.org/firstglance/fgix/capture.js

Attempting to save an animation from *Jmol_S* generates no errors, and 
the saved file contains the animation. It is not canceled.


Thus we are close to being able to save both static images and 
animations from buttons in FirstGlance. If you do not intend to disable 
these capabilities, I am very excited about developing the user 
interface in FirstGlance. I think this will make FirstGlance 
significantly more popular.


-Eric


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[Jmol-users] Saving files from JSmol

[Eric Martz]

Dear Bob,

It will be absolutely fantabulous if users of FirstGlance can save 
images and animations of the current view easily. Those animations (from 
the capture command) are gorgeous and attention-grabbing in Powerpoint 
slides.


With JSmol 14.4.1_2015.12.23, I have begun writing code in FirstGlance 
to make it easy. Saving static images ("write image" command) to the 
local disk from an online FirstGlance works from JSmol (no Java) in all 
popular browsers, both Windows and OS X, except for the Microsoft Edge 
browser.


Preliminary tests (from the JSmol console) indicate that saving 
animations (multi-GIF files) will also work in Firefox (only), although 
the capture command generates 360 frames /very slow//ly/ in JSmol.


Java:

Static images can be saved from the Jmol_S Java applet when the "write" 
command is issued in the Jmol console, but not from Jmol scripts built 
into the website. Jmol_S says "write <<< cancel" in an error message.


The inability to save "capture" files from Jmol_S Java applet when the 
command comes from the website is unfortunate since Java is enormously 
faster to generate the multi-GIF frames.


I plan to continue developing a user interface to make saving these 
files easy from FirstGlance ...


UNLESS you plan to disable this capability in JSmol as well. I hope not 
but I understand if security requires it.


Please let me know your plans so I don't end up developing a user 
interface that is inoperable in newer versions of JSmol.


Best regards, Eric


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[Jmol-users] FirstGlance with 14.4.1_2015.12.23

[Eric Martz]

I have released a new version of FirstGlance in Jmol that uses Jmol 
14.4.1_2015.12.23. So far I have found no problems in that version of 
Jmol that affect FirstGlance.

http://FirstGlance.Jmol.Org

I have tested browsers:

Firefox (best for JSmol!) in OS X and Windows
Safari in OS X
Chrome in OS X and Windows
Internet Explorer in Windows
Edge in Windows 10
Opera in OS X and Windows
Maxthon in OS X and Windows

I tested the Java applet in the browsers that support Java.
Browser performance summary:
http://bioinformatics.org/firstglance/fgij/notes.htm#browsers

Kudos and thanks to Bob and the Jmol community for the continued amazing 
progress with Jmol!!

-Eric

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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] more tests

[Eric Martz]

Dear Bob,

Hooray! I no longer see the 'color dots none' bug, and the one-minute 
freeze that I've been getting for 7ahl in FirstGlance is GONE!


So far my tests in FirstGlance reveal no other bugs.

Excellent work, my friend!
Enjoy some time with your family!
Eric

On 12/23/15 4:05 AM, Robert Hanson wrote:
see 
http://sourceforge.net/projects/jmol/files/Jmol/Version%2014.4/Version%2014.4.1/


*Download Jmol-14.4.1_2015.12.23-binary.zip (60.6 MB) 



*Jmol.___JmolVersion="14.4.1_2015.12.23"

bug fix: PyMOL 1.8 PSE files cannot be read
bug fix: dots broken when colored none
bug fix: color cartoons red blue not saved in state
bug fix: color cartoons red blue flipping red/blue in sheets




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[Jmol-users] Bug in 12/21 build?

[Eric Martz]

Hi Bob,

The good news is that the 12/21 build almost passed all my tests in 
FirstGlance.


Incidentally, while JSmol reports itself as 14.*4*.1_2015.12.*21*, 
Jmol_S reports itself as 14.*5*.1_2015.12.*16*.


So far I only noticed one place that both JSmol and Jmol_S hiccup. It 
only happens once, the first time I do a certain operation in 
FirstGlance, and only if I do a certain sequence. Sounds like an 
initialization problem?


This problem occurs in the 12/21 and 12/20 builds, but NOT in the 12/15 
build.


Before I spend more time on this (and trying to make something where you 
can reproduce this), maybe the info below is enough?


Jmol_S freezes with no message in the Java or Jmol Consoles.

JSmol says with set debugscript on
color dots none;
script ERROR: TypeError: this.bsColixSet is null J.shapespecial.Dots set 
color


and generates

TypeError: this.bsColixSet is null try/catch path:
0 function (b,d)
 args[0]=TypeError: this.bsColixSet is null
 args[1]=function (){a.instantialize(this,arguments)}
1 JS.ScriptEval.executeCommands(a,b)
 args[0]=false
 args[1]=true
2 JS.ScriptEval.evaluateCompiledScript(a,b,c,e,f,p)
 args[0]=false
 args[1]=false
 args[2]=true
 args[3]=false
 args[4]=null
 args[5]=false
3 JS.ScriptManager.evalStringWaitStatusQueued(a,b,c,e,f)
 args[0]=JSON
 args[1]=set echo middle center; font echo 100 sanserif bold; color e...
 args[2]=+scriptStarted,+scriptStatus,+scriptEcho,+scriptTerminated
 args[3]=false
 args[4]=false
4 JV.Viewer.evalStringWaitStatusQueued(a,b,c,g,f)
 args[0]=JSON
 args[1]=set echo middle center; font echo 100 sanserif bold; color e...
 args[2]=+scriptStarted,+scriptStatus,+scriptEcho,+scriptTerminated
 args[3]=false
 args[4]=false
5 JV.Viewer.evalWait(a,b,c)
 args[0]=JSON
 args[1]=set echo middle center; font echo 100 sanserif bold; color e...
 args[2]=+scriptStarted,+scriptStatus,+scriptEcho,+scriptTerminated
6 JV.Viewer.scriptWait(a)
 args[0]=set echo middle center; font echo 100 sanserif bold; color e...
7 JU.GenericApplet.scriptProcessor(a,b,d)
 args[0]=set echo middle center; font echo 100 sanserif bold; color e...
 args[1]=null
 args[2]=1
8 scriptWait(a,b)
 args[0]=set echo middle center; font echo 100 sanserif bold; color e...
 args[1]=null
9 function ()
 args[0]=set echo middle center; font echo 100 sanserif bold; color e...
 args[1]=null

-Eric
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[Jmol-users] JSmol speed vs. browsers

[Eric Martz]

I have provided data, methods and detailed conclusions here
*http://proteopedia.org/w/JSmol/Rotation_Speeds*
Briefly I found:

For JSmol (HTML5/javascript) Firefox outperforms Chrome, Opera and Edge 
by about four-fold.


Safari is as fast as Firefox with JSmol.

Internet Explorer 11 is unusably slow with JSmol, about 9-fold slower 
than Firefox.


Java is only 1.4-1.8 fold faster in Firefox, but more than 20-fold 
faster in Internet Explorer.


Curiously, rotating/spinning a spacefilled rendering is twice as fast as 
a cartoon rendering in Chrome and Opera (but not in Firefox, Edge or 
Internet Explorer 11).


Thus, in an update I'm preparing for FirstGlance, when using JSmol, 
Firefox will be recommended, and Internet Explorer will be strongly 
discouraged. This is a change since mid-2014, when Chrome outperformed 
Firefox with JSmol.


When using Java, the browser doesn't matter, except that Chrome and Edge 
don't support Java, and Opera threatens to follow suit.


-Eric
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Re: [Jmol-users] Let's try this one: Jmol-14.4.1_2015.12.15

[Eric Martz]

Excellent! JSmol/HTML5 appears to rotate acceptably in Chrome (still 
rotates more smoothly in Firefox), and Java works.


Preliminary tests with FirstGlance have revealed no bugs or issues.

I have replaced the jsmol in FirstGlance.Jmol.Org with the December 15 
jsmol.


Thanks so much Bob!!!
Eric

On 12/15/15 9:02 PM, Robert Hanson wrote:
*Download Jmol-14.4.1_2015.12.15-binary.zip (60.7 MB) 
 
*



Jmol.___JmolVersion="14.4.1_2015.12.15"

bug fix: Bad build for Jmol Java applet
bug fix: JSmol (JSmolCore.js) check for MS Edge browser, which does 
not support dataURI (so write xxx.png did not work in MS Edge)



--
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] JSmol 14.4.1 - Javascript error messages in Firefox 42

[Eric Martz]

Rolf, Bob and everyone, I, too, have noticed these numerous error 
messages in Firefox when running from local files in OS X. Since 
everything seemed to work, I didn't worry about them much. But it would 
be nice to eliminate them so it would be easier to find the errors that 
matter.


Thanks, Eric



On 12/16/15 4:00 PM, Robert Hanson wrote:

Ho, ho. What luck. A little web digging turned up the solution.

Add this to your page:

$.ajaxSetup({ mimeType: "text/plain" });


I will get that into JSmol.

Bob


On Wed, Dec 16, 2015 at 11:46 AM, Rolf Huehne > wrote:


Hi all,

with JSmol/HTML5 I get a lot of Javascript error messages in
Firefox 42
on Linux if I load the page locally from the file system. The error
messages don't occur in Chromium 31 or if the page is loaded from
a web
server.

Although JSmol still seems to work properly it seems especially
strange
to me that there are not only error messages for JSmol Javascript
files
but also for script files and data files loaded into JSmol (original
path names are shortened):

== Script and data file error messages ==
Error: not well-formed
Source File: file:///jmol-14.4.1_2015.12.15/start_script.txt
Line: 1, Column: 2
Source Code:
# ### REQUIRES Jmol 14.3.16_2015.09.22 or later ###
---
Error: syntax error
Source File: file:///jmol-14.4.1_2015.12.15/load_script.txt
Line: 1, Column: 1
Source Code:
set windowCentered on;
---
Error: syntax error
Source File: file: annotations_1.txt
Line: 1, Column: 1
Source Code:
observation_id entry_id entry_type entry_name species
---


== JSmol file error messages =
Error: syntax error
Source File:
file:///jmol-14.4.1_2015.12.15/jsmol/j2s/JV/OutputManagerJS.js
Line: 1, Column: 1
Source Code:
Clazz.declarePackage ("JV");
---
Error: syntax error
Source File:
file:///jmol-14.4.1_2015.12.15/jsmol/j2s/JV/OutputManager.js
Line: 1, Column: 1
Source Code:
Clazz.declarePackage ("JV");
---
Error: syntax error
Source File:
file:///jmol-14.4.1_2015.12.15/jsmol/j2s/core/corescriptcmd.z.js
Line: 1, Column: 1
Source Code:

(function(X,Y,Z,$,aa,M,H,N,P,Q,I,R,S,ba,L,D,T,K,U,ca,V,da,ea,fa,ga,ha,ia,ja,ka,y,la,ma,na,oa,pa,qa,ra,sa,ta,ua,va,wa,xa,ya,za,Aa,Ba,Ca,Da,Ea,Fa,Ga,Ha,Ia,Ja,Ka,l,W){M("JS");c$=Q(function(){this.e=this.vwr=null;this.chk=!1;this.st

=null;this.slen=0;P(this,arguments)},JS,"ScriptExt");l(c$,"init",function(a){this.e=a;this.vwr=this.e.vwr;return
this},"~O");l(c$,"atomExpressionAt",function(a){return

this.e.atomExpressionAt(a)},"~N");l(c$,"checkLength",function(a){this.e.checkLength(a)},"~N");l(c$,"error",
---
Error: syntax error
Source File:

file:///jmol-14.4.1_2015.12.15/jsmol/j2s/J/adapter/readers/cif/MMCifReader.js
Line: 1, Column: 1
Source Code:
Clazz.declarePackage ("J.adapter.readers.cif");
---
Timestamp: 12/16/2015 03:41:53 PM
Error: syntax error
Source File:
file:///jmol-14.4.1_2015.12.15/jsmol/j2s/J/adapter/readers/cif/CifReader.js
Line: 1, Column: 1
Source Code:
Clazz.declarePackage ("J.adapter.readers.cif");
---
Error: syntax error
Source File:
file:///jmol-14.4.1_2015.12.15/jsmol/j2s/JU/CifDataParser.js
Line: 1, Column: 1
Source Code:
Clazz.declarePackage ("JU");
---
Error: syntax error
Source File:
file:///jmol-14.4.1_2015.12.15/jsmol/j2s/J/render/MeshRenderer.js
Line: 1, Column: 1
Source Code:
Clazz.declarePackage ("J.render");
---
Error: syntax error
Source File: file:///jmol-14.4.1_2015.12.15/jsmol/j2s/J/shape/Halos.js
Line: 1, Column: 1
Source Code:
Clazz.declarePackage ("J.shape");
---
Error: syntax error
Source File:
file:///jmol-14.4.1_2015.12.15/jsmol/j2s/J/render/HalosRenderer.js
Line: 1, Column: 1
Source Code:
Clazz.declarePackage ("J.render");
---
Error: syntax error
Source File:
file:///jmol-14.4.1_2015.12.15/jsmol/j2s/J/g3d/CircleRenderer.js
Line: 1, Column: 1
Source Code:
Clazz.declarePackage ("J.g3d");
---
Error: syntax error
Source File:
file:///jmol-14.4.1_2015.12.15/jsmol/j2s/J/thread/MoveToThread.js
Line: 1, Column: 1
Source Code:
Clazz.declarePackage ("J.thread");
---

Regards,
Rolf


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Postdoc

[Jmol-users] "labels off" freezing JSmol

[Eric Martz]

Dear Bob,

This request could be titled "another conundrum" or "a holiday puzzle 
for Bob" or "how about another miracle, Bob?".

With the recent changes affecting rotation in Chrome, and despite your 
miraculous save, Firefox now outperforms Chrome for JSmol/HTML5 in every 
area, except one quite annoying issue.

For years, after loading a largeish model (e.g. 7ahl, 23K atoms, largest 
5% of PDB entries) into JSmol in FirstGlance in Firefox, the first 
operation to be performed (e.g. clicking the "spin off" button) freezes 
JSmol for about one minute. This is only for a minority of models, but 
it is quite annoying when it happens. It does not happen in Chrome (but 
rotation in Chrome is still very jerky compared to Firefox).

It only happens once. After recovery, when the same operation is 
repeated, it executes in about one second.

I have now narrowed down the culprit. A "labels off" command that occurs 
in FirstGlance freezes Firefox and JSmol for 45 sec. If the molecule was 
spinning, the spinning stops until JSmol recovers. During the freeze, 
one gets the OS X "beachball", indicating that Firefox is frozen. In 
Windows, you get the hourglass.

Well, its not quite that simple. In Firefox, at 
http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm (using JSmol/HTML5), I 
load 7ahl and spin it. I open the console, select all, and do "labels 
off". The command is completed in about one second. So it is not just 
the "labels off", but doing that in the state of JSmol in FirstGlance.

To reproduce the problem: In Firefox, go to 
http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm. Drag and drop the 
initial state of FirstGlance into JSmol 
(bioinformatics.org/firstglance/download/fgij-initial-state.spt.zip). 
7ahl should appear, spinning, in cartoon, colored by chain. (In Windows, 
when you unzip the script file, it makes a folder. The actual .spt file 
is inside that folder.)

Open the JSmol Console. Select all and enter "labels off". JSmol and 
Firefox freeze for 45 sec (longer on a slower computer). This occurs in 
both OS X and Windows 10.

So, Bob, what am I doing to JSmol that makes "labels off" take 45 sec? 
Can it be fixed or worked around?

Thanks, Eric

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[Jmol-users] 14.4.0 vs 14.4.1 and Java

[Eric Martz]

Yesterday I put Jsmol 14.4.1_2015.12.13 into the public version of 
http://FirstGlance.Jmol.Org. This enabled use of JSmol/HTML5 with Chrome.

Today I got around to trying Java. It does not work. In both Windows and 
OS X, the error message is "Application Blocked. Click for details. User 
has denied the privileges to the code." Clicking for details produces 
nothing.

The Java Console says (not sure if this is relevant)
CacheEntry[...JmolAppletSigned0.jar]:updateAvailable=true,lastModified=Sat 
Se 2- 16:03:20 EDT 2014,length=129547

Testing Java at java.com succeeds.

When I went back to an earlier version of JSmol, Java works just fine. I 
noticed that Java works at 
http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm but this is version 
14.4.0, not 14.4.1.

So I changed FirstGlance to 14.4.0_2015.12.13 and now both Java and 
Chrome work. In both Windows and OS X I needed to delete the Java cache 
before the applet worked. We've encountered this in the past when one 
goes to an earlier version number of an applet.

What is supposed to be the difference between 14.4.0 and 14.4.1?

Thanks, Eric

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Re: [Jmol-users] 14.4.0 vs 14.4.1 and Java

[Eric Martz]

Ah yes, I forgot to test rotation in Chrome when I went to 14.4.0. With 
14.4.0 Java works but Chrome does NOT rotate. With 14.4.1 rotation was 
great in Chrome, but Java did not work.


What puzzles me is that before your 12/13 version, rotation did not work 
in Chrome at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm even with 
caffeine, but now rotation is fine with Chrome in 14.4.0 there.


Bottom line is that I still don't have a FirstGlance that rotates in 
Chrome and runs the Java applet.


I have restored 14.4.1_2015.12.13 in FirstGlance for now because I think 
rotation in Chrome is temporarily more important than Java.


Eric

On 12/15/15 5:46 PM, Robert Hanson wrote:
difference should be just the Chrome issue in JavaScript, but I guess 
I messed up.


On Tue, Dec 15, 2015 at 2:41 PM, Eric Martz <ema...@microbio.umass.edu 
<mailto:ema...@microbio.umass.edu>> wrote:


Yesterday I put Jsmol 14.4.1_2015.12.13 into the public version of
http://FirstGlance.Jmol.Org. This enabled use of JSmol/HTML5 with
Chrome.

Today I got around to trying Java. It does not work. In both
Windows and
OS X, the error message is "Application Blocked. Click for
details. User
has denied the privileges to the code." Clicking for details produces
nothing.

The Java Console says (not sure if this is relevant)
CacheEntry[...JmolAppletSigned0.jar]:updateAvailable=true,lastModified=Sat
Se 2- 16:03:20 EDT 2014,length=129547

Testing Java at java.com <http://java.com> succeeds.

When I went back to an earlier version of JSmol, Java works just
fine. I
noticed that Java works at
http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm but this is version
14.4.0, not 14.4.1.

So I changed FirstGlance to 14.4.0_2015.12.13 and now both Java and
Chrome work. In both Windows and OS X I needed to delete the Java
cache
before the applet worked. We've encountered this in the past when one
goes to an earlier version number of an applet.

What is supposed to be the difference between 14.4.0 and 14.4.1?

Thanks, Eric


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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] Jmol 14.4.1_2015.12.13 released - IMPORTANT

[Eric Martz]

I have replaced jsmol in FirstGlance in Jmol with the 12/13 version.
Indeed the Chrome disaster seems fixed. And in a quick check, 
FirstGlance appeared to work correctly.


Hurray for Bob! I am constantly in awe! (And yes Yay for Mighty Mouse to 
the rescue!)


Mouse rotation in Chrome is still jerkier than in Firefox, but it is 
acceptable. (Better than Internet Explorer or Edge.)


zoomto *1.3 # default 1 sec

in a large Jmol (as in FirstGlance) is slower, jerkier, and takes 
several seconds in Chrome, but is smooth and fast in Firefox.


(At http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm, how about an option 
to increase the size of JSmol by 2.5 fold?)


My impression is that the jerky rotation in Chrome (jerkiness that 
remains in the 12/13 version of JSmol) has been present well before the 
disastrous version 47 of Chrome released December 1.


I wonder if you can do anything further, Bob, to make rotation-via-mouse 
smoother in Chrome, more like it is in Firefox? Just a thought. You've 
already worked a miracle overnight!


-Eric

On 12/13/15 1:56 PM, Robert Hanson wrote:

This new version is now available at SourceForge:

*Download Jmol-14.4.1_2015.12.13-binary.zip (60.3 MB) 
*



*IMPORTANT*: A very recent modification of Chrome makes Chrome 
unusable with all previous versions of JSmol, at least until sometime 
in January. The WebGL version of JSmol is not impacted.


This appears to be the result of a well-meaning attempt by Chromium 
developers to enhance smooth scrolling of pages by lowering the 
priority of setTimeout calls. However, the unanticipated fallout of 
that change results in extremely rough rotation of models. You can 
follow the issue here: 
https://code.google.com/p/chromium/issues/detail?id=568725 Note that 
one of the last comments on Dec. 11 indicates that there indicates 
this issue will not be addressed until sometime in January.


*But there is a workaround. *This release of Jmol 14.4.1 should 
correct that problem and, at the same time, may improve performance 
with Microsoft Edge.


I have put up two versions of JSmol that illustrate the problem and 
the fix:


(original) http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
(fixed) http://chemapps.stolaf.edu/jmol/jsmol2/jsmol.htm

Testing of that second site would be appreciated.

The work-around is simple, and if you want, you can implement this 
yourself on your site.  Really (in terms of this bug) it is just a 
single coding change in jsmol/js/JSmol.js, where one "setTimeout(f)" 
has been replaced with "requestAnimationFrame(f)". Thus, if you 
prefer, you should be able to just swap in a new JSmol.min.js or 
JSmol.min.nojq.js for the old one. I have not tried this. Of course, 
if you do that, then the other bugs listed below will still be there. 
If you want to try that, here is the link to that file specifically:


http://chemapps.stolaf.edu/jmol/jsmol2/JSmol.min.js

Bob

Jmol.___JmolVersion="14.4.1_2015.12.13"

bug fix: JavaScript Chrome/Edge fix for slow response due to 
setTimeout issues; uses requestAnimationFrame instead in JSmol.js

bug fix: zoomTo not setting time to 0 in the case of scriptWait
bug fix: set selectAllModels should restrict action of display/hide as 
well

bug fix: set selectAllModels not working appropriately
bug fix: set selectAllModels should not be saved in state
bug fix: JmolData.jar does not update atom screen positions upon 
REFRESH or select {visible}

bug fix: JmolData.jar -p flag does not work properly
bug fix: model 0 issued when more than one PDB file is open does not 
execute model *


--
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] jmolScriptWait vs zoomTo

[Eric Martz]

OK, no problem. Thanks, Bob! -Eric

On 12/13/15 8:42 AM, Robert Hanson wrote:
Probably a bug that the rest of the script is not executed, but 
there's no way to wait for a zoomto. Don't do that.


On Sat, Dec 12, 2015 at 6:33 PM, Eric Martz <ema...@microbio.umass.edu 
<mailto:ema...@microbio.umass.edu>> wrote:


Consider the following commands:

zoomto *1.3;
select protein;
color yellow;

In javascript, when these commands are in the string "spt",
jmolScript(spt)
produces a smooth zoom followed by protein turning yellow.

However,
jmolScriptWait(spt)
produces a zoom in one large step (snap zoom) and the remainder of the
script is not executed (protein does not turn yellow).

Is this a bug or a feature of jmolScriptWait()?

Thanks, Eric


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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] jmolScriptWait vs zoomTo

[Eric Martz]

Consider the following commands:

zoomto *1.3;
select protein;
color yellow;

In javascript, when these commands are in the string "spt",
jmolScript(spt)
produces a smooth zoom followed by protein turning yellow.

However,
jmolScriptWait(spt)
produces a zoom in one large step (snap zoom) and the remainder of the 
script is not executed (protein does not turn yellow).

Is this a bug or a feature of jmolScriptWait()?

Thanks, Eric

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[Jmol-users] Fwd: Chrome: rotation unusable in JSmol

[Eric Martz]

In April 2014, Chrome gave the best performance of JSmol: smoothest 
rotation and few if any long (~ one minute) pauses during loading of 
some modest PDB files (pauses seen in Firefox). I configured FirstGlance 
in Jmol, when using JSmol, to recommend Chrome over Firefox. Safari was 
good. Internet Explorer was unusably slow with JSmol.


Recently I began to notice jumpier rotation in Chrome, while Firefox and 
Safari continue to perform well.


Today I found Chrome to be unable to rotate any molecule (even caffeine) 
in JSmol. Although there are brief moments when rotation can be seen, 
these are broken by long freezes (> 5 sec) when no rotation can be 
accomplished.


The problem is worst when the mouse is moved quickly. The molecule 
freezes until the mouse is stopped. If you keep moving the mouse, the 
molecule may freeze for more than 10 sec. The molecule does rotate with 
very slow movements of the mouse.


The problem occurs in OS X, where Chrome has updated to version 47.

Rotation is still quite good in Chrome version 46, which happens to 
remain in my Windows 7 and 10 machines, despite version 47 becoming the 
stable release on December 1 
(http://googlechromereleases.blogspot.com/search?updated-max=2015-12-01T12:43:00-08:00=10). 
Presumably my Windows Chrome will shortly auto-update to 47 and then I 
will be very curious about performance.


I tested the OS X beta version of Chrome, version 48, in hopes the 
problem would be fixed -- but it remains in Chrome 48 in OS X.


Since Chrome stopped supporting Java on September 1, 2015, Chrome is now 
useless for JSmol websites.


We can hope this is a mouse-related bug in Chrome that will be fixed, 
but as I mentioned, a fix is not present in the current beta version 48.


This is a sad turn of events! Comments? Suggestions? Insights?

-Eric


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[Jmol-users] Bug or feature? (anomalous _P)

[Eric Martz]

Dear Bob,

While preparing a morph from 5cl3 to 5cle, I re-ordered the hetero atoms 
in 5cle so as to be in the same order as the homologous atoms in 5cl3. 
This separated [3DR]6:B.P from the other 3DR atoms. The result is that 
this phosphorus, while it remains hetero, is deemed by Jmol to be 
neither ligand nor solvent nor DNA. I can live with this, but I am 
reporting it in case it is a bug.


Tested with Jmol application dated November 18, 2015.

Example files:
http://bioinformatics.org/molvis/tmp/5cle-ligand.pdb
http://bioinformatics.org/molvis/tmp/reordered-ligand.pdb

Contents of example files:

ORIGINAL order from 5cle ([3DR]6:B.P is ligand)

HETATM1  O5' 3DR B   6  40.400  -4.134  11.144  1.00 
16.98   O
*HETATM2  P   3DR B   6  40.429  -5.572  10.443 1.00 
17.42   P *
HETATM3  OP1 3DR B   6  41.434  -5.662   9.357 1.00 
18.41   O
HETATM4  OP2 3DR B   6  40.671  -6.600  11.482 1.00 
19.96   O
HETATM5  C2' 3DR B   6  40.069  -0.707  13.038 1.00 
25.11   C
HETATM6  C5' 3DR B   6  40.150  -3.117  10.183 1.00 
20.01   C
HETATM7  C4' 3DR B   6  39.863  -1.817  10.934 1.00 
17.65   C
HETATM8  O4' 3DR B   6  38.569  -1.913  11.598 1.00 
19.68   O
HETATM9  C1' 3DR B   6  38.611  -1.154  12.821 1.00 
20.01   C
HETATM   10  C3' 3DR B   6  40.891  -1.550  12.055 1.00 
23.32   C
HETATM   11  O3' 3DR B   6  41.949  -0.747  11.542 1.00 
25.20   O
HETATM   12  N9  ADK B 101  38.704  -4.026  15.100 1.00 
24.10   N
HETATM   13  C4  ADK B 101  38.277  -4.217  16.354 1.00 
19.29   C
HETATM   14  N3  ADK B 101  37.775  -3.385  17.350 1.00 
35.42   N
HETATM   15  C2  ADK B 101  37.434  -3.931  18.532 1.00 
28.39   C
HETATM   16  N1  ADK B 101  37.558  -5.221  18.755 1.00 
24.56   N
HETATM   17  C6  ADK B 101  38.031  -6.073  17.825 1.00 
29.43   C
HETATM   18  N6  ADK B 101  38.164  -7.496  18.102 1.00 
23.29   N
HETATM   19  C5  ADK B 101  38.405  -5.601  16.602 1.00 
19.32   C
HETATM   20  N7  ADK B 101  38.896  -6.144  15.497 1.00 
17.81   N
HETATM   21  C8  ADK B 101  39.069  -5.183  14.606 1.00 
19.82   C
HETATM   22  C3A ADK B 101  37.649  -2.030  17.097 1.00 
31.68   C


REORDERED (coordinates differ because this was aligned with 5cl3; 
[3DR]6:B.P is NOT ligand):


*HETATM 2424  P   3DR B   6  59.344  -7.302  54.550  1.00 
17.42   P*
HETATM 2438  N1  ADK B 101  56.456  -6.944  62.856  1.00 
24.56   N
HETATM 2437  C2  ADK B 101  56.354  -5.651  62.639  1.00 
28.39   C
HETATM 2436  N3  ADK B 101  56.707  -5.105  61.460  1.00 
35.42   N
HETATM 2435  C4  ADK B 101  57.198  -5.940  60.462  1.00 
19.29   C
HETATM 2441  C5  ADK B 101  57.302  -7.327  60.703  1.00 
19.32   C
HETATM 2439  C6  ADK B 101  56.917  -7.799  61.923  1.00 
29.43   C
HETATM 2440  N6  ADK B 101  57.026  -9.225  62.193  1.00 
23.29   N
HETATM 2442  N7  ADK B 101  57.788  -7.873  59.597  1.00 
17.81   N
HETATM 2443  C8  ADK B 101  57.979  -6.911  58.711  1.00 
19.82   C
HETATM 2434  N9  ADK B 101  57.632  -5.750  59.210  1.00 
24.10   N
HETATM 2431  C1' 3DR B   6  57.593  -2.866  56.945  1.00 
20.01   C
HETATM 2426  OP2 3DR B   6  59.566  -8.339  55.585  1.00 
19.96   O
HETATM 2427  C2' 3DR B   6  59.058  -2.445  57.168  1.00 
25.11   C
HETATM 2425  OP1 3DR B   6  60.351  -7.404  53.467  1.00 
18.41   O
HETATM 2432  C3' 3DR B   6  59.869  -3.296  56.183  1.00 
23.32   C
HETATM 2433  O3' 3DR B   6  60.941  -2.509  55.677  1.00 
25.20   O
HETATM 2444  C3A ADK B 101  56.605  -3.747  61.214  1.00 
31.68   C
HETATM 2429  C4' 3DR B   6  58.840  -3.541  55.058  1.00 
17.65   C
HETATM 2430  O4' 3DR B   6  57.542  -3.618  55.718  1.00 
19.68   O
HETATM 2428  C5' 3DR B   6  59.107  -4.842  54.302  1.00 
20.01   C
HETATM 2423  O5' 3DR B   6  59.337  -5.867  55.258  1.00 
16.98   O



-Eric
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Re: [Jmol-users] Zoom calculation

[Eric Martz]

Initial zoom depends, if your Jmol is rectangular, on set zoomlarge and 
set zoomheight. Just in case you didn't remember those. With zoomlarge 
true I often set zoom to 110% to pretty much fill Jmol to the edges.
-Eric

On 12/3/15 7:05 AM, si...@publcif.co.uk wrote:
> Dear all
>
> If I do "rotate best;center visible;zoom 0;" I get a nice view of a
> model, but in most cases it wont entirely fill the applet because the
> zoom is optimized with respect to the 3d bounding box (I think).
>
> Does anyone know how to automatically zoom a model so that it is as
> large as possible in the applet but still shows all atoms?
>
> E.g. if I knew the 2D extent of the actual atoms as displayed after
> calling "rotate best;center visible;zoom 0;", I could work out how
> much space is available in order to apply an extra zoom?
>
> Any ideas?
>
> Cheers
>
> Simon
>
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[Jmol-users] DOCUMENTATION dotdensity

[Eric Martz]

Dear Bob,

The docs on 'dotdensity' seems obsolete.

It appears to me that the default dotdensity is 3, not 0.

Also a value of 4 is accepted.

Negative values don't seem to work as the docs would suggest.

Please update this section. Thanks! Eric

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[Jmol-users] DOCUMENTATION cartoon/hermitelevel

[Eric Martz]

Dear Bob,

Under 'cartoon', under 'See also', please add

set (structure)

Although hermite level is mentioned in the introductory paragraph, I 
don't necessarily look there and am more likely to look under 'see also' 
when I think there is a relevant setting.

Thanks, Eric

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Re: [Jmol-users] Capture inter-frame delay

[Eric Martz]

Thanks for banging me over the head, Bob -- I needed it! Indeed I never 
grasped that animationFPS determines the delay between frames in a 
multi-GIF from the capture command. I kept mis-reading it as spinFPS. So 
I've been frustrated for more than a year due to my own denseness.


Now I can control smoothness (number of frames) and speed of playback 
independently. Woo hoo!!


Eric

On 11/22/15 7:20 PM, Robert Hanson wrote:
I don't know about /spinFPS/. I am talking about /animationFPS. /I 
just tested it and had no problem.

​




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Re: [Jmol-users] Capture inter-frame delay

[Eric Martz]

Yes, I can adjust the frame rate with spinfps.
But the GIF file that is written unconditionally has a constant 0.1 sec 
delay between frames.


Here are some results:

# rotating 360 degrees in 2 sec gives only 60 frames
# with default spinfps 30 (frames per second).
# 4 sec gives 120 frames with spinfps 30.
# 4 sec gives 200 frames with spinfps 50.
# FPS SEC FRAMES SEC-PER-GIF-TURN
# 30  5   15015
# 10  5   50 5
# 10  20  20020
# 5   40  20020

set spinfps 30
set antialiasdisplay true

capture "rotate_capture.gif" loop
set waitformoveto true

rotate -360 5 branch {c9} {c8}

set waitformoveto true
capture end

On 11/22/15 6:12 PM, Robert Hanson wrote:

Eric, doesn't this work?

/Capture to an animated GIF file. By default, capturing will continue 
until the CAPTURE END command is issued. If the LOOP keyword is not 
given (see below), then whether the animation loops or not depends 
upon the value of animation mode 
: 
PALINDROME or LOOP results in a looping GIF (no distinction, as there 
is no PALINDROME option in GIF animation) or ONCE (no looping).*Frame 
rate is determined by animation fps 
, 
which has a maximum of 50 frames per second.


*/
Bob/*
*/
/
/


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[Jmol-users] Capture inter-frame delay

[Eric Martz]

Dear Bob,

I continue to be frustrated by the lack of control over the otherwise 
FABULOUS capture command. I first made this request on December 9, 2014.

The multi-GIF saved by the capture command plays back with a constant 
0.1 second delay between frames.

One cannot get a smooth, rapid animation. Smooth means many frames. But 
with many frames, the animation is way too slow. For example, a full 
rotation of 360 degrees, to be smooth, ideally would have 360 frames 
(one per degree). But playback would spin at 36 seconds/turn.

Again, I am down on my knees begging for a new setting to specify the 
delay between frames in the multi-GIF file saved by the capture command. 
For example

set gifDelay
or
set captureTimeBetweenFrames
or somesuch.

Thanks very much, Eric

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[Jmol-users] Writing from browsers

[Eric Martz]

I have tested "write pngj" and "capture" to write files to the local 
disk from an online HTML page. I also tested the ability to drop a pngj 
into Jmol in a browser. I tested these 5 browsers (all current versions):


Chrome, Edge*, Firefox, Internet Explorer 11* (IE11), Safari#.
   * Windows only.
   # OS X only.

Chrome and Edge do not run Java. The other 3 do.

Tests were done in Windows 7 and/or 10, and in OS X Yosemite (10.10.5).

All testing was done at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm

Commands used for testing (entered in the Jmol console):
   write pngj "filename.png"
   capture "filename.gif" rock 45

RESULTS

WRITING A PNGJ FILE: Works in Chrome, Firefox, IE11 in both Windows and 
OS X, from both JSmol(HTML5) and Jmol_S(Java). Works in Safari with 
JSmol(HTML5). Fails in Edge and Safari(Java mode).


DROPPING A PNGJ FILE INTO JMOL: Same results as writing pngj, except 
fails in Firefox(Java mode only, OS X only) because the image replaces 
the HTML page containing Jmol.


CAPTURE FROM JSMOL(HTML5):

From JSmol(HTML5) an error message is generated in every case. Samples 
are below. The error message opens in an alert subwindow, and after 
closing with the OK button, generation of the animation proceeds.


From JSmol(HTML5): Works in Firefox in both Windows and Mac, in IE11 
and Safari. Fails in Chrome (both Windows and OS X) and Edge. In IE11 
only, one must permit popups.


Generating the frames for a multi-GIF animation from JSmol(HTML5) is 
very slow (about one second/frame) except in Safari. From Jmol(Java) it 
is very fast.


From Jmol(Java): No error message. Works in Firefox in both Windows and 
Mac. Works in IE11. Fails in Safari. (Chrome and Edge do not run Java.)


The above results are re-iterated below in tabular form.

OS Jmol   Browser  Write-pngj Drop-pngj Capture
---
Win7   JSmol  IE11 YES*   YES* PopupBlocker+ErrMsg+YES (very 
slow!)

  FF   YESYES  ErrMsg+YES (very slow)
  Chrome   YESYES  ErrMsg+NO[1]

Win10  JSmol  Edge PopBlok+NO[2] NO[3]ErrMsg+NO[2] (very slow!)

   Java   IE11 YESYES  YES# (very fast!)
  FF   YESYES  YES (very fast!)

OS10.10.5
   JSmol  FF   YESYES  ErrMsg+YES (very slow!)
  Chrome   YESYES  ErrMsg+NO[1] (slow)
  Safari   YESYES  ErrMsg+YES (fast)

   Java   FF   YES NO[5] YES (extremely fast)
  Safari   NO[4] NO NO[4]

Safari fails to retrieve small molecules from NCI in Jmol_S, but works 
in JSmol.


* confirmed also for Win10; # confirmed also for Win7.

[1] Completes process, no error, nothing saved (even with popups enabled 
for the site).
[2] Seems to complete process and opens a new tab, but nothing, no error 
msgs.
[3] Cannot drop anything including an htm file into Edge. Did not find a 
setting to enable this.
[4] Error "Operation not permitted". Also the Java file save dialog does 
not show the directory/file list!

[5] Image opens, replacing the Jmol_S page.


Error message from Firefox below. From other browsers, some messages say

"TypeError: Unable to get property 'intValue' of undefined or null 
reference try/catch path".

TypeError: params.get(...) is null try/catch path:
0 function (b,d)
 args[0]=TypeError: params.get(...) is null
 args[1]=function (){a.instantialize(this,arguments)}
1 javajs.img.GifEncoder.setParams(params)
 args[0]={captureMode=movie, date=2015-11-17T11:00:25, captureFps=10,…
(etc etc)

-

-Eric

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Re: [Jmol-users] loading gzipped files in JSmol - Safari

[Eric Martz]

To anyone testing for Angel, CAUTION:
In the email below, the first link is labeled _ATPsintasa_mol.htm_ 

but the URL it goes to is _ATPsintasa_mol-2.htm!!_ 



The second link to _ATPsintasa_mol-2.htm_ 


__is labeled correctly.

On 11/17/15 11:59 AM, Angel Herráez wrote:

Hi

I have reports from 2 different people, accesing different pages of 
mine. When gzipped pdb files are involved, Safari fails to load the 
model into html5-JSmol


At least one of them reports "unrecognized file format" inside the 
Smol panel


Chrome works in the same systems.
So I think the problem is with loading zipped files via jsmol.php.  
Has anything changed in the way Safari deals with this? I acnnot test 
since I have no access to Mac


test case
a) with gzipped files

_http://biomodel.uah.es/metab/mitoc/ATPsintasa_mol.htm_ 




b) with plain pdb files

_http://biomodel.uah.es/metab/mitoc/ATPsintasa_mol-2.htm_

(it takes a whle to load and process the 3 consecutive files; that's 
normal)


--Note: you might encounter that Chrome fails to load the gzipped 
files. That is a separate problem that I am seeing with Chrome but 
only occasionally; to me, it  looks like related to a timeout in my 
server's php.


Thanks for any reports in general, and hints for Safari behaviour.




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Re: [Jmol-users] loading gzipped files in JSmol - Safari

[Eric Martz]

Test results on OS X Yosemite with all browsers up to date.

For me, since Yosemite, Safari seems broken. I never use it anymore. 
After you start Safari, there is a long pause, about 20 sec, before it 
will load any website. Often you get a "beachball". Sometimes it never 
loads. You may have to close the window, open a new one, and try again 
before the page loads. This is reproducible for me.


ATPsintasa_*mol.htm*:
Loads in Chrome and Firefox.
Safari (9.0.1):
Alert appears saying "JSmolCore.js: synchronous binary file transfer is 
requested but not available". After you click OK, JSmol has a red 
message at the top "unrecognized file format for ... _2wpd.pdb.gz".


ATPsintasa_*mol-2.htm*:
Loads in Chrome and Firefox and Safari.

-Eric

On 11/17/15 11:59 AM, Angel Herráez wrote:

Hi

I have reports from 2 different people, accesing different pages of 
mine. When gzipped pdb files are involved, Safari fails to load the 
model into html5-JSmol


At least one of them reports "unrecognized file format" inside the 
Smol panel


Chrome works in the same systems.
So I think the problem is with loading zipped files via jsmol.php.  
Has anything changed in the way Safari deals with this? I acnnot test 
since I have no access to Mac


test case
a) with gzipped files

_http://biomodel.uah.es/metab/mitoc/ATPsintasa_mol.htm_ 




b) with plain pdb files

_http://biomodel.uah.es/metab/mitoc/ATPsintasa_mol-2.htm_

(it takes a whle to load and process the 3 consecutive files; that's 
normal)


--Note: you might encounter that Chrome fails to load the gzipped 
files. That is a separate problem that I am seeing with Chrome but 
only occasionally; to me, it  looks like related to a timeout in my 
server's php.


Thanks for any reports in general, and hints for Safari behaviour.




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[Jmol-users] Jmol_S applet crash

[Eric Martz]

Dear Bob,

The following crashes the Jmol_S Java applet, version 2015.11.07, in 
FirstGlance in Jmol. It also crashes Jmol_S applet version 2015.10.17 at

http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED

It does not crash JSmol. I did not succeed in reproducing this in the 
application.

My tests were in Firefox and Safari, OS X (Yosemite), Java 1.8.0_65.
The same crash occurs in Windows 7 with IE11, Java 1.8.0_65.

To demonstrate:

Go the above StOlaf URL (default caffeine molecule).

Use the Jmol menu to open the Jmol Console.

Enter this command in the console:

isosurface delete

So far, so good, no crash.
(Note that there are no isosurfaces in the display.)

isosurface * delete

This crashes Jmol_S applet with the following in the Java console:

jmolApplet0__657817200757563__ couldn't find applet consoleFontScale
script 4 started
Script completed
Jmol script terminated
script 5 started
isosurface * delete;

java.lang.StringIndexOutOfBoundsException: String index out of range: -1
 at java.lang.String.charAt(String.java:658)
 at org.jmol.console.GenericConsole.outputMsg(Unknown Source)
 at org.jmol.console.GenericConsole.sendConsoleMessage(Unknown Source)
 at org.jmol.console.GenericConsole.notifyCallback(Unknown Source)
 at org.jmol.util.GenericApplet.notifyCallback(Unknown Source)
 at org.jmol.viewer.StatusManager.setScriptEcho(Unknown Source)
 at org.jmol.viewer.Viewer.scriptEcho(Unknown Source)
 at org.jmol.viewer.Viewer.showString(Unknown Source)
 at org.jmol.script.ScriptEval.showStringPrint(Unknown Source)
 at org.jmol.script.ScriptEval.showString(Unknown Source)
 at org.jmol.scriptext.ScriptExt.showString(Unknown Source)
 at org.jmol.scriptext.IsoExt.listIsosurface(Unknown Source)
 at org.jmol.scriptext.IsoExt.isosurface(Unknown Source)
 at org.jmol.scriptext.IsoExt.dispatch(Unknown Source)
 at org.jmol.script.ScriptEval.processShapeCommand(Unknown Source)
 at org.jmol.script.ScriptEval.processCommand(Unknown Source)
 at org.jmol.script.ScriptEval.commandLoop(Unknown Source)
 at org.jmol.script.ScriptEval.dispatchCommands(Unknown Source)
 at org.jmol.script.ScriptEval.executeCommands(Unknown Source)
 at org.jmol.script.ScriptEval.evaluateCompiledScript(Unknown Source)
 at org.jmol.script.ScriptManager.evalStringWaitStatusQueued(Unknown 
Source)
 at org.jmol.viewer.Viewer.evalStringWaitStatusQueued(Unknown Source)
 at org.jmol.script.ScriptQueueThread.runNextScript(Unknown Source)
 at org.jmol.script.ScriptQueueThread.run1(Unknown Source)
 at org.jmol.thread.JmolThread.run(Unknown Source)


Eric



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Re: [Jmol-users] Help to put Jmol on server for multi-GIF

[Eric Martz]

Dear Rolf and Bob,

I tested it in June and it didn't work.
In this message in June
http://sourceforge.net/p/jmol/mailman/message/34196031/
Bob said

" I don't plan on having capture available for the applet."

But today IT WORKS!!!

Indeed it opens a file save dialog and you can save to the local disk.
Hooray!
I hope this is intentional, not a bug.

Bob, please confirm that this will remain available -- before I spend a 
lot of time developing a user interface in FirstGlance to save an 
animation for Powerpoint.


-Eric

On 11/16/15 2:33 PM, Rolf Huehne wrote:

On 11/16/2015 08:24 PM, Eric Martz wrote:

Bob has said that the signed Jmol_s Java applet will NOT be able to
write files to the local disk.


Eric, do you mean the signed Java applet with the "unsigned" privileges
only (which was the unsigned applet in the past) or with the full
"signed" privileges?
With full priviliges saving should work.

Have you actually tried yet if it works or not?

Regards,
Rolf


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[Jmol-users] Help to put Jmol on server for multi-GIF

[Eric Martz]

I would like to add a feature to FirstGlance in Jmol. While using it 
(always in a web browser), I would like a button that generates a 
rotating multi-GIF of the current molecular view, for inclusion in a 
slide presentation.


In the Jmol application, a one-line command accomplishes that:

   capture “something.gif” spin Y # THANK YOU BOB!

Examples of such animations can be viewed in this Powerpoint:
https://www.dropbox.com/s/ki7wkuj8ojlvb0f/animation-examples-jmol.pptx?dl=0
(/You don't have to login to dropbox. Click "no thanks, continue to 
download"/.)


Bob has said that the signed Jmol_s Java applet will NOT be able to 
write files to the local disk.


Therefore I think the best solution might be to submit the current model 
and Jmol state script to a server, have the server run Jmol application, 
generate the multi-GIF file, and hand it back to the user for download.


1. Is this the best solution?

2. If so, will someone please guide me in how to do this?

Thanks very much, Eric

Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- Martz.MolviZ.Org <http://Martz.MolviZ.Org>

 * Top Five 3D MolVis Tools: Top5.MolviZ.Org <http://top5.MolviZ.Org>
 * FirstGlance: 3D Molecules in /Nature/: FirstGlance.Jmol.Org
   <http://firstglance.jmol.Org>
 * Protein 3D Structure Wiki: Proteopedia.Org <http://proteopedia.Org>
 * Education: Biochem in 3D at MolviZ.Org <http://MolviZ.Org>
 * Find Functional Patches in Proteins: ConSurf <http://consurf.tau.ac.il>
 * Atlas of Macromolecules: Atlas.MolviZ.Org <http://atlas.MolviZ.Org>
 * Interactive Molecules in Architectural Spaces:
   MolecularPlayground.Org <http://molecularplayground.Org>
 * Workshops: Workshops.MolviZ.Org <http://workshops.MolviZ.Org>

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Re: [Jmol-users] Help to put Jmol on server for multi-GIF

[Eric Martz]

DOUBLE HOORAY!!!

So I will begin coding a user interface to use capture from the applet 
in a browser.


Thanks Bob,
-Eric

On 11/16/15 6:34 PM, Robert Hanson wrote:

  public boolean allowCapture() {
return !isApplet || isSignedApplet;
  }

Eric, I must have misunderstood you -- I meant no capture for JSmol.
​




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[Jmol-users] PNGJ loading bug in OS X

[Eric Martz]

This bug may not be worth fixing since it is specific to OS X, and may 
be a bug in Java.


Using either the Java applet, or the Jmol application, the command

write "test.pngj"

saves a file that contains the atomic coordinates and the state of Jmol.

In *Windows*, dragging this PNGJ file into the Jmol *application*, or 
into the *applet* (tested in IE11 and Firefox), loads the molecule 
contained in the PNGJ file and renders it exactly as when the file was 
saved, after which it can be rotated etc. in Jmol. AMAZING!


In *OS X*, dropping the PNGJ into the application *works* PROVIDED the 
application happens to have *exactly the same pixel height and width* as 
the image (which is the size of the Jmol from which it was saved).


If the recipient Jmol application has a *different size*, an "Input" 
dialog opens asking to confirm changing the size of Jmol (or you can 
specify different height and width values). In Windows, this sizing 
dialog works. In OS X, once that "Input" dialog opens, *Jmol hangs* and 
has to be forced to quit by the system.


(For Windows, a size mismatch between the applet and the PNGJ doesn't 
matter. The molecule renders in the size of the applet without asking.)


In *OS X*, dropping the PNGJ file into the *applet* does not load it 
into the applet. Rather, it displays the image in the PNGJ file (in 
Firefox) or the drop fails (in Safari).


Tested in OS X Yosemite and Windows 7, with Java 1.8.0_65 in both.
Tested with the applet at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
which is Jmol 2015.10.17 and the matched version of the application 
Jmol.jar.


-Eric
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[Jmol-users] FirstGlance updated

[Eric Martz]

FirstGlance in Jmol version 2.32 is now available. As always,
http://FirstGlance.Jmol.Org
or google "firstglance" (with NO SPACE between t and g).

Java applet function is restored with the new certificate.
The JSmol (HTML5) menu can now be opened (thanks Bob!!!).

Browser compatibility and performance has been updated, and the Edge 
browser in Windows 10 has been included. See

http://bioinformatics.org/firstglance/fgij/notes.htm#browsers

As always, thanks to Bob Hanson for his responsiveness in diagnosing and 
fixing a number of bugs.


-Eric


Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- Martz.MolviZ.Org <http://Martz.MolviZ.Org>

 * Top Five 3D MolVis Tools: Top5.MolviZ.Org <http://top5.MolviZ.Org>
 * FirstGlance: 3D Molecules in /Nature/: FirstGlance.Jmol.Org
   <http://firstglance.jmol.Org>
 * Protein 3D Structure Wiki: Proteopedia.Org <http://proteopedia.Org>
 * Education: Biochem in 3D at MolviZ.Org <http://MolviZ.Org>
 * Find Functional Patches in Proteins: ConSurf <http://consurf.tau.ac.il>
 * Atlas of Macromolecules: Atlas.MolviZ.Org <http://atlas.MolviZ.Org>
 * Interactive Molecules in Architectural Spaces:
   MolecularPlayground.Org <http://molecularplayground.Org>
 * Workshops: Workshops.MolviZ.Org <http://workshops.MolviZ.Org>

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[Jmol-users] Installing & Enabling Java (Updated)

[Eric Martz]

These instructions for installing and enabling Java

http://proteopedia.org/w/Installing_and_enabling_Java

have been updated to include Microsoft Edge, a browser first released as 
part of Windows 10.

Edge does not support Java. However Internet Explorer 11 is also 
included in Windows 10, and works well with the Jmol Java applet. 
Instructions for accessing the (initially hidden) Internet Explorer in 
Windows 10 are in the above-linked document.

And of course Firefox can also be used in Windows 10 for Java.

In Windows, Opera currently runs the Jmol Java applet well, but Opera 
plans to remove Java support in the future. Opera has not operated the 
Jmol Java applet in OS X for a long time.

The above-linked document also includes instructions for enabling the 
old unsigned Jmol Java applet in legacy sites (examples of which are the 
tutorial on Hemoglobin, Antibody, and Major Histocompatibility at 
http://MolviZ.Org).

A summary of browsers vs. Java (and JSmol) is here:
http://bioinformatics.org/firstglance/fgij/notes.htm#browsers

-Eric

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[Jmol-users] JSmol in Edge, Chrome, etc.

[Eric Martz]

My tests of JSmol (in FirstGlance) in the Windows 10 Edge browser 
indicate that while Edge runs HTML5/Javascript much faster than Internet 
Explorer, it is still markedly slower than Chrome or Firefox.

Internet Explorer remains unusably slow with JSmol/HTML5. Edge is usable 
but sluggish, especially for rotation. While Edge rotates cartoon about 
as fast as Chrome, it rotates a spacefilled rendering much slower than 
does Chrome.

Curiously, the speed/smoothness with which Chrome rotates a cartoon 
rendering in JSmol/HTML5 has gotten much worse recently. Months ago, 
Chrome out-performed or equaled all other browsers in rotation. Now, 
Chrome is substantially slower/jerkier for rotation than Firefox or 
Safari. This is true in both Windows and OS X.

Opera remains very poor at rotating the molecule in JSmol/HTML5. For 
cartoon in OS X, Opera is slower than Chrome by about two-fold. In 
Windows, Opera is about equal to Chrome for both cartoon and spacefilled 
renderings.

Here is table summarizing my test results today:
https://flic.kr/p/z3Yh6J

A summary of browsers vs. Jmol/JSmol is here:
http://bioinformatics.org/firstglance/fgij/notes.htm#browsers
(This does not yet reflect the recent deterioration in cartoon rotation 
speed by Chrome in JSmol/HTML5).

-Eric


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[Jmol-users] Oct 17 Jmol works in FirstGlance

[Eric Martz]

Hey Bob, thanks so much for your prompt efforts fixing bugs. The Oct 17 
release (which is still named 14.4.0_2015.10.14, but shows the date 
below the version number as Oct 17) appears to work correctly with all 
FirstGlance operations.

And Halleleujah! Now the JSmol menu can be popped up in FirstGlance -- 
for the first time ever! (Gabriel Pons take note!)

I have not released a new version of FirstGlance yet but will announce 
it on this list when it goes public.

Great work, Bob! -Eric

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[Jmol-users] DNA sidechain bug

[Eric Martz]

Dear Bob,

With Jmol October 14:

Many DNA oxygens that are not sidechain atoms are selected with "select 
dna and sidechain", notably oxygens on phosphorus and in deoxyribose.

load =1d66
restrict none
select dna and sidechain
wireframe 0.3
spacefill 0.3
color cpk

You will see the sidechains of the DNA as sticks. Surrounding them are 
many oxygens "floating in space". These are not sidechain oxygens.

This bug was not present in earlier Jmols, e.g. it is absent in Jmol 
14.2.15.

Eric


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Re: [Jmol-users] All deployed Jmol Java applets are disabled

[Eric Martz]

Are you sure its *irrevocable*, Bob? That's quite unfortunate. As Angel 
says, it will take me some time to verify that current Jmol works in 
FirstGlance. Typically, I find one or more bugs/issues and have to wait 
till they're fixed (in my code or in Jmol) before I release a new 
version. And often I end up releasing with an earlier version of Jmol to 
avoid some problem or other. This means nobody can use FirstGlance with 
Java until I can get all those issues ironed out.


Well glory be to JSmol/HTML5 which will keep FirstGlance operational 
meanwhile!


On 10/16/15 12:48 AM, Robert Hanson wrote:
Well, it turns out that, following the instructions of an 
inexperienced representative from GoDaddy (where Jmol's secure signed 
certificate is managed) I just disabled permanently and irrevokably 
all standing Jmol Java applets.


Not kidding. *All deployed Jmol applets are dead*. Period. They will 
report:


Inline image 1


JSmol *JavaScript installations are not affected* (because they are 
not "signed").


Standalone Jmol JAR files are not affected (I am pretty sure).


In short, this is a mandatory upgrade for any site using Jmol or 
JSpecView.

All Integrated-Graphics signed Java applet installations must upgrade.

I am compiling now.

And it was such a good week

Bob

--
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] Unsigned Jmol Java applets still work

[Eric Martz]

Curiously, very old websites that still use unsigned Jmol java applets 
still work, despite the certificate for newer signed Jmol being revoked.

For example, the tutorials on Hemoglobin, Antibody, and MHC at 
http://molviz.org. These still work in Firefox on OS 10.10.5 Yosemite. 
An alert complains, but seems harmless, and sometimes you have to give 
permission more than once for the applet to run, but basically, after 
you get the unsigned applet configured to work, these still work with 
only minor fussiness.

Instructions for getting unsigned applets to work are included here:
http://proteopedia.org/w/Installing_and_enabling_Java

-Eric

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[Jmol-users] 14.4.0 problem with HTML5

[Eric Martz]

Dear Bob,

While developing FirstGlance, I test by running from local files in 
Firefox (on OS X; currently Firefox 41.0.2). All tests below were done 
using *HTML5* (no Java).


My current in-progress version of FirstGlance loads and displays 1d66 
using JSmol from *Sept 20*. Function appears OK.


When I use JSmol from *October 13*, the molecule does not load/display. 
My error reporting code says that JSmol is saying:


script compiler ERROR: invalid context for end if

(but the same Javascript and JSmol commands work with the Sept 20 JSmol).

When I look in Firefox -> Tools -> Web Developer -> Browser Console with 
JSmol *Sept 20, there are 27 'syntax error' lines* all referring to 
JSmol code (not FirstGlance code), even though the molecule displays and 
function seems good.


With JSmol *Oct 13, there are only 6 syntax error reports* (listed 
below). I have marked the 'syntax errors' in red.


-
element_focus_changed_caller: 3682822
no browser or host: 3682822
element_focus_changed_caller: 3682822
no browser or host: 3682822
before ff_id generation
ff_id generation 1
ff_id generation 2
ff_id generation 3
after window.setInterval
before "linkedBrowser.addEventListener"
before "addEventListener"
element_focus_changed_caller: 7769794
no browser or host: 7769794
element_focus_changed_caller: 7769794
no browser or host: 7769794
tab_id_created_sent: 7769794
process request - let's do: 


unreachable code after return statement main_cs.js:140:1
unreachable code after return statement main_cs.js:397:1
JSmol load jmolApplet0 loadClazz... JSmol.min.js:273:477
JSmol load jmolApplet0 start applet... JSmol.min.js:273:477
process request - let's do: 


JSmol exec jmolApplet0 loadClazz null -- OK JSmol.min.js:272:366
xhr.open async=false url=jsmol/j2s/core/package.js JSmol.min.js:178:297
Synchronous XMLHttpRequest on the main thread is deprecated because of 
its detrimental effects to the end user's experience. For more help 
http://xhr.spec.whatwg.org/ JSmol.min.js:178:0

xhr.open async=false url=jsmol/j2s/core/package.js JSmol.min.js:178:297
process request - let's do: 


not well-formed package.js:1:1
xhr.open async=false url=jsmol/j2s/core/corejmol.z.js JSmol.min.js:178:297
element_focus_changed_caller: 7769794
no browser or host: 7769794
element_focus_changed_caller: 7769794
no browser or host: 7769794
not well-formed package.js:1:1
syntax error corejmol.z.js:1:1
xhr.open async=false url=jsmol/j2s/java/net/UnknownServiceException.js 
JSmol.min.js:178:297

xhr.open async=false url=jsmol/j2s/JM/Structure.js JSmol.min.js:178:297
syntax error UnknownServiceException.js:1:1
xhr.open async=false url=jsmol/j2s/J/io/JmolBinary.js JSmol.min.js:178:297
syntax error Structure.js:1:1
xhr.open async=false url=jsmol/j2s/J/g3d/PrecisionRenderer.js 
JSmol.min.js:178:297

syntax error JmolBinary.js:1:1
JSmol exec jmolApplet0 start applet null -- OK JSmol.min.js:272:366
xhr.open async=false url=jsmol/j2s/core/corescript.z.js JSmol.min.js:178:297
syntax error PrecisionRenderer.js:1:1
syntax error corescript.z.js:1:1
element_focus_changed_caller: 7769794
no browser or host: 7769794
element_focus_changed_caller: 7769794
no browser or host: 7769794
element_focus_changed_caller: 7769794
no browser or host: 7769794
element_focus_changed_caller: 7769794
no browser or host: 7769794

---
I interpret this to mean that some change in JSmol between Sep 20 and 
Oct 13 is a bug. Let me know if I can help.


-Eric
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