On 29 Nov 2009 at 9:54, Andy Lu wrote:
> In Jmol, the default setting for selectionHalos on is all of the atoms, or
> you can select more
> specific types of protein residues, ex. Arg, His, Aromatic, etc.
The setting is to show halos for all SELECTED atoms. You define what you want
selected.
This happens at times with pdb files that have the wrong position of atom IDs
(typically,
shifted by one column position). Jmol does not identify the element, then makes
it unknown,
with is colored pink and sized as a smallish sphere.
Don't know how the NWChem specifies the element, but looks a
El 30 Nov 2009 a las 16:34, Graeme Kidd escribió:
> Although it looks like I could use {atomno=1}.spacefill
Right. It seems that all these 3 are synonymous:
{atomno=1}.radius
{atomno=1}.spacefill
{atomno=1}.cpk
--
El 30 Nov 2009 a las 16:34, Graeme Kidd escribió:
> Although it looks like I could use {atomno=1}.spacefill
Right. It seems that all these 3 are synonymous:
{atomno=1}.radius
{atomno=1}.spacefill
{atomno=1}.cpk
--
On 2 Dec 2009 at 13:33, Brian Moldover wrote:
> So do you load the pdb file multiple times? I´m reading the documentation
> but obviously
> not clear on how to do this or I wouldn´t have asked J
Hi Brian
No. You load the file once into each applet.
Actually, since it has been loaded in
In addition, Brian, you can even load a single model into each applet (so as to
reduce the
load), using "load models"
http://www.stolaf.edu/academics/chemapps/jmol/docs/#loadMODELS
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Try by all means to avoid "restrict". Use "display" or "model" = "frame"
Restrict acts on the atoms and bonds radii, and is not reversible, while
display is wholly
reversible (that is, you don't lose your atoms style). For models/frames, the
proper
command is model
-
Olga, can you please specify what version your are using?
I just tested 11.8.7 application and both the jpg and pdf are OK
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Olga, I still cannot reproduce your problem using now 11.8.11
What are you exactly doing to export the image?
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Hi Henry. How are you doing?
> A Windows program called Multiconversion appears to do the trick
> (but I have not yet found a download site).
Seems to be here:
http://stereo.jpn.org/eng/stphmkr/
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Brian, I suspect your latest problem may be due to lack of syncronization. That
is, when the
page contains several applets, they take some time to load, in parallel. Then
the scripts may
be called after some applets but before others. So some of the scripts will
fail. It can also
depend on the b
Yes, pages with many applets behave unpredictably and depending on the browser.
That0s
difficult to control.
Myabe you can try a trick by Bob for loading applets in sequence, one after the
other has
finished. It's somewhere on this list archive.
First time I opened your page in my Firefox 3.5
Dear Eric
As you'll know, I'm a Windows-only person. But this is what I've learnt related
to your query:
1. The "-g" parameter in the command line sets the window size, but there's no
way to
indicate the window position AFAIK
2. For me (WinXP), the application window position and size, the co
Otis, I'm surprised. As far as I know, Jmol has no wedge bonds. Can you provide
an
example (a model file, or an image) of such a result?
On 8 Dec 2009 at 11:19, Otis Rothenberger wrote:
[snip]
> This works very nicely, but the resulting 3D Jmol
> structure retains a wedge shaped bond.
Hi again Otis
1. I did not receive your first post or the image, but now I've seen it inside
Jmol
2. I'm astounded. Never saw that wedge bond before. It must be a relic from old
Jmol
versions.
3. I cannot follow your source code enough to see what it is you are passing
into Jmol. It is
not
I see. You must be using JME format to pass the data. Jmol has indeed a reader
for JME,
though is is declared as "not fully supported".
If I request Show > File Contents from Jmol, I see it as e.g.
8 8 C 9.44 -7.81 C 9.44 -6.41 C 8.23 -5.71 C 7.02 -6.41 C 7.02 -7.81 C 8.23
-8.51 C 8.23 -
4.31
> I don't know why I got it in my head that I had to pass the JME file.
> At one point, I seemed to be having CR/LF problems with molfiles going
> in via the Jmol DATA MODEL route. That's when I switched to the inline
> approach. I guess I just had this problem with molfiles via DATA
> MODEL in my
Otis, I thought this couldn't be done, but a search told me that onMouseOver is
supported
for the applet tag, so I've done a few tests and (at least in Firefox) both
applet and object
are supported. So, using Jmol.js to insert the applet, you can do
document.getElementById("jmolApplet0").onmou
El 11 Dec 2009 a las 19:10, Otis Rothenberger escribió:
> The pickCallBack works in Firefox, Chrome, and MISE. On my test with
> an alert() to look at the return arguments, I think I understand all
> the returned arguments except the last. I got two alerts on a click -
> mouseup mousedown??
While
Hi Vincent
Don't be concerned about asking, this is the place for that. We all
learn from each other.
> 1. I'm trying to select residue of the protein within a given cutoff
> distance from a previously selected set of atoms.Currently I'm using :
>
> select amino and within(5.0, STP2) ;
> co
El 14 Dec 2009 a las 16:12, Vincent Le Guilloux escribió:
> I think I have what I want with that. I didn't saw that within could
> be combined like that... I really need a full day to make my hands on
> Jmol scripting :)
If you can do it in just one day, we'll give you a medal ;-)
> What I
Inline data and newlines tend to eb asource of trouble...
Jonathan, have you checked it's not a quotes problem?
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Dear Andy
These are places where you can read about the way to use callbacks:
http://chemapps.stolaf.edu/jmol/docs/#k617
(from a Jmol script)
http://jmol.sourceforge.net/jslibrary/#jmolSetCallback
(from Javascript in a web page, using Jmol.js)
About "function name" in
set ScriptCallback "funct
I've been away and couldn't participate on this discussion.
The color picker looks great. One possible addition would be to use a
more suggestive icon rather than the little table: a palette maybe?
http://commons.wikimedia.org/wiki/File:Nuvola_apps_kcoloredit.svg
Maybe you didn't notice there was
Jonathan wrote:
> question to the community is do you want one .js file or would it be
> better to have to load separate files for each widget and possibly
> separate supporting .js files as well?
As a first thought, I'd vote for separate files for each widget.
> As an aside, what o
Bob G., thanks for reporting this.
I've run a quick check with a local copy of the offending page, and it's not an
issue of
linefeeds.
It's a bug in Jmol. I can trace it back to between 11.8.7 and 11.8.11.
11.8.15 (the current version at the website) and 11.9.13 fail too.
jmolLoadInline() wor
I've narrowed it down to between 11.8.10 (works) and 11.8.11 (fails).
That's 20 to 28 nov. 2009
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This is a bug introduced between 11.8.10 and 11.8.11 that affects
jmolAppletInline(), but not
jmolLoadInline()
The topic is being followed in another thread ([Jmol-users] Jmol demo page
hangs)
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Yes, I see the same: the applet ends loading, but stays empty.
Try changing to JmolApplet 11.8.10
It works for me with your code
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Robert Hanson wrote:
> OK, I know what it is. You can't give
>
> jmolApplet(...)
> jmolLoadInline(..)
>
> right in a row like that.
>
> After jmolApplet the browser is busy creating the applet. VERY unwise
> to fire commands at it while that is happening.
Yes, I've often had similar proble
Hi all
I have a problem with translating terms related to the recent multi-
touch features. Not having one such device is not helping either.
Specifically, what is exactly the action denoted by "swipe"? How is
it different from "drag"?
General definitions of swipe are not helping me much to und
El 14 Jan 2010 a las 11:45, Grossman, Robert B escribió:
> With Jmol 11.9.18, Safari 4.0.4, MacOS 10.5.8, and the following code:
I'm not sure, but probably 11.9.18 has the same bug as 11.8.15,
11.8.16 and 11.9.13. The fix has been done recently and is not yet
available for download. You can ei
Sorry Bob, what red button?
The applet hasn't got such
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El 14 Jan 2010 a las 11:24, Robert Hanson escribió:
> A "swipe" means you drag and the motion stops at the exact moment
> that the mouse is released.
So the key is whether you release the button (swipe) or not (drag).
Thanks
> You really can't do it with a mouse
Well, I'm quite sure I did it
El 14 Jan 2010 a las 12:48, Grossman, Robert B escribió:
> The version I have most recently downloaded, 11.9.18, is the one from Bob's
> site.
Current is 11.9.19_dev, dated 14 Jan.
Try that, so we can clarify the issue
---
Sorry for the possible confusion, I see that the date of the latest
file in Bob's site is 14 Jan, but the popup menu reports 12 Jan.
A better idea: I remembered about one of Bob's tricks: you can view
any Jmol webpage using any version of the applet.
This is documented at
http://wiki.jmol.org/i
Bob, the problem with saving images or whatever is that Java applets are not
allowed to
access the user's disk. That's why the signed applet exists, and can do it, as
Paul has said.
> - using the signed applet, you can send the script
> save IMAGE PNG "filepath/imagename.png"
And apart from
Hi Jeff
Easy.
When you load 2 files, Jmol puts them in 2 "frames" (or "models"). You have
found that you
can select them, using 1.1 and 1.2, but that doesn't make them visible.
You must use the "frame" command, see
http://www.stolaf.edu/academics/chemapps/jmol/docs//index.htm#frame
Example:
fr
Robert Hanson escribió:
> calculate hydrogen # adds the hydrogen atoms to C,N,O,and S atoms,
> respecting bonding but not considering formal charge (for now).
This sounds exciting, Bob!
> minimize addHydrogens # minimizes and then adds H atoms at the end
I have one wonder here. In my experie
Hi again, Bob
I think you have a problem related to applet IDs.
Please review
http://jmol.sourceforge.net/jslibrary/index.en.html#jmolApplet
By default, applets receive IDs like 0, 1, etc. That means they get named
jmolAppplet0 etc.
Since you are giving 'jmolAppplet0' as the ID, your applet will
Hello Ansari, and welcome to Jmol world
Jmol does not use any connectivity table, and does not treat differently
standard amino
acids from other chemicals/residues/groups. It just makes bonds when the
interatomic
distance is below the sum of van der Waals radii of both atoms (there may be a
t
> The next option might be to detect when the user clicks on one of the
> "Colour+Colour Glasses"
> menu items and switching the images accordingly.
Graeme, you can customize the popup menu so that it will do that switch
automatically.
That way you avoid to have a detection routine or
Dear Eric:
What I remember is that Jmol by default doesn't differentiate chain IDs by
case, but it can
be pushed to do so by setting one of its state variables.
Do you find a different behaviour in older versions?
Ah, there it is:
set chainCaseSensitive FALSE
http://www.stolaf.edu/academics/che
On 17 Jan 2010 at 18:39, Graeme Kidd wrote:
> Should I maybe convert this thread into a feature request?
Go and do it.
I have no idea whether it's technically possible, but a FR won't do any harm
and so things
get registered and are more manageable.
-
> write "3hyd.jvxl"
>
> (from the application or signed applet)
Or pop-up menu > File > Save JVXL Isosurface
with a nice Save As dialog that lets you see/choose where it is going
:-)
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I've seen the same with e.g. methylamine
Some times the minimization manages to pull both Hs apart, other times not.
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Dear Jmol users,
The pop-up menu has some entries under Select > Hetero that I'd like to reword.
- They are only fully understood by those knowing the script language (and the
popup menu
should be clear for naive users)
- In English, some are redundant
- In other languages, they are confusing, s
Hi Tom
This all dates back to compatibility with Rasmol and Chime scripts. Rasmol was
designed to
be used mostly with pdb files, and Jmol 10 wanted to inherit that functionality
(which is just
wonderful for us biochemists ;-) ).
So, these are Rasmol tokens that shouldn't change, but I think t
You have a point, Rich, but what kind of options could we have for nonprotein
molecules?
There is select by element and by symmetry already. The list of selectable
elements could
be certainly expanded (ideally, to cover all elements present in the model, as
it is done for
amino acids).
The wh
Hi Henry
At least for echos, it can be done. I let you find about labels:
http://biomodel.uah.es/Jmol/multimodel/11-1.htm
click a button to load a model and you'll see all sorts of funny symbols at the
right inside the
applet
I reckon the way is unicode, not html codes
-
> right -- just use unicode.
And it seems that you need to enclose it in double quotes --at least in my
tests today--
label C\u03B1 # shows just that
label "C\u03B1" #shows C and alpha
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Hello, Norwid
We have had little experience with production of PDF files, so your
experience will be very helpful.
The output should display atoms and bonds as they are rendered in
Jmol when you invoke the export. It is certainly possible to have
some atoms as ball & stick, others as stick-on
In case it's of any use, I am seeing no problem with
* WinXP, Firefox 3.5.7, Java 1.6.0_15
* WinXP, Firefox 3.6, Java 1.6.0_18
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If this can be implemented, I think it needs to be done for both the app and
applet. This
could be a way:
* for the app, similarly to what is done for macros (a little known feature of
Jmol app, with its
own menu entry; macros are stored as text files in the user's home folder,
which is named
I don't think so, Jonathan. Better to have such thing done
consciously.
Also, if I want to delete a view from the list, I must select it
first. If the view in Jmol changes automatically, then I've lost the
view I had in favour of one I do not want to keep.
I think it is OK as it is now.
Hi Chuck
I cannot reproduce what you see, so I must understanding something wrong.
Can you provide the sequence of scripts that you are using?
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El 9 Feb 2010 a las 9:06, Jonathan Gutow escribió:
> Angel,
> I'm not sure I understand this objection.
Sorry to have disturbed you ;-)
> 1) When the user selects a single instance in the webexport list of
> instances, the viewer reloads that instance.
That's what I understood.
>
Sorry, Otis, I cannot help with your problem (but the feature looks
exciting! One more step towards a Jmol editor, even if a simple one.)
Your post prompts a question: is this "valency" property a shortcut
meaning "number of bonds"? Bob?
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After "calculate hydrogens", "minimize" does nothing and locks any
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"minimize addhydrogens" produces the same lock
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Otis wrote:
If you are after a web application, I don't think there's an
alternative, but do you know Avogadro? It's an app, lets you build 3D
molecules in real time.
> The clean up at the end of my current routine is really not bad
> visually. I had to do it to keep the growing molecule in t
It seems that minimize does not work after "set picking deleteatom" has been
used
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Hi Albertsson
Using a script:
http://chemapps.stolaf.edu/jmol/docs/#writemodel
says "only selected atoms are saved"
>From the popup menu, I think you can only do this in MOL format:
"Show > Extract MOL data"
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Can you define more precisely what is you are doing to position according to
the boundbox?
Jmol has, since ancient times, commands to orient according to Top, Bottom,
etc, which I'd
say are related to the boundbox. In fact, I've never seen much advantage in
having them in
the menus for exampl
Hi Andrew
Yes, that's an uncoommon format which reader might have some problem.
But first, have you tried with the Jmol app included in the
distribution? We should know first if it's a problem with your
compilation.
-
Tom,
maybe "within molecule" ?
http://www.stolaf.edu/academics/chemapps/jmol/docs/index.htm#text10
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Rob, I'm quite sure this has been discussed before on the list. Try searching
the archives
Don't remember now, but the outset was not very encouraging I'm afraid.
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The syntax is not correct:
measure RANGE 1.8 3.2 (within(molecule,_F)) (not within(molecule,_F))
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Rob, Nico is the man for your problem.
>From what I've experienced and guessed, yes, the standard build script does
>not make the
signed applet. It may have to do with what/how/who holds the signature.
I think there's some advice somewhere as to how to apply your own signature
when
building.
I am trying to generate a molecular isosurface for a set of atoms in the model.
Before, by default any isosurface made with "isosurface select(myAtomSet)" was
open.
Now I find that the surface is closed around the atom set, despite I have bot
set an "ignore"
option.
Is this a change, or a bug?
Ah. numeric chain IDs! They are not common, so this passes
unnoticed.
Charles, that's probably a bug, but I guess you can safely remove the
dot asterisk part and get the same result you are expecting
select {[GLY]100:V or [THR]1:2}
# 2 atoms selected
>
> scriptcompiler ERROR: unrecognized ex
Bob, it's on the email subject:
2b9n.pdb
one of the ribosome ones
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An idea just popped up for Eric:
As a "roundabout" solution:
Maybe you could load just the selected frames, in the desired order, using
"load models"
and then animate them?
So,
> http://proteopedia.org/wiki/index.php/Sandbox_5_Eric_Martz I would like to
> animate just 2 frames, 1.1 and 1.10.
Hi Alan
Maybe you can use this:
http://www.stolaf.edu/academics/chemapps/jmol/docs/#setbondstyles
set bondTolerance (decimal)
When autobonding, the value of bondTolerance is added to the two bond radii
of atoms
being tested for a bond. A larger bondTolerance allows atoms that are further
Hi Nick
I think you can do it by including the model/frame spec in the atom expression,
either */1,
*/2 syntax or model=1.1, model=1.2
Say
connect 1.0 1.2 (carbon and model<3) (hydrogen and model<3) single
connect 1.0 1.2 (carbon and model>=3) (hydrogen and model>=3) partial
connect 1.0 1.2 (
I'm guessing, but I see 2 potential problems there:
On 3 Mar 2010 at 20:42, Rolf Huehne wrote:
> Let's assume an initial size of 600x600 pixel. Then the browser zoom
> setting is changed to 130%. Now the applet is 780x780 pixel. But CSS
> will still report 600x600 pixel.
Have you checked that?
El 5 Mar 2010 a las 8:58, Robert Hanson escribió:
> Jeff, be sure to check that out with 11.9 and get back to us.
If it's of use, I tried with 11.9.29 earlier today and it fails as
Jeff describes.
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If I remember corectly, the b-factor is read using this command:
color tenperature
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Hi Durga
Search the online scripting documentation for "colorscheme". That's
what you need. Apart from the standard schemes, I'm quite sure you
can impose your own. You may need to use a JmolScript variable for
that, I'm not sure.
Piero, you must be careful with the quotes. Javascript gets confused
Try this way, combining double quotes (for Jmol) and single quotes
(for JS):
function setPackaging(){
jmolScript('load "" {' + parseInt(document.pack.par_a.value) +
parseInt(document.pack.par_b.value) +
parseInt(document.
Hi Andy
I'm not sure I understand what you mean by adding a trajectory point (I haven't
worked with
trajectories), but regarding the addition of atoms without generating new
frame/model, there
is
set appendNew false
Don't know if that would fix the slowness.
-
Robert Hanson wrote:
> was there a question here?
The question is in the email subject line, Bob.
Charles, that PDB file only has alpha carbons for the Y chain. Not Jmol's fault.
The model has just 5A resolution, so it seems that the whole protein has not
been solved.
-
> 1.select an atom in a pdb file and make it the center of rotation
see Scrpting Documentation, commands "select" and "center"
> 2.restrict rendering to only those atoms or structure at a given
> radius away from the selected atom (center of rotation)
select within
and then
display
Maybe change the color, or the traslucency
You also have halos
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> I don't recall the exact parameters now. See
>
> file:///C:/jmol-dev/workspace/Jmol-
> documentation/script_documentation/index.htm?ver=11.10&search=callback
> #setcallback
There's also a bit of info that may be helpful about how to deal with
callbacks at
http://jmol.sourceforge.net/jslibrary/
Piero,
always starting from
http://chemapps.stolaf.edu/jmol/docs/
(which is linked from Jmol's website)
so
http://chemapps.stolaf.edu/jmol/docs/index.htm?ver=11.10&search=callback#setcallback
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I've never attempted f(w,x,y,z) directly, but you can assign custom properties
to atoms, so the
xyz could be coordinates and the 4th datum be assigned to a property, and later
used e.g. for
a color.
See "atom properties" in the Scripting Documentation
http://www.stolaf.edu/academics/chemapps/j
Hi Peter
Yes, Jmol can open .gro files. I'm not sure though if there is more than one
format output by
GROMACS.
http://wiki.jmol.org/index.php/File_formats/Coordinates#GROMACS
I used gro files coming from a molecular dynamics calculation once, but at the
time Jmol still
couldn't cope with the
Hi Frieda
I don't think you can do it for any two applets in one go. Either one or all.
I'm assuming you use Jmol.js.
jmolScript() takes as its 2nd argument the ID, which may be "all".
For buttons, you need to use jmolSetTarget() which I'm not sure if it accepts
the special "all",
but give it
Hi Frieda
> I am getting a Javascript
> alert that Jmol cannot find Applet0.
By using custom names you probably need to specify the applet ID always, using
the target
parameter in jmolScript or the jmolSetTarget() command for buttons etc.
> This message appears only on the
> first time I
Piero,
Sorry, I'm lost. Please be specific about what you have and what you
need to do
El 6 Apr 2010 a las 13:09, P.Canepa escribió:
> Rob, Angle
>
> I did as you said. What I see is: the file location as b, the name of the
> file as c and the title of the file as d.
> What's the way to ex
5 Sep 2014, 9:12, Robert Hanson wrote:
> On Fri, Sep 5, 2014 at 8:29 AM, Scalfani, Vincent > wrote:
>
> P.S. An STL writer in Jmol would be AWESOME!
>
> show me the spec.
The info I see for STL in Wikipedia speaks only of triangles. We'd
need cylinders and spheres too for a go
Bob, I added the links for the 2 presentations in the Wiki
http://wiki.jmol.org/index.php/Events
Good job!
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I've added that in
http://wiki.jmol.org/index.php/Troubleshooting/Local_Files
accesible from the front page > Running Jmol > Troubleshoot
that's a new page; I suspect this may need merging with information in other
pages, but at least it is set until I find them. The whole troubleshooting
needs
Otis,
your Automator scripts are know at
http://wiki.jmol.org/index.php/Troubleshooting/Local_Files/MacChromeAutom
ator
http://wiki.jmol.org/index.php/Troubleshooting/Local_Files
On 3 Sep 2014 at 9:07, Otis Rothenberger wrote:
> On the Chrome (37.0.2062.94 on Mavericks) issue that I wrote about
Dear Bob,
Can you explain the difference between Info.z and Info.zIndexBase?
For now, I am setting both, but would prefer to be more specific
--and also complete the doc
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Info
Thanks
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Hi
I have problems with JSmol/Html5 version 14.2.4
Both with my major pages (complex) and with a very simple test page,
I get the same error on page loading with a single Jmol object:
The Jmol box displays:
Jmol._Canvas2D (Jmol) "myJmol"[x]
Smol/j2s/core/package.js
And the browser JS conso
> There have been 1400 downloads of that, and I just downloaded and
> tested it again, and it worked fine. I suspect something is wrong
Well, who knows, could be cache or anything. But it got fixed when I
tried the other version.
Now I am testing 14.3 (because of other problems with sync) and i
Hello Anders
If I may come into the question, here are some ideas that may or not suit your
situation.
1. I know that your file has no connectivity info. Have you tried having Jmol
to determine
bonding? Looking at your script, it seems that you define bonded based on vdw
distance. SO
I guess J
Hi Michael
> No atoms are shown. If I click on "show" / "file contents", the
> information is there. So it would seem to be a problem of interpretation.
> Do I need to explicitly say it is a pdb file ?
Yes, it's possibly that.
You can check trying yo put that text in a file and load it in Jmol
Yes, it is not the need for other than the ATOM line. I did a quick test (in an
old Jmol version)
and it reads as pdb but does not display anything, for whatever reason
Add e.g.
spacefill 23%
and you see the atom
> I also tried that, but I'm not sure how to do it with Visual Basic.
> Essenti
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