Hello Benjamin
Your problem is probaly related to the "Java cache" in the browser.
This a browser-specific problem, per user.
You can fix it by manually clearing the Java cache before each
reload. There are instructions in the Jmol Wiki, Running Jmol,
Troubleshooting:
http://wiki.jmol.org:81/i
Thanks, Bob
> well, you can do whatever you want with the callback, right? If you
> want to know if an atom is in a certain set, I think you could use:
>
> if ({whateverSet} and {atomno=_atomHovered})
Yes, I am already following that line -and have a working test-.
It is atomindex, not atomno,
It can be done with the frame callback method, but it seems we don't
need to go that way. Based on my quick test, the connect command
works for all frames in one go without trouble, and the redefined
bonds are kept across the animation.
So, you may just need to disable autobonding and then apply
Karol, I think what Bob suggested is
1. there is no implementation of custom covalent radii
2. you can use the "connect" command to substitute for that: have
Jmol calculate and render bonds base on your radii
3. you must do that for each and every frame in your
animation/dynamics
The callback is
I see (11.5.50, 11.7.28) that the "biopolymers" entry in the pop-up
menu is greyed out. May that be a hint?
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Following my previous post, here are some other ways to do it:
If you want to keep the command in a single place, you can either use
a javascript variable or a function as you were trying to do (even
though I said before it could not be done):
var rotateModel = "rotate {atomno=20} {
Hello Aya
You seem to have several different issues. Let's try to sort out
things with your problem.
Your "function rotateModel" should be a Javascript function. First,
you need the proper javascript syntax (you are lacking the braces and
you should not use "end"). Second, the call to Jmol.js
> I often wondered
> why there isn't another way to do it---a different command key or
> command key combination.
There's also Ctrl + right-drag
(if you have a mouse with more than one button)
--
Apps built with t
> "a) Java allows malicious activity that could damage the system"
"Letting users use the computer allows malicious activity that could
damage the system" ;-)
And, does this mean that Flash is foolproof?
> "b) Java is an outmoded way to provide educational resources as everyone
> is using Flas
Alex,
it is possible to do that from the javascript side with the applet,
using pickCallback, as well as from the JmolScript language:
http://jmol.sourceforge.net/jslibrary/#jmolSetCallback
http://chemapps.stolaf.edu/jmol/docs/#setcallback
so I bet that there is a way inside the code to have it
Hi Dan
I'm afraid there is not much that can be done:
1. you can put commas instead of "or"
select atomno=3,atomno=5,atomno=18,atomno=26
2. if the file is MOL format (not sure about others like XYZ,
certainly not in PDB), you can use a combination of element symbol +
atom number, like
select C
Hello Inbal
Time ago, someone wrote a script for doing that (maye in Perl, not
sure now) but I'm not sure if it is still available and how trustable
it may result, particularly for recent Jmol versions; in any case,
I'd rather do it manually.
The tasks are:
1. substitute embed tags by applet
Hello Umanga
If you mean seeing the 5 models side by side at the same time, no.
You'll need 5 applets.
You can load the 5 files into a single applet and show them one by
one using the "load files" or the "load append" command. Or show them
superimposed at the same time, but they will overlap.
Yes, Dan, it is implemented. I put it into practice recently and
found a bug which has been fixed.
Read it all in the Wiki, including 2 examples.
http://wiki.jmol.org:81/index.php/Custom_Menus
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> Can you say to me where I can downloaded Jmol?
http://jmol.org
and follow the links
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Hi Ewen
That's pdb format, right?
I've done a quick test and it's working for me in both 11.4.6 and
11.6.16
Check the column positions of the atom numbers, might be that.
Not an explanation for your problem, but you could also dispose of
CONECT records and use Jmol "connect" command -- it's cl
Hello Yi
Not sure it this is enough to solve your problem; I don't think Jmol
can do the calculation of surface and volumen but, yes, you can save
the isosurface data.
>From application and signed applet, you can directly save to disk,
using
write isosurface
>From unsigned applet, you c
Egon, this page of mine
http://biomodel.uah.es/en/water/p3.htm
was built from Gromacs data of a molecular dynamics simulation.
Since Jmol did not read the gro file, I converted the data to pdb
format (see details at the bottom of the page).
We discussed about providing Jmol support for gro files,
This is an interesting feature, and rather surprising to me. One
never ends to marvel at Jmol wonders. Great work, Bob!
And now that I'm sensitive to the topic (having mused around it for
my home page in the last few days), this feature would contribute to
web accesibility, if the arrow, plus,
Hello Norman
That's quite unexpected. The Java installation should take care of
everything. I have never seen such problem.
Some things to try, as non-privileged user:
* Can you see Jmol applets in web pages?
* Can you open another Java application (another .jar file)?
* Is this happening only w
Hi Arjan
It is possible, provided that:
- you use Windows
- you use a PC where you have installed a certain piece of software
- but you really are embedding a webpage that includes a Jmol applet;
this has the advantage that you can also include controls like
butttons and so on
The software is c
Steve, It sees to me that instead of
"RELOAD {444 666 1}"
what you want may be the next menu entry,
"RELOAD {444 666 1}; display 555;"
Is it so?
And this is what these menu entries do, respectively:
save orientation; load "" {444 666 1} ; restore orientation; center;
and
save orientation; load
Jaime, I was writing a post for the Proteopedia list explaining just
this. Here is my advice:
I haven't looked at the source code, but this may help:
the sensible thing for pre-programmed surfaces in web pages is to
have Jmol save them as jvxl files, then make the page load that file -
- much fa
Henry, I've devised a (very) dirty solution:
duplicate residue 1 as nr. 9
The trace or cartoon is very sharp at the connection, so things get
better if we shift the residue numbering, such as making
1 -> 6
2 -> 7
3 -> 8
4 -> 1
5 -> 2
6 -> 3
7 -> 4
8 -> 5
9 is a copy of the new residue 1 (former 6
Well, it is not based on residue numbering.
A possible way to deal with this ould be to parse the pdb information
in LINK records.
Henry's file (2HK4.pdb) has them:
LINK P C A 1 O3* T A 8
LINK P C B 1 O3* T B 8
Hi Henry
Nice molecule! I had only known cyclic DNA molecules as in
"circular" DNA, e.g. procariotic DNA and plasmids. Chemicaly there is
not much difference.
I don't know the exact code being used fior calculating and rendering
cartoons et al., but I guess it is based on phosphorus IDs and
r
Hi Eran
Translation should be possible using "move", if I remember correctly.
Not sure about zoom; I think it only works in percent.
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> Thank you for the tip, but I noticed that "write state" doesn't support
> in the Applet version?
Yes, as everything that writes to disk, it is not available for the
unsigned applet. You can use application or signed applet for that.
Or just save to memory in a Jmol user variable to wich the ou
Hi Umanga
When you have the initial view as you want it, use
show state
and store that script (in an internal variable* or saved to a file,
"write state"), then later restore it either calling that script or
loading the script file.
*) may be using Java, o Javascript, or even a Jmol use
Today I am playing with VRML export. Models export very nicely
(restricted to atoms and bonds, it seems; not a complain, I knew that
features were limited).
Jmol offers by default the .vrml extension for files.
To see the vrml files, I have installed Flux Player (application and
browser plug-in
A paper that may be worth reading in this respect:
* (2008) Adapting a single-user, single-display molecular
visualization application for use in a multi-user, multi-display
environment.
http://www.cliftonforlines.com/papers/2008_forlines_molvis.pdf
(now linked from MultiUser_Jmol and Jmol_Lite
Hi Eran
> moveto timeSeconds {x y z} degrees zoomPercent transX transY {x y z}
> rotationRadius navigationCenter navTransX navTransY navDepth
> Can anyone offer some help as to what "{ 102 -219 -970 176.64}"
I'd say the 176.64 matches the "degrees" parameter. The braces are
ignored, just t
Hi Phan
I agree with Duan.
It may be a problem with the file path. Open the Java console and
copy the exact error, and post it here.
For a safest test, put the pdb file and the Jmol.jar file in the same
folder, then open the script console and type
load yourfile.pdb
(do not use the top menu,
El 15 Dec 2008 a las 11:46, Raphael André Bauer escribió:
> it seems that your observation is right and using the jmol.js breaks
> the GWT. However it is easily possible to use jmol without jmol.js and
> thus avoiding this problem. An idea is to use the Firebug plugin for
> Firefox that gives you t
El 15 Dec 2008 a las 11:46, Raphael André Bauer escribió:
> it seems that your observation is right and using the jmol.js breaks
> the GWT. However it is easily possible to use jmol without jmol.js and
> thus avoiding this problem. An idea is to use the Firebug plugin for
> Firefox that gives you t
Hi Umanga
Yes, that's the behaviour.
If you want a single label you must select a single atom -- or a
single coordinate, maybe at the center of the atom set. But that is
not done with "label", because labels are objects attached to atoms.
So you may either:
a) choose one of the atoms (manuall
El 10 Dec 2008 a las 18:34, Robert Hanson escribió:
> Something's not right.
>
> mayscript = false in no way prevents jmolButton from being created,
> and with mayscript=false, the jmolButton still works fine.
>
> Something else is going on there.
I though it weird, but that is tested on an in
> All -- I'm pretty sure that if you invoke _jmol.noEval = true in your
> wiki code, you will completely shut down any JavaScript functionality
> of Jmol except callbacks. This setting cannot be changed within Jmol
> -- it is checked upon applet creation and cannot be changed within the
> applet. S
Hello Umanga
Jmol will always use the residue numbers that are written in the pdb
file (not the order in the chain or in the file).
So, your problem seems to be in the exact data you have in your pdb
file.
That said, there may be a way for Jmol to find out the length of
chain A and add it to t
El 9 Dec 2008 a las 14:03, Nicolas Vervelle escribió:
> For example, I think you can stillrun Javascriptwithscripts
> calling other scripts:
> * Create a wiki page with contents corresponding to a Jmol script with
> Javascript in it.
> * Add a tag in a page with a script calling the ot
I'd like to keep this discussion going, so here is a little bit more,
picking up on the possibilities to have Jmol supported in Wikipedia
and other Wikis:
On 30 Nov 2008 22:53, Nicolas Vervelle wrote:
>
> On the matter of security issues, there are at least 2 things to do :
> * Being able to
I understood that there was a mechanism (setting) to prevent error
messages from being translated. From the recent discussion, I am not
clear as whether that is not working as I thought it would.
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Hi Gerard
Thanks for the suggestions.
Jmol is already fully internationalized and localized, over 10
languages:
http://wiki.jmol.org:81/index.php/Internationalisation/Current_Status
I'm not sure if the MediaWiki extension would need any further
localization.
Does the testing environment th
Brilliant, Frieda!
How about putting an animated gif as background image in Jmol? I
think we can put images as background, of course I don't know about
animated ones.
Or try the weird transparency trick that was recently discovered and
put the animgif as an image in the webpage behind the tran
El 20 Nov 2008 a las 22:09, Ondrej Certik escribió:
> Wow, all those applets work perfectly in my browser. So the problem
> seems related to some communication between the applet and javascript,
> right?
Yes, that confirms it. These pages do not use Jmol.js (in fact, they
are rather old are wer
Dear Jmol users:
-- For your information --
I have found a Java bug repainting Jmol's pop-up menu when the latest
Java (6u10) is installed. It seems to be related to the display
driver/graphics card. I see it in Windows XP with any browser, only
in my notebook but not in my desktop PC. It is
El 18 Nov 2008 a las 14:29, Ondrej Certik escribió:
> do I need to install some files as well? I thought it will work out of the
> box.
Right. Working with the demo pages is the safest way to assure that
your system works. Nothing to set up on your side.
> > http://www.javasonics.com/support/c
Hi Kris
I'm no expert in Linux, but it seems that your system doesn't know
how to open jar files. So, you must invoke Java for that file:
java -jar Jmol.jar
adding the proper paths to java and Jmol.jar, if needed
Another option is to try the script file included in the
distribution, which
Hi SC
You need to give details about the errors you get in the Java
console, or the URL for testing, so that some of us can see where is
the problem.
(If you don't know how to find the Java console, see here
http://wiki.jmol.org/index.php/Solving_Java_Problems
--
Maybe that is being affected by the setting (and / or) of
set bondMode
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El 13 Nov 2008 a las 16:45, Rolf Huehne escribió:
> This copy doesn't seem to be fully functional. The version selection
> doesn't work and also the examples. Passing parameters to the HTML file
> doesn't seem to be allowed.
Thanks for checking Rolf. I just viewed the main page and didn't test
i
Thanks for raising this, Rolf
To me it sounds as a very interesting suggestion. From here in Spain,
the page load time from the StOlaf server is regularly rather long.
An alternative server would hence be of help.
Of course, I'm not sure of how difficult it may be to maintain an up-
to-date cop
Frieda, I'd say that you can set a custom range for charges, then the
color range effectively used will be widened.
(I don't remember the syntax right now.)
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David, a very quick response; I'll need some more time to check
details:
> would like Jmol to be able to display H-bonds between amino acid side
> chains and main-chain atoms
I agree that this would be very interesting, but it seems hard from
the coding side (or we need a volunteer programme
Hi Paul
I'll bet that the variable you need to read is not called
"background"
1.- Ask for the state and look for the real name.
2.- Better use "color background xxx", as "background xxx" is
deprecated.
-
This SF.Net ema
El 30 Oct 2008 a las 13:44, FyD escribió:
> Why not simply taking the column of the FF atom types available in the
> Tripos mol2 file format & display it "as it is" ?
I think it's not a question of just "displaying" them, because they
must be converted (mapped) to element names, or you'll get t
OK, I've got it
Jmol is not using the atom name for element identification; mol2 has
an "atom type" field which seems to be both the cause and the cure.
http://www.tripos.com/data/support/mol2.pdf
In your DMSO file, the atom type for the offending atoms is CT and
H1.
This is not supported by m
FyD wrote:
> At http://q4md-forcefieldtools.org/RED/index-test.php, one can see the
> DMSO molecule (Tripos mol2 file format loaded).
>
> I am surprised by the color of the carbons/hydrogens is pink
That's Jmol color for non-identified elements.
> I guess it is because the name of
> the a
FyD wrote:
> Quoting Angel Herráez <[EMAIL PROTECTED]>:
>
> Thanks a lot Angel...
>
> >> http://q4md-forcefieldtools.org/REDDB/
Today I see the models in this page correctly. Behaviour of the
"spin" checkboxes is disconcerting, though. The models keep rotating
and changing even with the check
Hello, Max
> I tried to run Jmol on Linux/Fedora but just after I type ./jmol I only
> get a blank screen with only one icon menu(open a file).
> Could anyone help me?
Do you get a Jmol window? with black background?
Is there a menu at the top?
Try running it with
java -jar Jmol.jar
Give more
Hi Zeyar
1. The "zap" command is what will clear the display.
2. Whenever you load a new molecule, the old one will be removed; no
need to zap it.
3. I'm not sure if you can quit Jmol application from a script. I'll
try to find out.
Frieda, how about
{*}.partialcharge = {*}.property_temperature.all
?
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El 9 Oct 2008 a las 18:12, Robert Hanson escribió:
> Very slick, Angel! Files loaded for me in about 5 seconds. I forgot
> that you could zip up the data files. Of course!
In fact, they had been gzipped from the beginning; my friend doing
this has some disk space constraints (he's running rather
El 6 Oct 2008 a las 6:46, Robert Hanson escribió:
> I recommend leaving the envelope radius at 10. It is used to define
> the outer limits of the molecule, thus defining what the openings of
> the cavities look like. Feel free to try different settings, though.
In my very short experience with
My problem with
{selected}.y = 0
has been solved too in RC18
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Grand
I am with 11.6.RC18 doing something I've done before, but I am
finding a strange effect.
If it makes any sense, I will investigate further and report details.
1. I draw a small sphere using
draw pru diameter 0.3 {3.6 -1.35 1.4}
2. Then I activate
set picking draw
3. and move the object using A
Using 11.6.RC17 I get this error:
eval ERROR: el argumento no es válido
line 1 command 64 of file null:
{ selected } . >> y << = 0
The offending script is
select 2.0; spacefill off; wireframe 0.04; color [xFF00FF];
{selected}.y = 0;
It worked in 11.5.41 at least
(I seem to re
Hi Jennifer
Thanks for reporting this. However, I am seeing no problem.
Please,
1.- Clear your Java cache
(procedure described at
http://wiki.jmol.org:81/index.php/Solving_Java_Problems#Java_cache
2. Clear your browser cache. Quit your browser and reopen it
3. Try the page. If the problem still
Small additions to Bob's reply:
> The cavities are totally created within Jmol. No additional program.
The command is "isosurface", with "cavity" keyword
> Animations. 100 PDB files is not a problem. You can either load them
> as one file
Or load them one file at a time, using "load append"
I've added some information about clearing Java cache and other Java-
related stuff into the Wiki: main page > Running Jmol > Solving Java
Problems
Also linked from Running Jmol Application and Running Jmol Applet
Any confirmation or correction of that info from the Mac or Linux
users will be we
Just found this (well, not me, Google of course):
Clearing Java cache on Linux, Mac, Windows:
http://www.uwplatt.edu/oit/howto/java-cache.html
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Vinu manikandan wrote:
> Sir I restructured the program in such away that the different values
> are provided in the same page for example
> 1)1-55,
> 2)100- 120,
> 3)130-140 and
> I want to select these regions in the Jmol with out loading the
> protein structure again and again on the PDB Stru
Hi Vinu
El 25 Sep 2008 a las 12:31, vinu manikandan escribió:
> I had mailed the Jmol users blog couple of times, may be i was not
> clear in my question that's why ididn'tget any answers.
Maybe. Anyway, the list is so active that sometimes messages just
drop down too quickly. Don't hesitate t
Re: draggable applet
Here is a partial copy of my previous post (4 Sep.)
--- Forwarded message follows ---
[...]
I've tested it and it works. The applet detaches (Firefox 3 and
Chrome) and stays as a borderless window with a tiny close button
(that returns it to the browser), no way to
El 24 Sep 2008 a las 17:35, Thomas Stout escribió:
> Oh, I restarted everything - including the computer and re-downloaded
My experience with Firefox (Win) is that on some occasions it caches
the applet and insists on using the cached copy even after restart
and even if a new applet version is
El 24 Sep 2008 a las 16:06, Robert Hanson escribió:
> OH, OK, I'm glad that worked. I had heard about that and was
> wondering about it. Is that what then allows one to drag the applet
> out of the window and onto the desktop?
As I understand, the "draggable" is a feature of applets in the new
(following my previous post)
Rob,
You could also try to **delete** the unwanted frames (I think it's
done with a variant of ZAP) then play the animation
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El 24 Sep 2008 a las 21:17, rob yang escribió:
> Hmm, that does the trick. What if I want to animate only selected
> models too?
I'm quite sure that there are options for choosing the frame range
involved in animation. Check the doc. But maybe not possible for non-
contiguous frames.
> includ
In case it is of help, I found in our library a 56th edition (1975-
76) and a 77th edition (1996-97) of the CRC Handbook of Chemistry and
Physics. Both have tables entitled
"CRYSTAL IONIC RADII OF THE ELEMENTS" (pages F209 to F210 and 12-14
to 12-15 respectively)
with these values:
> > (8
Avehna,
It appears to me that your solution is to have each checkbox call
only the part of script specific to the relevant piece of protein.
So, all your problem is a scripting one.
> They are several segments, so I will need several
> combinations if I'm using just jmol commands.
No, you s
Dear Frieda
I've never tried that. From the doc
http://www.tripos.com/data/support/mol2.pdf
it seems that atoms can have IDs and residue IDs; they quote an
example:
1 CA -0.149 0.299 0.000 C.3 1 ALA1 0.000
BACKBONE|DICT|DIRECT
1 CA -0.149 0.299 0.000 C.3
[...] the atom is named CA and is [...] It
El 10 Sep 2008 a las 5:13, Robert Hanson escribió:
> http://www.umass.edu/molvis/bme3d/materials/jmoltuts/antibody/contents
> /contents.htm
> Jmol Version 11.3.13 2007-08-28 16:07
>
> really?
I'm quite sure that tutorial was written some time ago, and does not
use Eric's newest JTAT. So it's pro
just a record for the future...
> fascinating. So one would simply need to write a U3D file format
> exporter. Very good project for someone.
http://sourceforge.net/projects/u3d
Universal 3D Sample Software
Set of libraries to write, read, extend, render and interact with U3D-
formatted data, a
Amazing!
Thanks for pointing this out, Wayne. I have missed the last two email
ToC for TIBS, which I regularly review.
Movement of the model is very smooth. The quality of the renderings
is not so good -- must be related to file size, since PyMol can have
a very good quality.
El 5 Sep 2008 a
Chris Weichenberger escribió:
> It also seems to be
> inconsistent since the 'load' command asks for consecutive integers
> starting with 1 whereas the 'frame'/'model' command requires the PDB model
> number.
I've checked the doc and it's correct, "frame" and "model" will use
the PDB MODEL
[ Was:
Re: [Jmol-users] At request of AHerraez, discussion of feature
request moved to this list ]
sorry for the mess of postings :-)
Second part of reply, regarding the generation of images.
David Halitsky wrote:
> If (1-4) are possible as specified above, the next question is
> whether t
king Jmol in FrameB
> and again in FrameC and letting the user manipulate settings in the
> console, as you suggest.
No, I won't suggest so, you can indeed preprogram what you want.
> Thanks very much again for your time.
A pleasure to help.
> -
I am following this thread on the SF feature request system
El 23 Jul 2008 a las 15:02, [EMAIL PROTECTED] escribió:
> Rolf Huehne of JenaLib has told me that Jmol does not currently have
[...]
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Thanks, Bob.
It's not doing what I was imagining, though.
set labelGroup on {44-58};
So the atom expression says which atoms the label setting will be
applied to, and not which atoms the label will keep in front of?
(I am trying to label protein helices with a label that stays in
fron
To me, it looks like an error in the pdb data. Indeed, ALA 140 is the
end of the chain, so a sheet from 137 cannot go farther. The position
looks good to pair with the other strand, although quite wavy.
As far as I know, the HELIX and SHEET records, if present, are put
there by the authors to f
The doc
http://chemapps.stolaf.edu/jmol/docs/?ver=11.4#setlabels
says that you can put an atom expression, between braces, after
"set labelFront" or "set labelGroup"
I cannot get this to work in either 11.4.5 or 11.5.47, as I get a
syntax error:
set labelgroup {44-58}
·
ER
Jonathan, this looks a very interesting idea.
I will work through it and make suggestions later on. A Spanish
traslation could be very useful too. I likely will work on both
during August and come back to you.
First and quick impressions:
* The link on 2nd line, Jmol "Eport to Web..." Tutorial t
El 17 Jul 2008 a las 10:24, Bob Hanson escribió:
> Jmol Protein Explorer is ready for testing and may be considered in
> "beta" state.
Wow, Bob!
I know a bit about PE internal complexity, so that must have been a
huge effort.
Congratulations!
---
Thanks, Bob
> I think that is intentional -- how you light the surface is not a
> characteristic of the surface itself.
> It's a property of the state.
If that's so, then Ok; I'll just have to add the fullyLit parameter
when loading from disk.
But the jvxl file does include it on line nr.12:
> Web: load /*file*/"http://chemapps.stolaf.edu/jmol/docs/examples-
> 11/data/quartz.cif" {1.0 1.0 1.0};
> DW:load /*file*/"file:/Volumes/nggroup/external/test/histidine.cif";
> (this is on Mac OS X)
> Both fixed paths.
Yes. I now remember seing this before, though I don't use state
often.
Th
I also think that a fixed path is not good.
However, from Nick's quote
>
> # Jmol state version 11.4.4 2007-12-20 06:37;
> # fullName = "jmolApplet0[343951889313757]";
> # documentBase = "file:/Users/ngreeves/Sites/external/JmolPopup.htm";
> # codeBase = "file:/Users/ngreeves/Sites/external
Bob Hanson wrote:
> Newly available in Jmol 11.5.46
> (http://chemapps.stolaf.edu/jmol/docs/examples-11):
>
> You can now use the FUNCTIONXY keyword after the MAP keyword
This is wonderful, Bob!
It's working and great-looking.
I found a bug (in 11.5.46, haven't tested other versions yet):
l
It seems that my question was not clear, so here I go again:
I want to know if there is a way to (contour) color a surface without
relaying on an external (cube) file that provides the color mapping.
For example, to color based on the z coordinate of the surface's
points, or by distance to a cer
Thanks, Bob. Loading functionXY isosurfaces from disk is now working
OK with 11.5.46_dev from your site
A separate question: I see that there is a jvxl.jar file in your
Jmol.zip Is this file needed for the applet? What's its purpose? I
don't think I've read anything about it.
-
I am making an isosurface using a math function and would like to
color it according to the z value.
All examples of contouring and colormapping I find are based on an
external (cube) file with the coloring data. Is there a way to color
the surface without external data?
Thanks
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