Sorry, Andreas, I don't get it
How should we used this color table?
What color is chain A, etc?
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Chain A is 104BA9
B ... AA00A2
C ... C9F600
D ... FFA200
E ... 284A7E
etc
does that make sense?
Ok, let me try
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El 18 Nov 2010 a las 8:31, pieremanuele canepa escribió:
2) can you expalin me again how you would add a new atom, into a pre-
existing structure, knowing its Cartesian coordinates. I lost the e-
mail you sent me 1 or 2 weeks ago.
Piero, the email list is archived at the Jmol web site and at
That sounds terrific, Rolf!
Good work!
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Spend less time writing and rewriting code and
Andreas,
first save the script to a file (or implement it inside your web page)
then load the script file
script colorchain.spt
or drag and drop onto the Jmol app
load a file
and then, type at the console
color_by_chain()
It has worked for me
Hello Martin
Getting the right syntax is a bit tricky, bust most likely you can do
it in javascript using jmolGetPropertyAsArray,
jmolGetPropertyAsString or jmolGetPropertyAsJSON
http://jmol.sourceforge.net/jslibrary/#jmolGetPropertyAsArray
and in JmolScript using the equivalent
Nico, please check out
http://wiki.jmol.org/index.php/Jmol_in_Pop-up
that should be enough, don't you think so?
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Maybe, but it's not working for me with the current Jmol wiki.
With Chrome, I get an empty popup about:blank...
That reminds me about something I found previously. Let me see...
the HTML code of the main window as Javascript (so it's quite complex). I
am looking for a
function
Maybe, but it's not working for me with the current Jmol wiki.
With Chrome, I get an empty popup about:blank...
It's something specific to Chrome.
Other browsers work, including Safari (Windows)
I'm trying to find out what it is...
Hello Nico
I have no strong opinion on this new way for the extension you are proposing,
but I will share
some thoughts. Anything that can put Jmol in Wikipedia will be a great
achievement.
1. The Chrome problem with jmolWikiPopupWindow().
As far as I can test (Windows only), this is
Some follow-up on these topics:
1. The Chrome problem with jmolWikiPopupWindow().
This is now fixed in the latest Extension in SVN. It was something
specific to Chrome --not displaying applet that is part of a pop-up
window wholly generated from javascript-- and has been now
circumvented
Good news for jQuery : it's already used by MediaWiki !
Ha! How surprising.
We would also need jQuery UI, but maybe we culd add it or duplicate the needed
functionality.
For MediaWiki 1.16.0, you have jquery.js version 1.3.2 in skins/commons
There's also a jquery.min.js : Idon't know if
Hi Yingjie
Mike's solution seems the best thing you can do.
It basically means that instead of using jmolButton() you use your
own input type=button with jmolScript(). That way you have more
control --or easier at least.
You could probably still use jmolButton() giving it the ID parameter
and
Dear Jmolers,
Has any of you tried to use connect between atoms that belong to
different models (1.1 and 1.2)?
Is there an option to do that?
(This was prompted by a post by Gian Garduque on the MolVis-list, to
whom I am copying this)
The 2nd question was: can we have monitor lines without
OK, so I'll reply to myself:
To turn off just the labels, use set measurement OFF
It's
set measurementLabels OFF
Bob, so there's a typo in the online doc
http://chemapps.stolaf.edu/jmol/docs/?ver=12.0#k477
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I have two files with DNA, obtained time ago by trimming the protein
out of 1d66.pdb (Jmol version of Eric's DNA Tutorial, now in 6
langauges). I am trying to upgrade to 12.0
On both 12.0.24 and 12.1.25,
hbonds calculate
reports 0 hydrogen bonds
Previous versions of Jmol (11.4) produce the
Ah, here are the files:
http://biomodel.uah.es/model4/dna/dna.pdb
http://biomodel.uah.es/model4/dna/1d66-pwz.pdb
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After looking at the online doc I have found, quite by chance, a hint
for the change in behaviour.
The file in question has 2 hydrogen atoms (added manually since that
is a non-H pdb file). Other 2 files that I use (single nucleotide
pairs) have a full set of hydrogens.
On any on them,
Thanks, Bob.
That's sort of what I was imagining. I'm still uneasy about such a
change in defaults. I've already added a description to the Wiki,
http://wiki.jmol.org/index.php/Backward_compatibility
Can you confirm if this only affects pdb files?
By the way, I have no idea where that H3O atom comes from in that
file you are using. It's certainly not in the original 1d66. It's a
terminal H, I guess, but it isn't HO3 or HO3'. Maybe Eric inserted
that.
Yes, it was inserted manualy (either Eric or me), and it's meant to
be the 3'-end
Hello Jan
First, make sure what version of Jmol you will be using --this has
changed historically across versions.
I do not remember details right now, but I have some (old) example
page from where you can likely get the key:
http://biomodel.uah.es/Jmol/inicio.htm
and then Reading information
Dear Anbang Li,
Thanks for bringing this to attention. It's great that you are
interested on localization of the Export to Web module.
First of all, no matter what language I choosed, the text below the
label of Introduction is always in English. I want to ask, how can I
translate them?
The
Sorry, my mistake. The Chinese translation is complete in Jmol
12.1.26
So your problem, Li, must be in the part of the interface that needs
separate translation. I will come back to you this evening with
details.
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The same code is still valid to get the atom info.
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Jonathan Gutow wrote:
http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/openscience
/jmol/app/webexport/html/
That's right. I don't think there is another way to do this. All is explained at
http://wiki.jmol.org/index.php/Internationalisation/Offline/Export_to_Web
Regarding the
Hello, Yingjie
There is some limitation in your approach: a part of the model ca have several
styles
simultaneously, like ballstick, trace, ribbon. They are not exclusive of one
another. Then,
there is a numeric parameter indicating their size or thickness, and a color.
I'm not sure if there
Eric, apart from what Nico has pointed out, there is a category in the wiki
that collects pages
that use the applet:
http://wiki.jmol.org/index.php/Category:Pages_Using_Jmol_MW_Extension
(pages must be added to that category manually; see any of them for the source
wikicode
needed)
Eric, thanks for the detailed report and suggestions.
I will take care of those changes in the jscolors webpage (next week)
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Is there some way I can delete every other alpha carbon? Or filter to
get only the alternate ones, or every third or fourth?
Would it be a solution to pick them by residue number? I think it should be
possible to check
that in JmolScript / JmolMath and whether it divdes by 2 or 3 without
Eric, you description was -of course- precise and correct. I have
checked that the source code was designed to do what you were seeing
in assigning colors to chains.
The erroneous description must have been either a misconception in
the doc or an obsolete description.
The documentation has now
On 17 Jan 2011 at 14:48, Jonathan Gutow wrote:
2) I am not aware of a way to pass the path to use to Jmol on launch
except as a script.
At least in Windows, a batch file should be able do that. Not sure now what
exactly you are
needing. (I haven't followed the thread fully)
Just my 2 cents:
Evidently, a fair number of PubChem's sdf's have partial charge data.
I see aproblem here. The format shown in your example is not
according to SDF spec (I think it does not suppor partial charge,
only formal charge). They shouldbe using a different format, like
MOL2.
So
Something to check out:
http://depth-first.com/articles/2011/01/19/jmol-without-applets-using-websockets/
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Hello all
This must be trivial, but I'm stuck
I need to extract the minimum and maximum residue nurmber from a one-chain pdb
file into
a Javascript variable.
The Jmol commands are
m1 = {*}.resno.min
m2 = {*}.resno.max
but I don't know how to pass those to a javascript variable (I need to
Great, Alex, thanks
I had forgotten about jmolEvaluate()
This does the trick:
alert( jmolEvaluate( {*}.resno.min; ) );
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Mmmm... I see that jmolEvaluate() is not in the doc for Jmol.js
Maybe we should add it there (under Advanced)
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On 26 Jan 2011 at 9:53, Robert Hanson wrote:
oh, yes! It's very valuable.
2011/1/26 Angel Herráez angel.herr...@uah.es
Mmmm... I see that jmolEvaluate() is not in the doc for Jmol.js
Maybe we should add it there (under Advanced)
Done. Will be online in the next update
Dear Jmolers,
A failure has been detected to display Jmol when using the Chrome browser under
MacOS.
The reason has been tracked down to a change of behavior in Chrome (and future
versions
of Safari or other WebKit-based browsers) together with an old browser
detection routine in
the Jmol.js
I realize that my previous message may sound too alarming, so I will be more
specific.
The changes introduced into Jmol.js affect only the way the JmolApplets are
inserted into the
page depending on the browser. So you just have to see if the applet shows up
or not and if
the javascript
New downloads are available, but I still cannot browse the SVN
Guess I'm not the only one
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I am experimenting with an Amber set of files (topology + coordinates
from a molecular dynamics calculation).
The files load fine into Jmol (load trajectory) but I cannot get any
cartoons or trace renderings.
Is this a limitation with the TRAJECTORY option, or a problem with
the Amber format?
Possibly related to this:
I cannot select atoms based on atom name
e.g.
select Lys # 88 atoms selected
select Lys and *.CA # 0 atoms selected
select Lys and alpha # 0 atoms selected
Hover displays them correct
label %a # works fine
Hi David
It could be done, but I don't think Jmol is the right tool for what you intend,
and it wuld hardly
worth the effort needed.
Jmol is just the graphical end for whatever data you give to it. Although you
can do basic
calculation and move the atoms, for your idea you should rely on some
Part of the problem there may be that, as far as I understand, Jmol
algorithm for protein is more complex than identifying amino acid
residues by name (that's what amino does).
I think I read about the algorithm inside the source of
JmolConstants.java
I do not mean to defend that every atom
Maybe this:
select amino and not protein # will pick those anomalous atoms
select protein,amino # will pick all protein atoms
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Probably the jQuery solution is better, but in case it's of use I
have a couple of simple slider demos at
http://biomodel.uah.es/Jmol/sliders/
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Thanks everyone. Angel I like your solution.
I thought so. It's more logical and general.
Why do we need both protein or amino?
amino is rasmol-compatible. protein is Jmol chemical intelligence,
particularly to account for funny cases like yours. Also, I think, it
includes
Hello Vineet
I'm not sure what you mean.
If you want to load several files, you can do
load files molec1.pdb molec2.pdb molec3.pdb
You could also set them in a loop, like
for (var i = 1; i = 4; i = i + 1)
var x = molec + i + .pdb;
load append @x;
end for
Hello Adam
There is no reason why the bond should be deleted. This must be a
bug.
Please provide details of the exact version of Jmol you are using
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Oh, I didn't know this feature existed.
To me, changing bonds
1. is not suggested by the word picking
2. makes sense only in the context of ModelKit mode
3. could be implemented, if intended out of ModelKit mode, in the callback
function, e.g.
using connect
Having bonds dissapear in normal
Hello Nick
Thanks for reporting. I think this is a known issue with newest
Chrome versions that I tried to fix recently.
The fix is in Jmol.js, and it seems that the pages you have tested
are using different versions of that.
For examplehttp://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
Evgeny,
Yes, you can add dummy atoms using a script. See
http://www.mail-archive.com/jmol-
us...@lists.sourceforge.net/msg16573.html
for some more info and an example.
You should best use the existing Xx notation for an undefined
element. Then you can select Xx to act on it, set its size,
Otis,
from the top of my head, it used to be set picking none
But maybe the others are/were also valid
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Hello Sam
Welcome to Jmol
I'd advise that you browse the website and then the Jmol Wiki.
There is the Jmol Scripting Documentation, but that's better suited
for a more special use, when you have doubts about how to use a
command. First, you need to know that such a command exists.
The wiki
OK, bad assumption on my part. I was assuming it was identifying beta turns.
The Colors document on the
Jmol site does indicate blue for beta turn.
My fault. So we should say just turns, right? Will do that
Aha, that's why I put beta in parentheses last time!
strand [255,200,0] FFC800
On 5 Mar 2011 at 13:50, Robert Hanson wrote:
instantaneously.
Is that different compared to moveto 0 (etc.)?
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Hi all
I am tryng to write a script that will detect paired bases (A-U, G-C) in a RNA
molecule.
Before I start trying, any ideas about how to address it would be welcome.
For now, I am thinking of using WITHIN with distance.
(I am assuming that in large pdb files maybe the hbonds detection is
Thanks, Bob, that's what I needed
It seems that your 2 solutions work the same.
I'm finding out which one is the best solution for me. Of course,
working with RNA is mroe tricky, but that's why I need the algorithm.
Jim, since a JAR is a zipfile, I'd say that you just need the same
syntax as for loading a JMOL or ZIP file. Maybe it's LOAD ...
FILTER. Check the scripting doc
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Alex, I think I am not getting the whole picture. Can't you use the Jmol script
console for that?
Maybe together with a few script files.
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Hi Paul
select *:y
is the notation I use regularly
Not sure about why *y gets you all atoms; looks like it has something to do
with coordinates
(xyz)
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Hello
On a colleague's site, I am getting this error in the Java console
when he pages tryes to load the applet:
java.lang.ClassFormatError: Incompatible magic value 1008813135 in
class file JmolApplet
What is this about?
(It's an old Jmol version, maybe 11.6)
Thanks for any tips
you have a mix of versions or a bad file.
Thanks, Bob. We'll check that
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Hello Yingjie
You can probably use the atoms array, and either use their geometric
center (not for a label, but an echo) or the first atom in the array.
The result will probably not look very nice.
I cannot give you the exact syntax, but check the doc under atom
expressions. It will be
Hello Yingjie
1. Are you sure that when your jmoEvaluate() call is executed the
applet has finished loading? That could be a reason.
2. I doubt that boxSize is predefined. Or do you mean YOU have
defined it? Jmol predefined variables start with an underscore, like
_version
Hope this helps,
Hello Yingjie
Below is an example of usage I found on
http://jmol.sourceforge.net/jslibrary/#jmolEvaluate
alert( jmolEvaluate(a) );
// Displays the value of the 'a' variable if set in Jmol script.
I think the example might be a bit confusing for newbies like me :)
Why do
Hi all
I'd like to use jmolSetTarget() to target two applets but not a third one.
I started using all as the parameter when I only had 2 applets in the page,
but after adding
the 3rd one I'm stuck.
Any solutions?
Thanks
Yingjie, I think it's easier
I have a variable X in JavaScript, and I am looking for a way to pass it back
to Jmol.
How about
jmolScript(var myJmolVar = + myJSvar)
that would pass the value to the 'myJmolVar' variable in JmolScript.
Or do you need something more complicated that just
Hi Yingjie
Both #2 and #3 are calling a script befire the applet has had time to load.
That's what you
must avoid.
Maybe this would work:
jmolInitialize(../jmol/);
jmolApplet(600, ..; set pickCallback 'moveBox'; )
because the 2nd parameter in jmolApplet() is not run until the applet has
Michael, I have no experience with VB, but regarding Javascript calls to Jmol,
all support is in
the Jmol.js library, and it supports html IDs for both applets and controls.
Maybe that's what
you need.
That immediately leads to the question of how to obtain a list of available
functions
Hi Eric
I'm no Mac person, as you know, but one of your descriptions ticked a neuron.
Long time ago, I read that one of the new Java updates was bringing the
possibility of
detachable applets. At that time, I tried it and it worked for Jmol (tweaking
the Jmol.js, I
guess). Then I lost
El 28 Mar 2011 a las 23:54, Yingjie Lin escribió:
Is there a way to disable translation with double clicking and hold?
As far as I know, you can redefine mouse gestures by attaching
behaviours. Search the online doc or the email list archive
On 30 Mar 2011 at 14:46, Eric Martz wrote:
Chrome:
PROTEOPEDIA fails: It thinks java is disabled but it is not. I
suspect this may be a problem with the java detection routine in Proteopedia.
Eric, this may be a known problem I detected some time ago with browser
detection in
Jmol.js,
Hello Yingjie
I don't understand what is exactly the problem you are seeing. Your
page works well in my Windows Firefox 3.6
There is an alternative: you can put jmolApplet inside a DIV and then
resize that div rather than the applet
div id=jmolContainer
script
jmolApplet(100%)
/script
/div
Very promising. Congratulations!
the popup example link opens a window with this content:
could not be loaded.
(This is Firefox 3.6 WinXP)
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Hi Lamar
Sounds like a timing issue maybe.
I'm not sure why it fails, but try using
label %a;
instead of
set label '%a';
just in case
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Some further ideas:
1. try loading the menu before the model
2. select ALL; is not necessary right after loading
set autobond OFF;
load menu http://130.18.154.148/~lamar/jmol.mnu;;
load http://130.18.154.148/~lamar/JmolInput.txt.xml;;
label %a;
Dear Bob,
I don't remember any discussion about Android.
The question, of course, is how are Java apps run in Android, what's the JVM
and
compatibility.
Should we open a page in the Wiki for this?
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There it goes!
Two primers. Please fell free to add your comments, experiences, links...
http://wiki.jmol.org/index.php/Support/Android
http://wiki.jmol.org/index.php/Support/iOS
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This is the original message
http://sourceforge.net/mailarchive/forum.php?thread_name=BANLkTi%3DR%2BnAP_yaq9g
Ph-if_BQd6%2B8xy8A%40mail.gmail.comforum_name=jmol-users
Currently I have Jmol loading a script at startup that loads a file and
custom menu. However, I would also like it to show the
Hello, Jaime
I'd say you cannot use labels, but you can use echos with 3D
coordinates. Also, you can draw an arrow pointing to the bond
midpoint.
Regarding selecting bonds, I'm not sure. You really select atoms
always I think. But it makes no difference.
More difficult will be to aim at all
Bob, it seems that connected and connect do not accept ssbond
as a parameter. Would that be too dificult to implement?
e.g. I can do
select all; hbond calculate;
select connected(hbond,cys);
but cannot do
select connected(ssbond,cys);
Hey! I forgot we have
select cystine
Jaime, maybe
Jmol, not JMol, please!
I support that, and it is stressed in the website, but -for the
record- actually Will York's JMol vanished into thin air time ago.
There is no way to find it on the web.
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Laurent, are you sure youhave the whole set of jar files in the server? If it
works with
jmolAppletSigned.jar and not with jmolAppletSigned0.jar, it sounds like that
may be the key.
As Bob said, you better use Jmol.js. That will invoke *0.jar, so the comment
still aplies
My copy of IE9 (both 32 and 64 bit versions, under 64bit-Win7)
says there is a problem with the page and that IE has had to close and reopen
the tab
whatever that means.
In fact, the page is displayed briefly (black Jmol) and then dissapears.
Same happens with my page :(
May be something with
I have added some description based on this thread at
http://wiki.jmol.org/index.php/Support/Windows
for future reference
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Hello Reinhold
You are right, rotation, zoom etc. affects all frames/models.
The only way is to use the rotateSelected command. But that doesn't
work by mouse, only does defined angles.
I think there is no way to do interactive rotation of a single model.
I can no longer copy text output to the Jmol script console (like
show orientation)
This seems to be related to the update of Java. I have just installed
1.6.0_25, under WinXP
I think there was recent discussion about this in MacOS. Any ideas
will be welcome
I don't know if this was there in 1.6.0_24 (but I have used this way
of getting orientation moveto many times before).
I have now found a workaround:
I'm using the unsigned applet script console.
I select (mouse drag) what is in the upper panel, output area; press
Ctrl-C, but it cannot be
Thanks, Wayne
I was quite sure I had read similar issues here, thoughtit was with
the Mac.
I cannot confirm if 1.6.0_24 was working or not for me. 25 is not,
and it's the first time I've noticed but there may have been several
updates in between.
Bob,
thanks, now I see that the output of
Jay,
Otis knows better abaout this, but there is a chnce that your problem may not
be his.
There have been changes in Chrome support of the APPLET tag, and that has been
fixed
recently in Jmol.js. So, it's important that you check and tell us
1- what is your OS
2- do you see the applets using
Thanks for the details, Otis.
I just tested my Chrome WinXP:
2) Chrome supplies some command line line switches to turn off features,
including the the Java
version police (editorial sarcasm). In my hands the Java related command line
switches do not
work:
--always-authorize-plugins
Dear Jmol users,
You may remember that I published an introductory manual for Jmol.
Unfortunately I haven't yet found the way and time to write the
promised volume 2 with more advanced content.
However, I have just released an update to Vol.1 in the form of a 30-
page supplement. It updates a
Hello Néstor
I'm afraid that dashed bonds cannot be changed. You can change thickness and
color, but
not the dashes.
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Dear users,
I have two models that I want to display at the same scale.
I know I can use set scale3d = set scaleAngstromsPerInch, bot that
disables zoom.
What I would like is display the two models at the same scale, then let the
user zoom (I'm
adding sync so the 2 models change at a time)
Hi all
I am using for the first time save state and restore state. Sounds great!
But restore takes quite a time, seemingly it loads the model again. Is that so?
Would there be a way to restore the state without reloading the file?
I am seeing that re-running the initial script (which I have in a
Hi again Néstor
Rather different, but may useful for you:
you could use solid translucent sticks for those bonds
It would be something like
select connected(partial);
connect (selected) (selected) single yellow translucent;
Dear Eric,
Not sure where I got that trick, but look at the source of
http://biomodel.uah.es/quimica/get_structures.htm
The model command removes the Ramachandran plot and goes back to
the structure.
The current doc says that ramachandran is an obsolete command
superseeded by plot ramachandran
Thanks, Bob.
set rotationRadius is my best choice. I have also applied it now
to other pages that were hardcoded by hand. Great!
For anyone interested, please note that any moveto command contains
rotationRadius as one of the parameters, so it will effectively alter
the initial setting.
Otis,
I have not IE9 now at hand, but in part this sounds like the last
problem reported in Jmol-users list: IE was closing down the page.
I'm not sure what the fix was then (some saw it, some not), but
yesterday in a colleague's PC we had the problem again (she had just
upgraded to IE9) and
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