Chuck, as far as I know isosurfaces are controlled with the isosurface
command. display
only affects atoms and bonds, labels probably too.
If you want to see a portion of an isosurface there is probably a way to do it,
like using the
select and ignore tokens in the isosurface command.
Hello, PM
I am a new Jmol user and would like to learn more about smol files (Spartan,
Wavefuction)
Maybe this is not the best place to ask. You should address some Spartan
community.
1. What is the MIME type for smol files to be correctly read on a server?
As far as Jmol is concerned,
Hi again
It is probably true on a desktop, but I do not think this is correct on a
server. If a MIME type is not
set, a file like.smol (or even jvxl) will not be read by the web app.
I'm quite sure of this: Jmol does not care about MIME type. It may be that your
server serves
the files
When the JME editor creates a molfile with JME.molFile(), it saves the
same stereo information contained in the SMILES and the proprietary JME
file. Where the JME file uses -1(up) and -2(down), the JME created
molfile puts a 1(up) and 6(down, go figure) in the connection table's
first
Hello Michael
Your problem is quite strange, but first we must be sure that we are talking
the same
language, so to speak.
1. You do not install Jmol, just unzip the contents of the downloaded file.
Then, there are 2
separate components in Jmol: the application and the applet. So it's
Piero, if you just want to select, just need to refer to the list and
its element:
assuming you have an ID, like
select id=mySelect
then to select the 4th item:
document.getElementById(mySelect).selectedIndex=3
It can also be done using the NAME of the select
Hi Jay,
I don't use povray export, but have you tried
write povray myFilename
?
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Jay, the key issue is security.
(In my former reply, I was thinking of the application, didn't
realize you talked about the applet)
An applet that comes from the internet is not supposed to do anything
to your computer; even with the signed version, it needs to request
your acceptance before
Alex, if you have just loaded the file, you should be able to use
something like the last frame number, wouldn't you?
http://chemapps.stolaf.edu/jmol/docs/#jmolmath
_lastFrame
_modelNumber
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Similar finding here.
This is my impressions:
loadStructCallback
Called: upon successful file loading.
but... not before the model has finished loading, so its info is not ready yet
Do you need to use it in loadStructCallback? Because if I do it in the script
line that loads the
file, it
El 13 Jul 2010 a las 11:57, Alexander Rose escribió:
by the way, were can I find the parameter list for all callbacks? were in the
jmol code are they defined?
Alex, I'm trying to document those in
http://jmol.sourceforge.net/jslibrary/#jmolSetCallback
but I'm doing mostly by trial. If you
jmolLink(script, 'img src=path/to/image.png /', id, title)
If that doesn't work, you can also do:
img src=path/to/image.png onClick=jmolScript('spacefill on') /
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What will
Piero, I don't get the whole picture of your problem, but you have
select name=colourbyElementList id=colourbyElementList size=1
class= onchange=elementSelected(value)
var scriptColor = ;
function elementSelected(element){
scriptColor = ' color + element + $COLOR$';
return
I still think you are mixing javascript with JmolScript. The
elementSelected() function is called by onchange of the select
control
El 13 Jul 2010 a las 14:59, P.Canepa escribió:
yes u pass it to Jmol with strApp+=JmolColorPickerBox( + scriptColor +
,[255,255,255]); \n
On 14 Jul 2010 at 17:58, Robert Hanson wrote:
I'm pretty sure you are wrong about the word must there. Can you find that
specific requirement
in the second of those references?
It seems that was dropped in recent versions of the format; I have a local copy
of
pdbguide2.2 where for
Van der Lee wrote:
Yes for sure; it would be nice if we could verify the intermediate
steps; so I repeat my question: is there an independant idtf/u3d viewer?
Arie I have installed Deep View from Right Hemisphere, and it opens
U3D files. (I think you need the Complete version, it is free.)
Well, so I've managed too to create my own 3D-PDF following Bob's
instructions. (Windows) Wonderful!
The procedure is now documented at
http://wiki.jmol.org/index.php/File_formats/3D_PDF
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On 16 Jul 2010 at 9:25, Andreas Prlic wrote:
That seems very useful! Would it be possible to mail me such a PDF, so I can
see how it gets
displayed ?
Haven't got it here now, but will post it next Monday. (Cannot install the
latex software in my
too crowded laptop at home, needs 300 MB
Phil, I heavily advocate the use of only relative sizes for content in web
pages.
And I have never seen any problem with browsers.
The situation is more complex than just screen resolution: today's browsers
allow a variety of
toolbars, side panels, etc., and there is also the zoom utility
On 18 Jul 2010 at 12:21, Philip Bays wrote:
I assume then, that if you are putting the applet into a table cell that you
want to fill, you must
specify the cell height and width in some sort of screen percentage as well.
Yes, that's a way. But table cells will expand automatically to fit
Works fine for me; the path has underscores, the filename has spaces
www.uwosh.edu/faculty_staff/gutow/Jmol_Web_Page_Maker/JmolColorPicker/Jmol
Color
Picker Test.html
On 19 Jul 2010 at 9:32, Thomas Stout wrote:
FYI, I wasn't able to locate that web page. I suspect the culprit is the
spaces
Jonathan,
there is an error in the instructions on that web page
http://www.uwosh.edu/faculty_staff/gutow/Jmol_Web_Page_Maker/JmolColorPicker/Jmol%2
0Color%20Picker%20Test.html
it says
Usage
Where ever you want a popup color picker box include a script like
script type=text/javascript
var
Piero, there is a misprint in the doc
Do not use
jmolColorPickerBox(Colorscript, 'rgb(100,100,100)');
But use
jmolColorPickerBox(Colorscript, [100,100,100]);
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What
Hi Paul
Chains with no ID... yes, I remember hittting that problem once. Not
sure of what I did in the end, but probably something like 10:? or
10:*. Problem is that does not exclude 10:A, 10:B etc
If I remember or find the solution, I will tell you.
Meanwhile, maybe try adding extra braces:
Tom, by any chance you have ONLY IDTFConverter.exe in the c:\idtf\
folder ?
It needs other files in the zipped distribution.
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Phil,
it's there:
http://wiki.jmol.org/index.php/Jmol_Applet_Deployment_Local
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MiKTeX rendering an empty pdf doc has already been mentioned, and was
in the instructions in the wiki. I've now added more clarification
regarding the need for the several IDTFConverter files.
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Hi Phil
Don't despair.
But I also read that using the server and accessing by
http://192.blah.blah.blah will behave like the
eventual campus web site site will -- and that the above arrangement of files
is not necessary.
1.
If you read the pages from a server, yes, any folder arrangement
script type - text/javascript
Make sure to fix that - which should be =
I've put up a pge with your same code, it works in my Firefox 3.6 Win (first
time the model did
not load, timing; upon page reload it's ok)
http://biomodel.uah.es/angel/Phil/pages/Phil.htm
Phil, your test page in my Firefox WinXP:
first time: empty applet, no errors
reload: model displays OK
I read this as timing problem: the page tries to load the model before the
applet has finished
downloading. Second time it is cached, so it works. And no Java errors anytime.
Your problem:
El 22 Jul 2010 a las 10:35, Robert Hanson escribió:
Let's get this
in bold print in the Wiki.
There's not much use of bold in the style of wiki or the website, but
it's already there:
http://jmol.sourceforge.net/jslibrary/#jmolSetCallback
[cite]
Please, note that all these parameters are
Matthew Betts wrote:
Please see my most recent post, and/or you might have to ask
your IT Support for help (I found it a bit tricky anyway).
That's now also at
http://wiki.jmol.org/index.php/Troubleshooting/Applet#The_applet_is_di
splayed.2C_other_problems
Henry, it's a long time since I did my small contribution to
exporters and so don't remember well the support (well, in fact I did
not work on idtf export, only vrml and x3d), but I did one molecular
isosurface the other day, so they must be supported. Maybe it's
related to size.
Hi Piero
I think I know where the problem may be, but it will help if you can specify
precisely which
version of jmolColorPickerBox.js you are sing --where did you get it and when
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Hi Tom, and welcome to Jmol!
Try executing (double-click) the Jmol.jar file
I'm afraid the batch file is not often looked at. If there is a difference, we
will try to fix it.
Also, please specify the version of Jmol you are testing.
Thanks for the fast reply! The same problem occurs whether I start JMOL via
the batch file and/or JAR file. I am using the latest version downloaded
today from SourceForge.net.
Tom, pleas quote version number. 12.0.x or 12.1.x ?
There are two latest lines of releases.
Piero, I think your problem may have originated in some mismatch that existed
between
instructions and the actual functions in JmolColorPicker.js.
var colorScript = [setAtomColor, 'atomColor'];
I'm not sure why you have that. it should be a string with a Jmol script, not
an array.
Hi Henry
A similar example works fine for me.
You certanly must use double quotes around filenames, and you are missing the
'files'
placeholder before the file names. Like this:
jmolRadio('set frank off; background white; load files file1.pdb file2.pdb;
rotate z 0;
rotate y 60; rotate x -90;
On Tue, Aug 17, 2010 at 6:23 PM, Tom Hammond t...@uakron.edu wrote:
We are trying 12.0.6 but cannot get past the splash screen. Should we try
12.1.x instead?
Tom, comparing versions is just for tracking down the problem, in case it is a
bug. But
certainly 12.0.x should work too.
It
I am forwarding this to the list.
On 18 Aug 2010 at 15:20, Sara Shi wrote:
Hi, sorry to bother you, but I couldn't post to the maillist yet.
We have exactly the same problem (stucking at the splash screen) if we use
Jmol 12.0.6 and Java 1.6.0. Following the suggestions by Bob, we just
Shouldn't that read starting Jmol 12.1 ?
On 19 Aug 2010 at 8:56, Robert Hanson wrote:
Let's get a prominent note to that effect in the files download page or
somewhere in the release
notes. Java 1.5 required. Nico, I am fully convinced this was a VERY good
idea, despite the fact
that
Hola, Tomás
Just to be sure, you already know what Jmol can do in anaglyphic rendering,
don't you?
It's not clear to me whether you would like a different implementation or you
haven't yet found
the existing one.
The command is stereo,
On 30 Aug 2010 at 9:26, Pshemak Maslak wrote:
Is there a way to display hybrid orbitals in Jmol? I am thinking at
least about sp3, sp2 and sp hybrids, or better any sp^m hybrids
(variable m).
Yes. Find under lcaoCartoon command
Piero wrote:
2) I cannot find in the script guide how to get the number of atoms
of a
certain frame. For instance I have a MgO cell with 4Mg and 4O atoms
how
can I know that the structure has 4 Mg and 4O?
Maybe
{1.1 and _O}.length
or is it .size ?
Piero, I have no experience with hovering or clicking on isosurfaces,
but this is what I would expect or guess:
pickCallback would only respond to objects like atoms and bonds,
maybe also others like draw, but not to a certain point on an
isosurface (how many points are there on an
Sérgio,
Java security policy has grown less tolerant in the last months,
particularly for Firefox. Are you sure your other scripts currently
still work, in the same Java+browser version?
Check out
http://wiki.jmol.org/index.php/Jmol_Applet_Deployment_Local#Examples_o
f_folder_arrangement
and
On 10 Sep 2010 at 16:03, Robert Hanson wrote:
Say, that's a really NICE wiki page, Angel. Good job!
Thanks. It needs some more work and combinations, but I run out ot time at that
point.
Right. Local
Jmol sibling, models sibling
was the surprise new security issue. All the others have been
I've reported this in the Wiki
http://wiki.jmol.org/index.php/Troubleshooting/Applet#The_applet_is_displayed.2C_other_pro
blems
Please edit if the description is not acurate.
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Eric, you can indeed insert JmolApplets in Jmol Wiki pages. The procedure is
called using
the Jmol Mediawiki Extension, special wikisource tags do that.
http://wiki.jmol.org/index.php/Wikis_Using_Jmol
and links therein:
http://wiki.jmol.org/index.php/Jmol_in_Wikis
Currently the documentation says to use ignore {water}implying that without
this, water will be
included in the surface.
Eric, have you tried to use the select token in the isosurface command to
force water
included?
Back to the original thread purpose...
The section is up in the wiki
http://wiki.jmol.org/index.php/Jmol_in_the_Classroom
Feel free to add your bits
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Hi all
I have added
http://wiki.jmol.org/index.php/File_formats/Chemical_Structure
Those of you who have experimented with loading either SMILES strings or JME
strings into
Jmol, you are welcome to visit the page and make any corrections or
enhancements to it,
based on your experience.
Hello Aiswarya
It can be done, but very much depends on how your database is
organized and you query it.
Please provide a sample page or page source code so we can give you
some advice on specific terms.
- The script for many molecules would be the same as for one. Or do
you want to load
Looks wonderful, Bob, though I have no knowledge of the DSSP
algorithms.
This is going to be a big bonus to Jmol.
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I'd bet that's a copy of the Log from Export To Web session, but it should not
affect the
working of the applet.
Maybe there is some bit of code unfinished, like an open tag?
I assume that the problem is not present when your students have the files in
their local
folder, right?
i am trying to implement in my blog (http://pinostriccoli.altervista.org) JME
TO JMOL (or
JChempaint as in http://biomodel.uah.es/en/DIY/JChemPaint3/draw.en.htm), so
that the two
applets will be displayed in just one window.
At the moment there is a link to Molinspiration that i would
I already have JME working in my page on my weblog, Actually i can see
the molecule in 3d on molinspiration.com. I would like to use just Jmol
in the same page with JME or Jchempaint.
What do I need to display the two applets working and connected on the
same page ?
Jmol will accept
Hello Pino
On 12 Oct 2010 at 20:15, Mio_libero wrote:
When i try to transfer the structure to Jmol, nothing happens and
firefox gives me an error
Errore: jmolLoadInlineScript is not defined
What has gone wrong?
That sounds like you don't have Jmol.js accesible. Check your files and
You need to have all the jmolApplet0*.jar files available for the page.
The error I'm getting in your page is not what you mention, but this:
File reader was not found:Mol
which suggests that some of the applet files are not available
Also, the Jmol applet popup menu is not opening.
On 12 Oct 2010 at 22:21, Mio_libero wrote:
Yes true. This error i found after fixing the path. is it as if it can
read the molfile?
I would say that it is not finding some of the needed jmolApplet0*.jar files
Make sure you have all files from the Jmol zip distribution present in the
Wonderful, Pino! Bravissimo!
I'm glad that you could make it work. Congratulations.
It will be appreciated by other users if you write the details
relevant to how to configure WordPress for JmolApplet (and maybe JME
applet) in the wiki,
http://wiki.jmol.org/index.php/Jmol_in_Wikis_and_Blogs
Hi, i forgot to tell that i had to use the tag applet to insert
Jmol. WIth the Javascript code it doesn't work, giving always the error
JmolAplet.class not found. Maybe it cannot find Jmol.js?
Usually, when Jmol.js is not found the error is jmolInitialize() is not
defined
The potential
Angel, in Wordpress i can use just jmolapplet.jar and i receive
no
error of reader missing.
Of course. That is the monolithic applet that contains all
components. The standard procedure (e.g. when you use Jmol.js and
jmolInitialize() with no special parameters) calls jmolApplet0.jar
Bob, this is a great addition.
I am adding this info about the new DSSP method to the Wiki,
http://wiki.jmol.org/index.php/Protein_Community
calculate structure # default DSSP -- new way
calculate structure RAMACHANDRAN # old way
No way to recover the structure assignment based on the PDB
Bob, I see a conflict in coloring of Hbonds
In beta sheets,
calculate hbonds;color hbonds type
renders them in yellow. That was the standard coloring.
The new
calculate hbonds structure;color hbonds type
renders them in cyan or white (parallel/antiparallel strands). That's nice, but
these
Oh, I see.
I don't have a strong feeling about this. You can leave it as it is.
I was mostly thinking on documentation (colors page at website)
Any opinions on this from other users?
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top menubar.
I have added **Available in the next 12.1.x release**
File Reload
that, right now, calls the command
load
(that is, reloads the current model)
Bob has mentioned that it could do
How do you usually drag the molecule?
Ctrl + rightDrag
or
double-clic and drag
as far as I remember, there are no other ways
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Hi Jeff
1. In the lastest versions of Jmol, including 12.0.18, there are two
different colors for helices, most of them magenta as before but some,
mostly short helices, a shade of purple. What is the significance of
the two colors? Are the purple ones variant (e.g. 3-10) helices? Does
This is interesting and intriguing... What is the reason why Jmol
minimizes correctly the model coming from JME string but not the MOL
string?
As I said, I'm quite confident this is only a cyclohexane problem.
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Ha, ha
I think I remember that Bob implemented something to get
preferentially the chair conformation when the JME string was loaded
(and to automatically add hydrogens and run minimize). That is JME-
input-specific, and so does not apply to MOLdata.
But try and see what happens when you draw
Thanks, Otis. You're right.
There is some doc about the filters, particularly for JME strings, in
http://wiki.jmol.org/index.php/File_formats/Chemical_Structure#JME
I don't think I collated this info for MOLfiles.
Hi Piero
I'd like to draw a sphere of
radius distance around the point. Is it possible ?
Yes, use the DRAW command
I know there is an option for isosurface, can I use it ?
Probably you can too, but draw is easier
Bob said:
That command works for applet or application.
Good. But if you have to enter it into the console (every day that you open a
page with a
model, or maybe every TIME that the browser opens the Jmol app), then it's
just as easy to
use the menu for changing the style, I guess.
I was
Hi all
I've had some weird behaviour today while working with my students. Maybe some
of you
have seen this before and can give a clue?
We were in a computer room, all PCs configured the same in principle (WinXP in
Spanish).
The students connected to www.pdb.org and clicked on the View in
how bizarre. Is it reproducible on those particular machines?
I didn't have the time to check that. I will report if I can collect the
evidence (not easy for me
these days).
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Hello again, Xiao-Ping
I think the key is the way you instruct Firefox to invoke Jmol for opening .pdb
files.
I would like to use Jmol as a firefox application
I think the proper name for this situation is use Jmol as a helper
application that is, Firefox
downloads the file and then calls
Yes, that would be nice. But I don't know how to do it. I believe that
Jmol should be recognized as a Firefox plugin as Chime in order to do
so.
No, Jmol is not a plugin and cannot be. It is an applet, so it can be embedded
in a web page
by the web page author.
It all depends on who
Sorry, make that
$command -Djmol.home=$JMOL_HOME -jar ${JMOL_HOME}/Jmol.jar $@ -J trace only
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Hi Andreas
I have not used ED maps, but if they are isosurfaces you can generate
them only for a subset of atoms.
isoSurface select... does not seem to have a related
option either.
How not?
isoSurface select(resno=24) ignore(resno!=24) molecular
Sounds interesting, Jan
Can you give details, what is a Google site?
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* 2.2 WordPress
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Hi Piero
You mean changing its chemical identity, not just its name, right?
See http://chemapps.stolaf.edu/jmol/docs/#atomproperties
{atomno=6}.element=F
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will look at it
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Done and committed.
Bob, can you please take a look at the code additions? I think they are ok,
but...
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Hello Jmol users
It's been several weeks now that every time I open a web page with
Jmol applet I receive a Java security warning saying that there is a
mixture of signed and unsigned content in the applet and requesting
permission to continue (in fact, recommending not to do so).
I'm quite
This looks like a good explanation of how to fix this, both at user
level and at developer level:
http://download.oracle.com/javase/6/docs/technotes/guides/jweb/mixed_c
ode.html
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Thanks, Otis
I think that what you mention is a different issue. I also saw some
changes in security rules related to paths some time ago.
But this says it is the use of mixed signed and unsigned features
**in the code***. I am speaking of the unsigned applet, that of
course is not supposed to
Yes, I am seeing it with the unsigned applet (sorry I failed to
mention this important bit initially)
And it doesn't seem to be dependent on the Jmol version, but I
haven't checked that systematically
After playing with the Java Control Panel options the warning is
gone, but I chose one of
Might be something with my system, but I am seeing it at both
computers, and with different applets (Jmol unsigned, my campus
Blackboard environment, among others). Also in different browsers.
The warning jumps most often saying it's jmolApplet0.jar, but some
times it has been another
Piero, it sounds like a java cache problem. The browser may be
reading the old applet files from cache instead of the new ones
coming form the server.
Make sure that you close your browser, clear your java cache and
restart the browser
OK, so after a couple of silly symptoms, I sort of decided that the
system was mad betond reason. I have therefore applied the master
method for troubleshooting: uninstall Java, check that there are no
java files left behind, and reinstall. The problem has gone. One more
mistery on the list,
Sorry to meddle, but I thougth I would give my opinion in case it is
interesting for you.
- What if you check for this second column of atom names only for
files with the .p2n or .P2N extension.
Jmol does not rely on file extensions for reading any format.
- or we can add a header in
I just tested this file (mentioned in a different thread)
http://q4md-forcefieldtools.org/Tutorial/P2N/Metal-
complex/Mol_red1.p2n
in Jmol 12.1.15, which reads it as pdb format.
I'm curious: how is it that Jmol draws from the central cobalt 4
regular single bonds and 2 dashed, partial bonds?
Oh, I thought that Jmol completely ignored the CONECT records.
Quite exotic situation, anyway. No more fuss.
There's always place for new discoveries.
Thanks
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Hi Matt
I'm not sure of this, but rather than changing the Z translation I
would try changing the slab incrementally
When you say that it works manually using the mouse, are you zooming
in? That is what Z translation means. Or are you shifting the slab
plane? That is waht an incrmemental slab
(I was probably wrong when I said that Z translation and zoom are the
same, but the main point still applies)
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move has the slab parameter, but does not take a time.
moveto doesn't take slab
The for loop that Bob has suggested will be your best choice
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Jmol default colors for chains are historical, but -yes- too pastel
for my taste. Particularly the bluish and greenish, you don't need to
be color-blind.
Changing defaults is always a concern, but I agree that there might
be a point in this. Or at least not change default but have other
Paul,
If I remember correctly, color monomer is an alternative to color group,
that is, it colors by
residue, not by chain.
Andreas,
only blue and yellow? then it's sure hard.
The problem is, color chain relies on the chain ID, and you cannot assume
that all pdb files
will use chains A, B, C
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