Ok, after sorting out my problems with the JSmol file set, I can now --again--
assert that where one JSmol works, two don't.
This is my test code:
var myJmol1,myJmol2;
var myInfo = {
height: '50%',
width: '100%',
jarFile: "JmolApplet.jar",
jarPath: '..',
j
Yeah, I was just checking that.
I downloaded JSmol.zip this morning and I am getting error in loading
core.z.js
After checking the js console errors, I located many lines that have a strange
invisible character at the beginning of line. I could select one (together with
the next few letters) and
> 2) Entering the "mouse selection" mode by using the toolbar icon
> deselects all atoms. This doesn't happen if the popup menu is used
> instead
I see this logical. If I go into mouse selection I am not expecting
to work against an already selected full set. So the previous "select
JSmol in
http://chemapps.stolaf.edu/jmol/jsmol/test2.htm
is running fine for me in Firefox 17.0 (Win7)
both HTML5 and WebGL
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Thanks, Paul
It seems you are right. I was testing several pages successfully until I hit
the
2-applet page. But now the ones that used to work are not working, so I must
have changed something in the file set.
I'll have to check the files from scratch. Let's wait
-
Dear all,
I'm trying a page with two Jmols using Jmol-JSO. My code is like this:
var myJmol1,myJmol2;
var myInfo = {
height: '50%',
width: '100%',
jarFile: "JmolApplet.jar",
jarPath: JmolPath,
j2sPath: JmolPath + "/j2s",
use: 'HTML5',
debug:
Ciao Pino
I tested your page in Firefox Win7. All models load fine with links or buttons
except "cloruro di metile"
which gives a javascript error
Fecha y hora: 20/11/12 20:06:31
Error: NS_ERROR_FAILURE: Component returned failure code:
0x80004005 (NS_ERROR_FAILURE)
[nsIDOMCanvasRenderingContex
Bob, that sounds great!
Can you set an updated zip of all the needed js for download?
I'm trying to convert some of my (complex) page sets. I've been patching
what I downloaded initially with updated single files but I'm afraid of
missing
something and must be sure in order to chase down som
Hi Paul
I also tried Google Closure compiler a few days ago, but I was put off by the
warnings, like this one:
core.z.js:3435: WARNING - Suspicious code. This code lacks side-effects. Is
there a bug?
($t$ = java.net.URL.factory = fac, java.net.URL.prototype.factory =
java.net.URL.factory, $t$)
It's one or two weeks ago that I was testing JSmol and I quit trying
to do it locally, either in Firefox or Chrome, because of several
security errors. Only from server I could work reliably.
So it may not be exactly that version, but even a former one (I have
not tracked my version lately, but
Hi Otis
Try to set CSS style of the container div to be "position:relative"
at least, or maybe you need "position:absolute"
and see if it makes a difference
> The positioning works, but as I increase margin-left, mouse-zoom
> versus mouse-rotate creeps across the canvas from the right,
This script was working in former versions but throws errors in
13.0.8 and 13.1.8
var n = 2;
select resno = @{n+5};
How can I select by residue?
(This goes in a function where n is the argument)
Thanks
--
Everyon
> I am trying to save an image from unassigned applet and unable to do
> so. When I right click on the applet, I am not getting the option to
> save as JPEG or any image format.
> Is it possible to do so, as I am able to save image when I use signed
> applet.
> thanx in a
That's great!
Thank you, Rolf and Paul
"show chain" works nicely for me.
"{*}.chain.count().size" sounds better and is ok in Jmol 13, but I'm
tied to Jmol 11.8 for this case, and there "count()" is not
supported. "{*}.chain.size" gives the number of atoms, not useful.
:-)
--
and you must be using the signed applet for that to be possible.
Unsigned applets have no permissions for writing to the local disk,
even by user action.
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Hi all
I'm trying to set a JmolScript that counts the numbers of chains in a
model.
It seems that the data are in getProperty("chainInfo"), in the form
chainInfo.models[0].chains=new Array()
but I have trouble parsing this information into a number.
I've gone as far as
var chI = getProperty ("
Hi Rolf
> "jmolScript(command)" that became "Jmol.script(jmolApplet0, command)").
Exactly that
There is part of it at the Wiki (ongoing doc)
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object
Mmmm... maybe a "how to upgrade" table ?
Not much time now either.
> 3) I couldn't get rid of the structure load part below the canvas (input
> + menu + button).
I think it is this line in definition of Info:
addSelectionOptions: true,
try setting it to false.
This is my own note in
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object
"Info.addSel
Dear Jmolers,
We have started to collect some information on this exciting new addition at
http://wiki.jmol.org/index.php/JSmol
That page is not too obviously linked yet from others, but I will keep working
on that. After all, this is still in development phase and so not directly
addressed to
> I've put what we have so far into
> http://chemapps.stolaf.edu/jmol/jsmol/jsmol-10-29-2012.zip
Good! I wanted to give a try. Thanks
> Note that this will run fine from Firefox on your hard drive accessed as
> file:// but Chrome and
> MSIE require that you access files via the web, so it'
> Is there any cance to use jsut HTML5 so that, at least for simpler
> purposes, no java is used?
Yes indeed. You specify the method(s) you want when you write the page.
See
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Initialization_paramet
ers
But the JSmol javascript files are not
I can confirm that Jmol-13.0.8-binary.tar.gz is OK, but Jmol-13.0.8-full.tar.gz
has an error
(tested with WinZip under Windows)
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Hello, Pino
That page is currently set to use HTML5 JSmol, no Java, by default.
You can change options either clicking on the links inside the page or adding
a parameter in the URL
http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?USE=HTML5
http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?JAVA
Hello Sridhar
I think that
load "filename" {i j k}
// Loads a block of unit cells
may be what you need
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Hello Jen
print {*}.labels
seems to work fine, for the console (it outputs empty strings for
non-labeled atoms; there may be a more convoluted way of letting
those out)
For saving to disk:
xx = {*}.labels;
write var xx ?; //prompts for a file name and location
write var xx "listoflabels.tx
Hello Inbal
Yes.
First, try to allocate more memory for Java+Jmol
http://wiki.jmol.org/index.php/Jmol_Application#Giving_Jmol_more_memor
y_to_work_with
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Hello Dina
You can try this:
select protein,nucleic; ribbons only;
select !(protein,nucleic); spacefill only;
select all;
And by the way, Jmol applet does not run in the server, but in the client
browser!
On 17 Oct 2012 at 14:41, Dina Schneidman wrote:
--
Dear users,
I'm setting up a page that uses Jmol-JSO syntax (13.1.6)
I see that there are defaults for Info that suit the unsigned applet but not
the
signed applet.
This code works:
var myInfo = {
jarFile: 'JmolAppletSigned0.jar',
jarPath: '.',
isSigned: true
};
var myJ
Hi Henry
I have Windows 7 (64 bits) with Java 1.7.0_04-b22
no problems detected --at least in Firefox
Possibly I haven't tried latest Jmol. I can if you think such test useful.
Regards
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Is this what you mean?
http://chemapps.stolaf.edu/jmol/docs/#hover
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Sorry, hiding and displaying of ANYTHING is documented. You just
combine display command with atom expressions, which are described in
the doc (and used by most commands).
Good luck!
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Hi Andreas
You need to find out the chain IDs (usually A, B ... but not always)
Then
display *:A; // will also hide all the others
display add *:A; // makes A visible without hiding others
etc.
Check the DISPLAY and HIDE commands in the documentation
-
Hi Pino
Yes, this problem has been there always with reading MOLfile data. As
Bob says, using the JME format for the transfer fixes it. You can see
both demonstrated in my page (compare the 2 buttons)
http://biomodel.uah.es/en/DIY/JME/JME.htm
If you still need to use MOL (as I do in my pages th
> How would this command look like in your case? I'm trying: 'write
> IMAGE 200 200 PNGJ 8 /servlet/?POST?_PNGJBIN_'
> but according to firebug no POST is actually happening.
Maybe try to enclose the filename in quotes
write IMAGE 200 200 PNGJ 8 "/servlet/?POST?_PNGJBIN_"
---
Jiri,
We are confusing two menus.
There is the Jmol application top-bar menu, which has what you
describe.
And there is the **pop-up** menu, shared by Jmol application and Jmol
applet, which has a "File" subentry with export VRML
-
Nikolay, maybe you can add a dummy atom at the center, produce the
tetrahedron and then hide the atom.
Not very clean, but probably effective
I cannot advise however about generating the tetrahedron around the fake
atom
-
Hi Jiri!
Also available from the pop-up menu:
File > Export VRML
so you can choose the destination folder as well as filename, visually
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Those of you who are Mac users and are finding out the problems, if you are
keen to it, I invite you to summarise the situation at
http://wiki.jmol.org/index.php/Troubleshooting/Java_Problems
@Henry,
the "presentation mode" in Chrome sounds interesting. Is it very different to
Firefox in "full
On 3 Sep 2012 at 8:51, Robert Hanson wrote:
> OK, I've corrected that for 13.0.2 and 13.1.2
Thanks, Bob
Meanwhile I could trick it by using
translate x 0.01
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I have a page using Jmol 11.6.24
When updating to use 13.0.1 I have a mispositioning of the model
which seems related to
translate x 0;
doing nothing. Before, it re-centered the model.
translate x 1 // works
translate x -1 // works
translate x 0 // nothing happens
This is in anold and complex
Dear Jaim,
I find the doc for color-schemes misleading but then I have found a way; you
need to specify a property in order to use a color scheme. So:
color property temperature "roygb";
color property temperature "bgyor";
seems to do it
color temperature // by itself seems to use bwr (red b
> Example: http://biomodel.uah.es/Jmol/JSO/simpleJmol3-0.htm
>
> However -- Angel -- is that page supposed to load, or was that a demo of the
> problem we were
> having? I note that it does not load correctly in FireFox.
It was for demonstrating the problem with percent-sized applets, at le
This same issue seems to be reported as a Chromium bug,
http://code.google.com/p/chromium/issues/detail?id=115880
http://code.google.com/p/chromium/issues/detail?id=71525
but no solution is offered and it has been closed as "obsolete" ??
-
Well, I've looked into this a little and I see the error same as Mikko, only in
Chrome.
The error is there in both Jmol.js and JSO methods, but other browsers
seem not to notice or care about this.
And it happens the same with either doctype, HTML5 or HTML4 (4.01
Transitional)
But the interesti
> Example: http://biomodel.uah.es/Jmol/JSO/simpleJmol3-0.htm
That's my page. Be careful, since I am not sure what set of files that is using
(I cannot update the site now from where I am). I think that 3-0 page was
using the standard JS files included in Jmol distribution, but maybe I
changed t
Hello Sridhar
What the popup menu "View > Bottom" does is basically
moveto 2.0 bottom;
so you can use that. The 2.0 is a time in seconds that you can change. If you
also want the box effect, try concatenating "boundbox on/off" like in
boundbox on;
delay 0.5;
moveto 2.0 bottom;
delay 0.5;
bound
Don't know what was it, but now it is working after your tip. Probably I was
not using the @{ properly, somehow. Still a mistery :-)
Thanks, Bob
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Hi all
I am trying to custom-color per residue in a pdb file (color group does not
work here for some reason; it is not a protein chain but a collection of
separate lipids)
After several tries, this is working when entered in the console of Jmol app
12.2.17:
var ccc = ['xD9', 'xCC80FF', '
FYI, the new 13.0.RC version (downloaded a few days ago) is working fine
for me with my test example. So the existing problem was fixed, and what
Andreas is having now is a separate one.
I was using lowercase and forward slashes in the Jmol application as is.
Hello Mihai
Jmol can indeed be used offline. Only a handful of features require online
connection (yours is an example).
> /*file*/"MOL3D::http://cactus.nci.nih.gov/chemical/structure/methane/file?format=sdf&get3d=True";
I suppose you are using
load $methane
that needs to connect to the Cac
Ok, I see the same as Andreas, and I think there is a bug
Doc says "Starting with Jmol 11.8, multiple files may be loaded as
independent trajectories using APPEND TRAJECTORY"
So I'm testing this:
load trajectory "model_1.xyz";
load append trajectory "model_2.xyz";
load append trajectory "model_3
Andreas,
I have no direct experience with this, so you need to test.
> 1) I have to use files (?)
Maybe. As I said, I'm not sure if it's compatible with the DATA method.
> 2) What kind of filetypes have I to use or are supported.
I would say any type of file format.
> 3) When possible, how c
Hi Andreas,
1) Have you tried to use the TRAJECTORY option of load? (That only works
if all your models have the same atoms and bonds, but the memory and
speed improvements are large) Not sure if/how it may be combined with
DATA.
2) following Rolf's comment, ZAP may be used to delete models,
Hi Andreas
Yes, it seems that translucency cannot be permanently assigned to an
element. I don't think this is too bad an idea. Element color is
identity, but translucency is just cosmetic (like ball size).
But you can assign the color permanently, then apply translucency per
case:
color _H [
> We really do not want to be in the business of distributing other's
> code, I think.
I agree.
> There's no customization. Why do you think that?
There are several portions of code (with your explicit name) that
differ between the file at your site and the file downloaded from the
GLmol sit
El 22 Jul 2012 a las 17:36, Robert Hanson escribió:
> http://chemapps.stolaf.edu/jmol/glmol/test2.htm?GLMOL
>
> http://chemapps.stolaf.edu/jmol/glmol/simple2.htm?GLMOL
>
> should be working. I forgot to upload a change in JmolGLmol.js
Ok.
My concern now is:
- JmolGLmol.js is included in Jmol di
GLmol support seems to be broken. The test pages
http://chemapps.stolaf.edu/jmol/glmol/simple2.htm
http://chemapps.stolaf.edu/jmol/glmol/test2.htm?GLMOL
don't display the GLmol model and throw javascript errors
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My very first and rude attempt at writing a page with object-oriented Jmol.
Using RC1:
Error: TypeError: str is undefined
Archivo de origen: file:///F:/jmol-13.0.RC1/GLmol.js
Línea: 177
I am loading
I obtained GLmol.js v. 0.44 from http://webglmol.sourceforge.jp
--
Hello Jay
Two ideas:
1. you should not use FILE after APPEND. There must be a single word after
load. "Load files" is only needed when multiple files are loaded in one
command.
That is,
load "file1.cml";
load append "file2.cml";
2. I don't think that "select 2.1" is meaninful regarding the iso
Welcome, Sebastian
I hink I had something like this recently and could solve it
Try to add ID before the ID (it is not usually needed, but in this case solved
my problem)
So,
isosurface ID @iso_id cutoff 0.02 @cube_file
---
Hi Andreas
I don't think you can define your own symbols. After all, they are
element symbols with precise chemical meaning. The XYZ reader expects
to see them.
What you can do is choose any element for each type of fragment and
then assign custom colors and radii for each "fake element".
For
Hi again
Oh, you don't need to change all your model files.
The setting may go in your page, there are several ways to do it
I've looked at you demo page and file
Yes, it seems you are in the limit!
distance1.860.186 nmC8/1 #8 P4/1 #4// bonded
distance1.92
Hi Martin
I assume you mean
- hits a link,
that runs some JmolScript
- and then the "Back button"
the browser's back button, right?
I find it hard to think that this may be done, as they are at two very
different
layers - the browser interface, back means go to former page and it is not the
Hello Tian
Jmol draws bonds if the distance between the atoms falls within some range
of the sum of van der Waals radii for those two elements.
Or when the file includes bond information.
Or when there is an explicit connect command in JmolScript
> When I open my structure I can always see som
Otis,
maybe { model=i }
?
e.g. this works:
print {model=2}.atomindex.min
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Dear Eric,
Have you tried
color monomer
instead of
color group ?
That could do it. It works as you describe for interrupted chains, so
maybe too for your situation
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3rd try
Another way, without changing the newAppletWindow() function in new.js
The popup page cannot read variables from the opener page but can
execute functins there (as proved by the call to jmolGetPropertyAsString() )
So:
1. set a ***javascript function*** in the mother page that returns
2nd try
It seems that the popup page cannot read variables from the opener page
(at least in my Firefox Win), so I've changed the procedure:
1. set a javascript variable in the mother page which value is set depending
on
your choice ("left" or "right" in your example). Let's say that variabl
Ok, some suggestions for the popup:
The relevant code is in JmolPopup.htm within function getState()
It says
opener.jmolGetPropertyAsString("stateInfo")
jmolGetPropertyAsString() takes a target applet ID as its 3rd parameter,
http://jmol.sourceforge.net/jslibrary/index.en.html#jmolGetPropertyAsSt
Hi Nick
While jmolSetTarget() applies to UI controls, jmolScript() specifies its target
directly, as the 2nd parameter
http://jmol.sourceforge.net/jslibrary/#jmolScript
So you would use
javascript:jmolScript('load
model/miscellaneous/ene_reaction/1-pentene_decomposition.xyz', 'right')"
> I
I tried to test Bob's script, and it seems that the space after 80&
must be removed
x = "http://webbook.nist.gov/cgi/cbook.cgi?Mask=80&"; + script("show chemical
inchi")
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select _N, _O, _H and connected(_N,_O)
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wi
better:
http://chemapps.stolaf.edu/jmol/docs/
Read-Only Variables
_signedApplet
whether or not Jmol is running as an signed applet (Jmol 11.6)
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Martin, I agree with that observation.
My feeling is that the unsigned applet is what gets loaded.
1. Is the Jmol frank red or white?
2. I think there is a Jmol read-only variable that will say if it is
signed. Check the doc
--
Martin said:
> maybe you could also place the applet within a , and assign the
> onblur to the
I'm not sure that would work. But the applet itself has an ID
--either automatically assigned by Jmol.js or equivalent, or assigned
by you-- and you could define (on page load) the onBlur function I
On 23 Jun 2012 at 11:31, Otis Rothenberger wrote:
> This might be useful, but I'm frustrated that I blew getting the JmolScript
> history. Formerly, this
> text could simply be copied. Did something change in Java security related to
> this?
Yes, after some Java version update, text can no lon
More important than the time needed, the scripts may end up running in
parallel, not sequentially (maybe not, but you better be sure). Send them all
in one go as Paul says.
On 21 Jun 2012 at 20:56, Paul Pillot wrote:
> You should reduce the successive jmolScript calls to a single one, with
> d
a quick Google search says
"The standard installation of Fedora should install OpenJDK"
so that's the likely problem (AFAIK, OpenJDK => IcedTea Java plugin)
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Hi Martin
I'm no Linux guru, but a key aspect is to specify the Java brand and
version. For example, IcedTea has been reported to have problems
running Jmol
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Hello Maciek
I am not certain, but I think that you probably cannot get Jmol
looking for bonds between models. After all, atoms and bonds belong
to a model, they cannot be cross-model.
I'd suggest two possible workarounds:
#1 (probably will not work) Make all models visible before you try:
> It turns out, I was doing the load using "jmolScriptWait(...)". Using
> "jmolScript(...)", it seems to have no problem with permissions.
Ah! That clicks a memory
This is called use of threads. I have fixed security errors by setting
useCommandThread
Look for that word in the online scriptin
Hi Martin
Yes, I know the feeling. It has happened to me occasionally.
1. Make sure you clear up the Java cache. Maybe try another browser
to be sure it is not "contaminated" bu cached copies.
2. Check the paths of the files involved. Sister folders for example
are a cause of security exceptio
Jmol_object.js
sounds better to me
and
gl-matrix-min.js --> Jmol_GLmatrix.min.js
1. better use capitalized GL as in others
2. from what I've seen, a dot is common before min. You can choose it
minimized or not
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James,
> I also want to know if its possible to import and display unit cell data, on
> non-crystal molecule
> formats. The goal is for the user to create a unit cell around a molecule
> (designed in Modelkit for
> example) by inputting A,B,C,alpha,beta,gamma data.
I'm no expert and not sure
Bob,
This is a bit outdated, but I did some review of available 2D drawing
alternatives --AFAIK none of them did 3D --except ChemDoodle
and they are all html+javascript
http://biomodel.uah.es/en/DIY
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Hi Daniel
As Bob says, filter is rather tricky. However, there are basic
differences in your proposals (as applies to select atom expressions)
E.g.
- uper/lowercase is irrelevant anywhere in Jmol
- ":B, protein" means aither chain B or protein or both, so it's totally
fifferent to ":B and prot
More testing, now with MSIE 8 (WinXP)
> http://chemapps.stolaf.edu/jmol/object/test.htm
The applets displays fine, but the image does not (broken image icon)
> http://chemapps.stolaf.edu/jmol/object/test2.htm
"show info" ==> the info pane is put below the applet (which does not
hide). Also, I
Testing in IE9 (64-bit, Win7):
> http://chemapps.stolaf.edu/jmol/object/test.htm
First try: applet loads, white background, no atoms.
Reload: same.
Click on image link: the image is displayed (black bkg, molecule etc)
The IE console reports a javascript error at line 31,
jmol = Jmol.getApplet("j
Hi Paul
> http://librairiedemolecules.education.fr/molecule.php?idmol=336
Very nice!
It works in my Firfox 13 / WinXP but IE8 does not even display the
images (why is it so?)
On IE8, if I am quick to catch the link (which is located to the
bottom-right of the image space) and click on it, th
I am finding (12.2.2, 12.3.28) that
set fontscaling true
affects labels but not echo or measurements.
The doc does not mention measurements, but certainly says that echos
are scalable
What is the expected behaviour?
-
Pascal, each JmolButton has an ID. You can use that for custom CSS rules.
And you can specify which ID you want, instead of the automatically
generated ones.
See the doc for Jmol.js
http://jmol.sourceforge.net/jslibrary/
--
Hi David
I have no direct experience, but the IcedTea Java plugin has been
reported to have compatibility problems with Jmol.
If you can, change to Sun/Oracle Java
That is not restricted to version 12.2, is it?
--
Liv
This is not clear to me.
Are you loading several files together, or sequentially? (i.e "load files etc")
Otherwise, what does "the frame of a specific file" mean?
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_currentFileNumber
_currentModelNumberInFile
_frameID
_lastFrame
_modelFile
_modelName
_modelNumber
_modelTitle
described in
http://chemapps.stolaf.edu/jmol/docs/#jmolmathread-onlyvariables
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from http://wiki.jmol.org/index.php/Creating_Movies :
num_frames = getProperty("modelInfo.modelCount")
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Do you mean getting the total number of frames?
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Hi Daniel
without testing, I would use
load myzip.zip|structures/2L6F.pdb filter ':A/1, ![HOH]'
or
load myzip.zip|structures/2L6F.pdb filter 'MODEL=1 and :A, ![HOH]'
That is, model=1 not model:1. The forward slash notation dates back
to Rasmol compatibility, but it is handy. However I think
Hi all
Jmol 12.2.17
translate Y 12 // not recognized
translate y 12 // works as expected
As far as I know, Jmol is not case-sensitive in commands.
Is this a bug or is there a rationale?
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Otis,
http://jmol.sourceforge.net/jslibrary/#jmolEvaluate
is what you need?
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Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how I
Dear users
This is a poll for your opinions
The new addition in 12.3 of "calculate partialCharge" brings me the idea of
ading this
functionalty to the pop-up menu.
We have
Computation > Optimize structure
Computation > Model kit
I am thinkig of adding
Computation > Calculate partial charges
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