One further note:
I have just found out that the app lacks the FileSave dialog when
exporting to vrml and others, as we have discussed, but the signed
applet has the dialog form all exporters. I hadn'tnoticed anything in
the code I reviewed yesterday that separates app from applet. Must be
Dear developers,
I've been playing a bit with getting all the exporters open a File Save dialog
when called
from the app's popup menu. My changes for now affect only one java file, but
there are
some other things I'd like to adapt (like isosurface export) and I'm not sure
if that will affect
Jonathan's idea sounds great to me: standalone scripts.
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Hi Tzontonel
This is a link to my problem page:
http://ramandata.freehostia.com/minerals/calcite.html
Click to crystal structure to open panel with applet. I put ?NOAPPLET to
link and say: Applet
would be here.
http://ramandata.freehostia.com/minerals/jmol/
does NOT contain (at least)
Forget my former message. I see that you are calling the applet from Bob's
site, not from
yours.
So the problem seems to be that you are calling jmolApplet() BEFORE
jmolInitialize(), so it
probably trying to load Jmol from the page directory (you can only omit
jmolInitialize() in
special
More news:
I reloaded your page, still the yellow box. Then I opened your Jmol.js, then
went back, then
opened the Jmol.js at Bob's site, then went back and your page now loads
correctly!
So it may have been some browser cache trick. Please try to clear your
browser's cache
and retry.
Something has broken between 11.9.1 and 11.9.2 app:
When no molecule is loaded, pop-up Save (first entry) says
11.9.1: File zapped (greyed out)
11.9.2: File (not greyed out)
seems that the zapped special word is no longer being set; as a result, the
submenu
doesn't get disabled
Another
Hello again, Tzontonel
Yes works because I removed some code for jquery.
Yesterday I got intermitent behaviour on page/panel reload: sometimes the
applet,
sometimes the yellow box. Now it seems to work everytime.
The Jmol.js is the same version. If there are some incompatibility why works
So it seems that all this was due to a single bug. One of Bob's recent updates
(11.9.2) has
fixed both issues:
On 2 Sep 2009 at 8:41, Prof. Robert J. Lancashire wrote:
In converting a number of MOL files to WRL we found that the exported
filename is
not using the filename from the original
El 7 Sep 2009 a las 3:11, Robert Hanson escribió:
I think this is taken care of, right?
Right. The problems have disappeared in 11.9.2
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El 7 Sep 2009 a las 3:10, Robert Hanson escribió:
which would put it all together, perhaps with the state script also
embedded in a JPG. (If you haven't tried that, you should. It's quite
startling -- save a JPG, then just drag/drop it back into Jmol. Or
display the JPG on a web page, and
Bob Hanson wrote:
Angel, I think this is not a good idea. These two functionalities --
ExportToWeb and writeGaussan -- are part of the application, not the
applet. They have toolbar icons or drop-down menu items. It is not
reasonable to port them over to the applet, as they
This compressed Jmol file is a great advance, Bob!
write myfile.jmol
I guess this will fit nicely in the popup menu, right?
File Save packed Jmol file maybe?
that would be
write \?FILEROOT?.jmol\
isn't it?
or maybe just File Save as, and don't let users start scratching
their
On 8 Sep 2009 at 11:41, Jonathan Gutow wrote:
1) I don't think this belongs in the pop-up menu.
But we do already have in the popup entries for saving a copy of the file and
for saving the
state, so what's the difference? This is just a more convenient way of doing
the same.
And we'd be
El 10 Sep 2009 a las 10:50, I B escribió:
Hi Ira
What you need has already been invented. If not trivial, quite easy
to do:
How can I get atom name + x,y coordinates by clicking atom on jmol
applet?
You use the callbacks:
http://jmol.sourceforge.net/jslibrary/#jmolSetCallback
In your
The details are explained in the Jmol.js documentation, in the link I
posted before.
If you think that explanation can be improved, please say so.
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Hi,
I am using jmolGetPropertyAsJSON(chainInfo) to extract info from
the model and process it to get the sequence of a protein.
I am finding some funny results, which could be explained if this
method omits info about residues hidden using hide.
Does it make any sense?
I cannot use
select *.?
in 11.8 or 11.9, because I get an error
script compiler ERROR: unrecognized expression token:
Might this be related to the recent implementation of escaped ? (\?) ?
Documentation says it was added in 11.7.34
My copy of 11.7.32 accepts the command, but 11.7.41
On 13 Sep 2009 at 10:35, Robert Hanson wrote:
Thanks for spotting that, Angel.
Well, it broke my existing script :-)
So I had to downgrade Jmol version. Looking forward to 11.9.4
Thanks
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the default for that, I believe, is visible. But you can add any
atom expression you want as a second parameter:
jmolGetPropertyAsJSON(chainInfo, */1.1)
Great! That solves my needs nicely.
BTW, is there any difference between visible and displayed ?
Dear Nico,
There were links to Wiki pages in the form
http://wiki.jmol.org/index.php/Internationalisation
but now they don't work.
What is accepted is
http://wiki.jmol.org/index.php?title=Internationalisation
I've found this because of two of them which are in the pop-up menu (Mouse
manual
On 21 Sep 2009 at 20:52, Nicolas Vervelle wrote:
They seem to recommend the http://wiki.jmol.org/wiki/Title format.
What do you think ?
I think that makes links more complex and confusing, since we already have the
wiki at
the beginning.
What would be expected to be outside of the wiki
Hi Tzontonel,
I guess that onClick is not the expected way to use the drop-down items :-)
You may use this:
select onChange=document.jmol.script(this.value)
option value=selectSelect vibration by clicking here/option
option class=green value=frame 4T(Ca, CO3)/option
etc., as long as you don't
Andrei, you can put text IN Jmol, not OVER it. The web browsers do not allow
any contents
over applets.
You have echo for inserting text in Jmol, either in 2D or in 3D
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Good idea, Graeme. Thanks for bringing it.
I remember adding the 'label' tag to ease the use of controls.
I will work on this along the weekend. Other controls should then have a
similar feature.
Let's see what can be done.
Do you have any experience with screen readers? Do they really read the
Hi Graeme
What you are requesting was already implemented in Jmol.js (the 'title' is
there for the 'span'
tag that envelops the checkbox+text).
What version of Jmol.js are you using? Or may it's a browser problem?
I see the tooltip in both Firefox 3.5 and IE 8, WinXP
That's great news, Michail. Thanks for sharing!
Do you mind if I add a link to your file in Jmol Wiki?
http://wiki.jmol.org/index.php?title=File_formats/3D_Objects#IDTF
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Dear developers,
You probably know this already, but just in case, I thought better to
forward it:
--- Forwarded message follows ---
Subject: never use + to join lots of strings
While well known, this post nicely shows why concatenating lots of
string
shouldn't be using the +
On 13 Nov 2009 at 20:28, Jonathan Gutow wrote:
if (! nameSuffix)
nameSuffix = appletCount;
considers nameSuffix = 0 as True.
You mean it considers nameSuffix as false when it is zero, hence !nameSuffix as
true.
That's regular javascript. There is also the issue of undefined, but
Bob wrote:
if (xxx == undefined) xxx=yyy
as
xxx == undefined (=yyy)
same s
xxx != undefined || (=yyy)
I'm OK with any solution, but I find this very hard to read --
particularly the last one. If there is no advantage in peformance,
I'd rather stick to the original if
For the translation, I need clarification of this item:
click and drag to select selected OR this group of atoms (requires {0})
does the OR mean a combination of selection (those previously selected plus the
ones
dragged now, i.e. like in an OR command), or an alternative action?
click and drag to select selected OR this group of atoms
(requires {0})
Bob wrote:
Yes, it means the group of atoms will be added to the group of atoms
already selected.
Thanks, Bob. I will clarify in the Spanish locale.
Anyway, I think that may be confusing some users. How about
I cannot test this new feature, but it does sound exciting.
I understand there is a basis for this, but I would suggest to have a keyword
easier to
remember and less prone to spelling errors than
SparshUI
-multitouch-sparshui
multiTouchSparshUI
Wouldn't multitouch be enough? Or, if more
I've tested my ideas on
http://biomodel.uah.es/angel/Jmol/rounded/
1. uses just CSS (good only for Firefox, Chrome and Safari, but I guess you
already have
your solutions for rounded corners)
2. Jmol can position 4 images using echo, but seems to have problems with GIF
transparency in 3 out
I am testing the use of transparent gif files inserted into Jmol using
set echo myNamedEcho IMAGE myFileName
I created some GIFs with transparency. Jmol (11.8.11) does not respect the
transparency,
but instead makes transparent always the color of the top-left pixel.
And whatever was my
El 22 Dec 2009 a las 4:25, Graeme Kidd escribió:
Sadly my understanding is not good enough to know why it needs to look at
one pixel to determine if the image uses transparency and why the other
methods haven't picked up on it either.
Yes, I found that the first (top-left) pixel is used for
El 21 Dec 2009 a las 23:48, Graeme Kidd escribió:
I have attached the images if you want to add them to your example.
Unfortunately, those are good only for black applet. Jmol is still
using the first pixel for transparency.
What I wanted is that the corner images will be white outside and
Hi Aya
You can find the details you want reading the Scripting Doc for hover and
label, at
http://www.stolaf.edu/academics/chemapps/jmol/docs/
You can put any text as well as special symbols preceded by %, which are
explained in
label.
Particularly, for a line break you use a vertical bar
(We're talking Jmol 11.10 here, not a fix in 11.8)
As an aside, this is maybe an occasion to make it 12.0 -- that will simplify
explanations of
the different behaviour (if you have Jmol 12 is easier than if you have
11.10 or later).
Anyhow, there's already many new features to justify a new
That would be a big move. We'd need to see what Eric Martz and
company think, since that would definitely change the molecular
surface visualization for traditional PDB files. (It would, of
course, CORRECT the visualizations for H-containing PDB files, but I
think that's a small subset of
Hi Tzontonel
I'm quite sure that's xyz format with vibrations (called XYZ+vib in some
places, such as the
Jmol home webpage). For each atom, first 3 numbers are xyz coordinates, 2nd
group of 3
numbers define the vibration vector.
I'm sure there is a description somewhere, but don't remember
On 17 Jan 2010 at 0:22, Angel Herráez wrote:
I'm sure there is a description somewhere, but don't remember where.
There it is, in the Wiki:
http://wiki.jmol.org/index.php?title=File_formats/Coordinates#XYZ
Hello Mhairi
Second, the delay only works with `delay 2´, if I change it to `delay 1´
then it just freezes.
That's strange and shouldn't happen, but try delay 1.0.
Or try a different version of Jmol, to find out if it is a bug.
This command works but it has the wireframe for 2
I see this as a term that needs translation:
#: org/jmol/script/ScriptEvaluator.java:8998
msgid {0} struts added
Can you tell me what are these struts? The standard dictionaries do
not help me.
--
Oh, yes I had seen the airplane thing, but couldn't think of a way Jmol would
have anything
to do with that --despite the navigation mode ;-)
In Jmol this is a generally short bond-like piece that is thick enough to
support a section of a
protein in a plastic model created using rapid
Ha, ha, I know what it is. You are building a (nano)airplane to do the
navigation mode with
it, right?
x-D
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On 5 Feb 2010 at 17:12, Robert Hanson wrote:
The files read just fine on a PC with Cortona3D.
Yes, I've following this with Tzonzonel (must have been off-list, since I don't
see my posts in
the archive). I told him that the file displays fine in several VRML viewers I
have (different
from
Hi, Tzontonel
The relevant command is stereo. Look it up in the doc.
It is also available from the popup menu
(Sorry, I have no time now for more details, but it is easy to do)
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Those plots were made manually, for a limited set of data.
Extending to general data sets is not easy, if even feasible.
On the other hand, as Jonathan says, there has been recent progress on the
abilities of
Jmol to plot functions.
Status: Closed
Resolution: Fixed
Summary: water is not solvent
Comment By: Bob Hanson (hansonr)
Date: 2010-02-27 09:19
Message:
fixed for Jmol 11.8.19 and Jmol 11.9.31
sure enough. That's broken at least back to 11.6.
select ions
actually selects ALL
Good. I still have a
Robert Hanson wrote:
The JUnit test passes, so there may not be any problem. One thing I
could not find were Crystal Maker cmdf files, and as part of this I
am upgrading ShelxReader, which includes that.
Bob, do you need sample Crystal Maker files? I might get some from a
colleague.
Hi Moacyr
When you have some time, it would be nice that you insert some description of
your work at
http://wiki.jmol.org/index.php/MultiUser_Jmol
Sharing a Jmol model between several users across a network is something that
has a great
potential for scientific discussion and, particularly,
I would say yes, you would see it 3D.
Why don't you try and tell us?
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Hi Pravin
You certainly do NOT need the CDK for building Jmol.
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Hi Kent
So you're saying that the color part is an entirely separate command?
Certainly. Once you define bonds, they are treated as such, and
that's the command.
However, I would advise you not to use bonds for this. You can draw
objects (lines, cylinders), and they will be treated
R. Kent Wenger wrote:
connect (atomno=442) (atomno=410); connect (atomno=586) (atomno=266);
color bond green;
I end up with all of the bonds colored green, not just the ones I added.
If I make the whole thing one command, I get an error.
That's right. You need a select command to
Thanks much!
Good!
I forgot this: if you want to control later the connection visibility, color,
etc., it's better to give it
a name when created:
draw myConnectionA diameter 0.2 {atomno=442} {atomno=410} color cyan;
then
draw myConnectionA off;
draw myConnectionA on;
Hi Kent
Also, if I give two consecutive draw commands, only the second one seems
to take effect.
Try to assign a name/ID to each draw object:
draw ob1 diameter 0.2 {atomno=586} {atomno=266} color cyan;
draw ob2 diameter 0.2 {atomno=596} {atomno=276} color cyan;
(the ob1 and ob2 may be any
In general, cite the project's website. The citation is explained
there.
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I vote for 12.0. Enough new and radically new features!
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Bob, three small issues with the scripting doc page:
http://chemapps.stolaf.edu/jmol/docs/?fullmanual=1ver=11.10
1. the page loads 11.8 by default, not 11.10
2. All text is bold starting from by a molecular frame quaternion, as, for
example, retrieved by
q (within navigate)
3. links for JVXL
On 26 Mar 2010 at 14:56, Robert Hanson wrote:
works for me. Comes up 11.10.
Right.
Sorry, I pasted the 11.10 link. What I meant was that I was expecting
http://chemapps.stolaf.edu/jmol/docs/
to open with the latest. Since you say the design is to open the stable one,
everything's Ok
I had the
I agree that, at least for icons, a common place is better. More uniform look
after any future
restyling.
As for other 'resources' I can hold no opinion.
--
___
I've been playing for somewhat long time with connecting JChemPaint for 2D
drawing toJmol
for 3D rendering.
It's over a year that I have a working prototype, but haven't released it
public because I was
expecting to polish it up. In fact, that's the topic of one of my presentations
at BCCE
A few comments:
1. JCP has the advantage of accepting SMILES; which I think is more
widespread and feature-loaded than JME. I also allows more variety
when drawing structures. I have set quizzes that use SMILES to match
user-drawn structures against correct answers. I doubt that JME
string
Robert, do you mean that Chime would do 3D starting from a flat
structure? I've never seen that
El 28 Apr 2010 a las 17:34, LANCASHIRE,Robert J escribió:
this would then mean Jmol really does provide a replacement for MDL CHIME.
Would Jmol then read mol files where all the z coords were
LANCASHIRE,Robert J wrote:
sorry to confuse, CHIME was able to display a flat version of a 2D file where
all z coords were 0.0
Right, that's what Jmol has always done.
There was an extra piece of code in the commercial version that allowed some
energy minimisations
and movement of atoms
So, Egon, what does JChemPaint use for a minimization algorithm when
going from 2D to 3D?
Unless I'm totally wrong, JCP does no 3D. Only flat molecules, 2D
coords.
--
Robert Hanson wrote:
I note that the description on the WIKI should be changed:
Done!
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Bob, can you check if the info at
http://wiki.jmol.org/index.php/Support_for_stereochemistry
is correct and precise?
Thanks
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I've made some interesting observations, with flat MOL file models that have
the (newly
supported by Jmol) stereo bond codes (1 for up, 6 for down):
(All atoms have z=0)
2 programs that have a good support for the MOLfile standard:
ChemSketch opens the files and depicts them flat with the
On 1 May 2010 at 21:20, Egon Willighagen wrote:
However, with the current design, a sub 250kB applet should be possible...
That's interesting... Right now, just applet-core and applet-editor sum up 560
KB
--
I'm copying this from JChemPaint list in case it is of interest
--- Forwarded message follows ---
Date sent: Sun, 2 May 2010 12:59:57 +0200
From: Christoph Steinbeck steinb...@ebi.ac.uk
We need to be careful with statements about what should be possible
Dear developers,
This post in the CDK mail list may be of relevance to future Jmol
features.
Message: 1
Date: Mon, 03 May 2010 19:49:42 +
Subject: [Cdk-devel] [ cdk-Patches-2996119 ] Implementation of
CLOCKWISE and ANTICLOCKWISE stere
Patches item #2996119, was opened at
Windows Safari 4.0.4 (531.21.10)
I think I have not updated it too recently
1) go to http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
2) click on cmd just to the left of the input box under the applet.
The applet is frozen right now.
3) enter a command such as background red and
Some more testing:
Windows Google Chrome
userAgent says AppleWebkit/532.5 Chrome/4.1.249.1064 Safari/532.5
The console opens and the applets works OK
(Safari 4.0.4 says AppleWebkit/531.21.8)
I have just updated to Safari 4.0.5 (AppleWebkit/531.22.7)
still the same problem
1) go to
Jonathan Gutow wote:
So here's what I think we've got on Webkit Browsers:
Doesn't work:
Safari 4.0.5 (6531.22.7) MacOS 10.6.3 Java SE 6 (64 32 bit versions enabled)
OmniWeb 5.10 MacOS 10.6.3 Java SE 6 (64 32 bit versions enabled)
Safari 4.0.5 Windows (version info? Angel)
mine are
Not a problem, Bob?
What do you mean? It is not working properly in both 11.8.23 and
12.0.RC11.
El 19 May 2010 a las 1:24, SourceForge.net escribió:
https://sourceforge.net/tracker/?func=detailatid=379133aid=2933627group_id=23629
Category: User interface
Group: v11
Status: Closed
I've just found (from reading his recent paper in J.Cheminformatics)
that Peter Ertl is working on an open-source javascript-based
equivalent of JME. Might be a good complement for Jmol.
--
I just received news from Peter Ertl. The JME2 development is
currently stalled with no known date for resuming it.
;-(
El 21 May 2010 a las 10:39, Angel Herráez escribió:
I've just found (from reading his recent paper in J.Cheminformatics)
that Peter Ertl is working on an open-source
I've been updating the Spanish translation, mostly involving the new model kit
features.
I'm quite OK with lowercase, but the current convention is that menu entries
start with
uppercase (or even have several words in uppercase).
Before updating the translation, I can go and edit the source
I think it's premature to do much with the model kit. I don't consider those
permanent. Just a set of
menu items I whipped together over the weekend.
So I thought, but I like to see things as they will, and keeping the
translation up to date.
I can delay the translation until things ar more
There's an upper/lowercase problem that prevents the all frames button from
displaying in
the app toolbar:
org/openscience/jmol/app/jmolpanel/Properties/Jmolresources.properties
HAS
animateAllScriptImage=allFrames.png
BUT the file is...
org/openscience/jmol/app/images/allframes.png
I tried
I've commited a new image with a new name and modified the properties file
acordingly, so
this should be OK now.
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[ I'm taking this off the users list ]
El 8 Jun 2010 a las 18:53, Robert Hanson escribió:
jmolSetCallback(UseCommandThread,true)
[...]
* You can specify that the signed or unsigned applet or application
should
* use an independent command thread (EXCEPT for scripts containing
the
Jonathan Gutow wrote:
cartoon_fancy_sheets --- turn on antialias for cartoons
Also, and more important,
set hermiteLevel 4
and maybe
set ribbonAspectRatio 12
or some other value
(I'm guessing since I don't know the exact rendering Pymol uses, but
Jmol cartoons look much better with
Hi, Henry
http://chemapps.stolaf.edu/jmol/docs/ says (even for 11.8):
set measurementUnits [distance-unit]
Sets the units for measurement display to be Angstroms, nanometers, or
picometers.
where
[distance-unit] is ANGSTROMS, AU, BOHR, NM, NANOMETERS, PM, or
PICOMETERS
So is
Presently if you try to save a WebExport page with the same name as
one you've already made (ie update it), you end up opening the
existing directory and saving a new one inside of it.
Right. That's quite inconvenient to me, and I think it may be unpleasant for
users.
If not, I
On 16 Jun 2010 at 16:49, Jonathan Gutow wrote:
Oh, did the translation issue in the help go away? If not, I'll look at the
code again.
Last time I looked, the menu links in the header section were translated (I
think), but the
content of the help page still was not.
But I must do a clean
Ok, so I've just tested RC19
The WebPageMaker Help pages display all in Spanish, until when I click on the
link for
widgets, that page comes in English. And all further navigation with links
takes me to the
English pages.
Thanks for looking into this, Jonathan
Jonathan, the local path issue is still not working
12.0.RC19
I have .. set in both server and local paths in the ExportToWeb panel. The
page I get (both
PopIn or ScriptButton) has both local variables set as .:
var jmollocaljarpath = .; // where JmolApplet*.jar is to be found locally
var
Found it and committed a fix. You had missed a few links when
translating and were still linking to the English pages.
Oh,I see! I must use the _es links. Didn't notice that. Sorry
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Hello Kapil
I'm no expert at Java programming, but I see 2 possibilities. It
might be a bug, but others are not seeing it.
Most likely this has to do with the HotSpot VM. Have you tried using
Sun's Java VM? That's compatible for sure
I remember some discussion time ago regarding HotSpot, but
Hi Piero,
Yes, it looks like it may be a timing problem.
Have you tried to call set loadStructCallback before
set messageCallback ?
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What will you do first with EVO, the
El 7 Jul 2010 a las 10:42, Robert Hanson escribió:
You mean in Jmol.js?
Yes, that's Jonathan's idea, changing Jmol.js
I suspect there must be some reason why we have the two methods: use
appletID parameter for jmolScript() and similar ones, or use
jmolSetTarget() for the others, but
Piero,
Mostly, alerts serve to stop the flow of javascript and whatever
message you put in them just tells you that the flow is there.
I'm afraid I cannot offer any clear hitn as to what is happening
precisely in your case.
On the other hand, if your only purpose for defining a
I can do that change in the website.
But we should think whether the linked pages (old method of writing
the applet) should be removed altogether or left as now, with the
caveat added (they were old doc pages and until now I was reluctant
to remove and loose them for good)
Bob is probably more knowledgeable than me, but this is how I see things:
If you have the HTML4 doctype in the header, the browsers will interpret as
such. No problem
with applet. After all, this tag is already deprecated in 4.01, but the
browsers respect it.
After this dicussion, I have made some changes in what goes in the website,
advising about
the fate of the applet tag and the strong convenenice of only using Jmol.js
The update is already online. (Thanks, Nico)
http://jmol.sourceforge.net/docs/
http://jmol.sourceforge.net/scripting/
I wasn't
P.Canepa wrote:
Colud be possible to highlight the fact that Jmol can read CRYSTAL outputs on
the official page?
Piero, I assume that you mean to mention this format in jmol.org
webpage, right?
http://jmol.sourceforge.net/index.en.html#Features
I can do that. Please, provide a short
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