I can't make this work:
color selectionHalos cyan;
Works fine in 11.8.25, but not in 12.0.RC26
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Dear developers,
As far as I know I am not an admin or moderator for the jmol-dev list (and in
fact I cannot
access the link below with my password), however I have received this message.
Maybe it's helpful for you to know what's going on with auto generated
maintenance emails.
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problems with
my email server rejecting my own posts to the list. I have been unable to find
a cure, other
than adding my address explicitly as Cc to my own posts.
(In case you are interested, the issue is that my
Bob Hanson wrote.
-- proposing a NEW DEFAULT for Jmol for 12.1 and 12.0:
double bonds in the plane of the atoms, not twisty with
orientation.
I quite agree with Jonathan, I'm not sure I would like this default changed.
Must play with it
but haven't got the time now.
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Either the server is down or the url mapping is failing:
http://wiki.jmol.org/
gives an Error 404
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Yes, broken for me too. Apache's strike, maybe? :-)
The wiki is back on right now!
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Jonathan, I know what you mean. The idea is that zero may be taken as false (no
id
provided). However, my test now seems to behave (12.1.14)
The line in Jmol.js that does the trick says
nameSuffix == undefined (nameSuffix = appletCount);
but I really don't understand how this code works.
Jonathan, I'm running this test (out of Jmol.js):
var appletCount = 1;
function test(a,b,nameSuffix) {
nameSuffix == undefined (nameSuffix = appletCount);
alert(nameSuffix);
}
var x = 0;
test(0,0,x); // returns zero
x = 0;
test(0,0,x); // returns zero
So how are you setting the n variable?
I had assumed the problem was this test. But your results suggest
not. Is there something earlier or later in the code that is also
checking the appletID? I hadn't noticed anything.
Can't see what or where. jmolApplet() directly calls _jmolApplet()
which tests the ID.
What browser are
Jonathan, we have something to hold onto.
Your test page
https://141.233.197.45:4443/home/pub/0/
works fine in Firefox 3.6 Win. Both applets go to sleep and wake up correctly.
However, when I click to sleep for a second time, there are errors:
could not find applet jmolApplet0
(in a
I think it must be some change in the StubManager.
Nico, do you have any ideas about this?
See also
http://wiki.jmol.org/index.php/MediaWiki#Problems_yet_to_be_solved
http://wiki.jmol.org/index.php/User_talk:Jacksmind
Bob,
I don't think that has nothing to do with the problem, but it is an interesting
idea.
The problem is with the Jmol MW Extension generating the applet code from the
wiki tags. It
seems that the extension is working in old versions of the StubManager
extension, but fails
with new ones.
I
On 15 Oct 2010 at 22:28, Robert Hanson wrote:
Is this a case where the image/state could be useful? Upload the model file
and the PNG image
containing the state; they will be in the same mediawiki directory (I
suppose), so then loading the
IMAGE into Jmol (never loading the model
Right, I thought of that too. But then you do not have the PNG for display in
the wiki. (Which
was YOUR suggestion ;-) )
Anyway, I've found no way
1) to have both files uploaded together
2) to have the Jmol MW Extension code merge with the image insertion wikicode.
so I think it's a no-no
Has Nico taken a look at this?
Nico is travelling and cannot check the wiki config for some weeks.
It can't be too much of a problem since. One of
the guys in the mediawiki irc channel told me. he got jmol running in no
time.
though I cannot confirm what versions he used. And as you
Dear developers,
1.
As a result of my sessions with students, there is a recurrent topic that has
appeared in
previous years, and maybe now is the time to tackle it:
Using the applet and popup menu, one can color by chain, but there is no way to
select
chains other than from the command line.
The enabling/disabling of options depends upon the name of the menu
item in the resource. For example, PDB indicates that a file must be
a PDB or MMCIF file with residues (other than just UNK) for that item
to be enabled.
Yes, I remembered that later on.
But don't we have
Set
I suggest not having calculate structure Ramachandran on the popup menu. It's
too esoteric.
Why do you thnk so? It was the default until recently, so one may want that.
ANd particualrly
if I have done dssp, I may want to compare results.
To me, the command set should be complete: calculate
Christoph, how do you define current coordinates?
As far as I understand, the (xyz) coordinates of the atoms do not
change when you rotate or translate. So current=original at all
times.
rotateSelected does change the atom positions relative to the rest of
the model, so it does change the xyz
Hello Christoph
Not sure about the rationale of the error, but t be safe I think you should
create the isosurface
for what you have selected --is that what you want? Then whatever is visible
or not shouldn't
matter, I think
select 20-22:A and 2.1
isosurface isosurface_pdb1sbt_ent_19_21
I don't know if this is a bug, or just a limitation. Probably nobody has ever
come to using this
combination.
Anyway, I thought I'd rather report it.
When using set scaleAngstromsPerInch (aka set scale3D) and then set
antialiasDisplay
true, the size of the model shrinks (I guess due to the
Dear Bob,
Yesterday I had to work with a PQR file. I knew that Jmol opens them, but it
seems that it
was being interpreted as pdb (the partial charges were not right)
When I loaded using load pqr::xxx.pqr to force the format, ir came out good.
So my question is: how is the reader in Jmol
Ok, thanks, Bob
So it seems that PQR exported from Pymol lacks these fields (I don't
think that my colleague removed anything on purpose)
Regards
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Sorry, I don't understand what static fields mean.
Whatever I contributed to WebExport was based on duplicating or editing
exissting code. I
don't really grasp the inners of Java code.
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While testing 2D to 3D conversion with random drawn structures, I've noticed
that Jmol
sometimes fails to calculate a hydrogen for a carbon that has 3 substituents.
Today an example has shown this dramatically.
I am using minimize addHydrogens or just calculate hydrogens with same
result.
Nico, I'd like to help with this, but I'm loaded this month and the
next. I could put time after January 10th.
·
Dr. Angel Herraez
Dep. Bioquimica y Biologia Molecular, Universidad de Alcala
E-28871 Alcala de Henares (Madrid), Spain
Hello Alexander
Let's try to divide the problem
Do you get the error with a simpler example like this?
jmol
jmolApplet
/jmolApplet
/jmol
My LocalSettings.php just has the
require_once($IP/extensions/Jmol/Jmol.php);
I'm not sure about the $IP bit, you may know better. My test wiki has
The proxy feature is great news, Bob (I know it's not new, but I
never grasped its utility).
Nico wrote:
What are the exact URL used for SMILES and PDB ?
Documented at
http://wiki.jmol.org/index.php/File_formats/Chemical_Structure
Nico wrote:
Is it possible to configure Jmol for
I realize that certain localizations are still in an immature state,
but if the JmolApplet0_i18n_pl.jar file is included in the
distribution and the 'language =pl ' command is available and
accepted, shouldn't that language be available from the popup menu?
I have verified this situation with
El 13 Dec 2010 a las 10:56, Robert Hanson escribió:
go ahead and do that, Angel.
Now that's a challenge!
I will see if I know how to ;-) Can't promise
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El 13 Dec 2010 a las 11:03, Robert Hanson escribió:
Just follow the examples of the other languages.
Yes, I've found the code that does it (GT.java). It makes sense: only
languages with over 80% translated items get to the popup. The next
two candidates pt and pl are just above 50%. I doubt
Thanks , Nico
I'm not sure if it's worth the effort.
Recreation of the interface when switching language has improved in
latest versions.
There may be an easy way to add a language in the popup menu if is
choosen by the used.
More than chosen by the user, it's if chosen by script or if
I would rather see 3 things in the menu : the language code, the
language name in English, the language name in its own language.
That sounds great.
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I have found out that MOL files exported by Jmol, using the write command,
fail to be
opened in PowerMV, a free SDF viewer.
So I've gone into finding the cause, and it is that
1. PowerMV is picky on the MOL/SDF format
2. Jmol exports do not fit the MDL spec in some aspects
So I am working on
Well, we aren't exporting SD files, just MOL files. Let's just
implement an SDF file writer and do that right rather than faking it.
Bob, you're right, but that's not exactly the situation. I didn't
make myself clear enough.
MOL and SD formats are exactly the same except for the line
Bob, the doc
http://chemapps.stolaf.edu/jmol/docs/#writemodel
says
In the case of SPT, a script file containing the coordinates of the model.
How is that? Only the state script is saved (I always thought that was it).
Hi Bob,
I've looked at your commit to SVN.
Is there a reason why you want to keep the headers for the MOL export as they
were?
I think we should conform to MDL-Symyx for both SDF and MOL
The only thing different for SDF would be the line
Regards
Works great, Nico!
No complains building now.
All languages display well in the menu (I see blocks for those whose fonts I
don't have, but I
guess that's fine)
The addition of language per demand is wonderful addition
I have commited a small fix - English was being displayed only in Spanish.
Bob, the month is wrong (zero-based)
__Jmol-12_11181000533D 1 1.0 0.0 0
should be
__Jmol-12_12181000533D 1 1.0 0.0 0
That's why I added one
1+ c.get(Calendar.MONTH)
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(Sorry I sent this to the wrong thread: localizations)
Bob, the month is wrong (zero-based)
__Jmol-12_11181000533D 1 1.0 0.0 0
should be
__Jmol-12_12181000533D 1 1.0 0.0 0
That's why I added one
1+ c.get(Calendar.MONTH)
Also, I think the position of the
Bob wrote:
A satisfying day! After my development laptop died yesterday, that is
especially good new.
So you melted it down? ;-D
Angel, I need you to test those V2000 files to see if they really do load
into that viewer.
Sure. Later this weekend
I'm trying t find if there is a
(This is mostly for Jonathan bu I'm putting here for future reference and also
if someone else
has ideas. It follows from a report in jmol-users that pages generated from
Export to Web
display Chinese text worng in the widgets)
Jonathan, my first impression:
The problem is only in the part
Thanks, Egon, I had already found that page of yours yesterday.
But in practical terms I don't know what to make out of it. I haven't got CDK
installed (and will
not, since it exceeds my needs and understanding).
Now I'm worried that Bob gets a new laptop and so his development rate will be
and the very latest little fix I just checked in -- there was an extra 0
on the bond records.
Yes, I was just tracking that down that extra zero. That was the origin of the
error DS
Visualizer gives. Now V3000 is loading fine into both
-- Accelrys DS Visualizer 2.0 (3D viewer-editor)
--
Nico, thanks for the advice
I am aware of the encoding in the html files, but after looking at
this I think the problem is not there, but in the java.
I will need more testing for findignt he origin and the fix.
Your comments will be helpful, I hope. Thanks
Li An-Bang has brought to my attention that
And,I notice, the Jmol logo in What's new doesn't display correctly.
I am trying to find the location of the html template for that panel.
Jmol.properties says
# Resources for the What's New dialog box
#
Thanks, Jonathan
I had already looked at those
I think I've found it: it's out of the src folder, in
doc/source/JmolHistoryToHtml.xsl
But still struggling to how to reference the missing Jmol_logo.jpg file
It seems that the folder was moved between 11.6 and 11.8 from
Hello Kevin
El 26 Jan 2011 a las 20:03, Kevin Rosso escribió:
I tried reporting this to mol-develop...@lists.sf.net but was sent a
rejection email.
There's a 'J' missing there, maybe it was that:
jmol-developers@lists.sourceforge.net
I've tried your live demo pages
Sorry, a couple of typos slipped into my previous message:
jmol-developers@lists.sourceforge.net
is probably equivalent to
jmol-develop...@lists.sf.net
but I'm not sure. The first one is what I use regularly
The browser detection routine in Jmol.js is
old and does not take Chrome into
Clarifying Kevin's problem (some of the dialog between us went off-
list):
1.
in Mac OS Snow Leopard, same computer:
- Chrome 8.0.552.237 (latest) fails to display Jmol applet
- Safari 5.0.3 and Firefox 3.6.13 display OK
(so it's not a Java problem, in principle, but something specific to
Chrome
Kevin,
I fund my former testing page. Let's see if we can corner the problem.
Can you please test this page
http://biomodel.uah.es/angel/Jmol/test/test-object-tags.htm
and tell me which of the 4 Jmols you can see in Mac Chrome?
Got Miguel's and Kevin's reports and screenshot. Thanks
Will report back later or tomorrow
(dinner time :-) )
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Not sure what's going on.
Jmol.js in inserting an applet tag (Jmol #1) for Chrome and fails to display,
but when that
code is written directly (Jmol #2) it works.
I've read about changes in the way recent Chrome deals with object tags, but
not with applet
tags. And since Chrome/Win hasn't got
Bob,
problem is, I don't know what/where the bug is, so I can hardly file it --may
be taken as a
Jmol.js problem. As I said, the applet code (#2) works fine when entered
manually, but not
(#1) when entered by Jmol.js (on my v.1 page, using the regular Jmol.js)
So I thought I had it right, now I'm feeling uneasy ;-)
Jonathan reports:
MacOS 10.6 and FF 3.6+: no Jmol appears in the first box, page v.2
Kevin reports:
Mac OS X Snow Leopard and FF 3.6.13: ok
The Mac/Chrome issue seems located and fixed, but now Mac/Firefox steps in!
And as far as
On 28 Jan 2011 at 21:20, Jonathan Gutow wrote:
c. Set Mac/Firefox to do the same as other Firefoxes (Anyone knows of any
problems with
Mac/Firefox that make the applet tag more adequate than the object tag?)
Just tested this. Your version 2 page does not work with FF 3.6+ MacOS
10.6.
I think this is mainly for Bob:
Jmol.js has this:
function _jmolFindAppletInWindow(win, target) {
var doc = win.document;
// getElementById fails on MacOSX Safari Mozilla
if (_jmol.useHtml4Object || _jmol.useIEObject)
return doc.getElementById(target);
else if
I'm rather surprised about the last posts in this thread. Up to now,
I had the knowledge that the safest way to avoid timing problems
was to put the script in the jmolAplet call and not in a jmolScript.
Now it seems there are situations where the other is better (plus the
callback, of course).
El 4 Mar 2011 a las 18:29, Nicolas Vervelle escribió:
Do you think we should installUser_Merge_and_Deleteto merge the
spammers account and reduce the list of such accounts ?
It sounds the reasonable thing, but what I read on the web strongly
advised not to do so, unless hardly
Nico, thanks for the effort.
I haven't been able to test the new system yet, but it sounds
reasonable.
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Hi Bob
I agree that sounds much more intuitive and informative.
If I remember well, Jonathan had a page of the sort before he started
working on Export to Web
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Hi all
Today I've started some cleaning up of the user list in Jmol Wiki
(BTW we are still having spam user and page creation despite Nico's recent
preventive
measures)
1. cleared all users that had been blocked in the past because of spam ('clear'
means
merging them to the anonymous user and
On 11 Mar 2011 at 16:32, Robert Hanson wrote:
Thanks, Angel. Any reason not to just clear all the users and start over?
I guess we'd destroy all history, at least. And would offend fair users, their
existing user
pages, password etc. No need for that. In any case, users cannot be deleted en
And we still have a lot of new users each day, without any
contributions : it's not a big problem, but the user list will
probably grow again.
I've seen that. I think that maybe the new locks (like avoiding to
have URLs inserted) are preventing this fake users from creating
pages. But they
Under a particular situation I am finding that animation of a multimodel file
is blocked by
using hermiteLevel
This is a molecular dynamics trajectory fileset (topology file + coordinates
file, from Amber) of
a peptide. I am setting a thick trace for all protein + sticks or spacefill on
a
Hi Egon
I searched for volume in the Scripting Doc and this came:
isosurface VOLUME
Calculates the volume of the current isosurface and stores that
value in the isosurfaceVolume variable. The VOLUME parameter may also
accompany any other parameters in the construction of an isosurface.
Hi Jonathan
I have not strong confidence on this, but I will drop a couple of comments
1. I'd guess that changing the archive parameter on the fly will need thorough
cross-browser
evaluation. Do your Sage pages have a single JmolApplet in them? Otherwise,
the shift will
not work. As I
Dear developers,
I have committed code that updates the definition of the 'carbohydrate' atom
set. This is
based on a list of residue IDs (provided by Eric some time ago).
While working with some glycans in glycoproteins, I have found out a few common
residues
(N-acetyl-galactosamine and
I have NOT removed the obsolete IDs. They are still there for
backwards compatibility. I just moved them all to the last line so
they are easily identified as such.
After all, we are supporting old atom and residue names like A T G C
in DNA, both 3' and 3* etc.
Unless the same IDs are now used
Bob Hanson wrote:
Don't get me wrong
I didn't. No worries.
PREHEADER HYDROLASE (O-GLYCOSYL) 06-DEC-79
I think that date is the key here. PDB has been doing a lot of
change. But on the other hand we all keep old files around in our
disks and webpages, so the conservative attitude is
Jonathan, have you tested the output of show isosurface or list
isosurface?
Probbaly too basic for your need, but maybe...
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Ries, the creator of
write myfile.pdb
is producing a file that uses commas as decimal markers (I guess this comes
from my
Spanish locale in Java, although my Windows is configured to use the decimal
point, not the
comma)
As a result, the pdb file is not correctly read (some missing atoms and bonds).
A full
Sorry, I am unable to reproduce this problem now, in 12.2.RC5
I will repost if it happens again.
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Jonathan, I'm trying to use this idea of replacing the applet with
the signed vesion on request.
Coud you share the scripts you use for retrieving the state and
applying ti again after the applet has been replaced? I'm stuck
trying jmolEvaluate('state'), show state, print state...
Thanks
Thanks Bob!
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Good; thanks, Jonathan
I vote for having this jmolToSigned() added to Jmol.js
I know it may need further testing, but it seems to work fine and
having it there is the good way to have it tested.
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What's the goal of JmolToSigned?
Looks to me like it just returns a file name.
It **assigns** a file name to the _jmol.archivePath variable. This
allows the page to destroy an applet and replace it with the signed
applet.
Or that's the idea
There is a huge number of phrases that are now untranslated in the current .PO
files, I guess
this is a consequence of the recent refactoring. But many of them were already
translated
before.
Why have they been lost?
It's going to be quite a task to retranslate them all
It may be that they were (translated) in the applet PO file and now they are
also (new, and so
untranslated) in the application PO file
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I just tested kiosk mode in latest 12.2_dev at StOlaf
The instructions at the top say to type exitJmol but this is not recognized
with that case; all
lowercase exitjmol does close the kiosk
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Have we got the translation issue sorted out for this release?
I mean, that bunch of new untranslated phrases in the Jmol.pot and po files,
which already
existed translated in the applet.
I think that having full translations is important for a release version.
If all translators will need to
In my opinion, being able to make distinctions between phrases that
translate different. There are a few other instances that I would
like to improve in the future (like no, none, ...)
It is of course clear that we need a mechanism that does not break
existing translation and requires the
Nico wrote:
* The code removes [...] in the displayed text when it is at the
beginning or the end of the text
Unless this has been changed recently, that is not correct. The
removal is done specifically in those two entries, per case, not by a
general algorithm.
I agree that a
That is correct. But there is a potential problem, Sam:
the two models must be in the same coordinate system. Otherwise, you
will see only one because the other is far away.
So, if you find something strange when you try Bob's suggestion, it
may be this.
Hello Sam
All can be done:
Is there any possibility of viewing both the protein and the ligand in the
same frame,
which will enable me to view the ligand's docking with the protein?
either of these:
frame all;
frame *;
will do that. They are not in the same frame, but you see both. If
So, Bob, is that a simulator of Android running in the PC?
What's its name? I searched for something like that with little success
:) great work! That'll beat iThings aside. Real molecules in the phone!
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Hello Moon
There are a couple of web applications that do that, but it is not an easy task.
Please, let us know in more detail what you need. For example, do you know in
advance
what is the sequence you want highlighted, or is this a generic need that
should work with
any protein?
For
Why not?
If you manage to extract the sequence programmatically, then you must just call
Jmol with
the script that
1. loads the pdb file
2. selects atoms by the sequence
3. highlights the selected set
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Hello, Moon
You can probably achieve that using hoverCallback
http://jmol.sourceforge.net/jslibrary/#jmolSetCallback
For output, you may use echo, or a textbox in the page, or other ways.
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In principle, callbacks work in Javascript, so in a web page.
Windows is not the problem, you can write a webpage and run it
locally in Windows :)
I'm not sure if there is an equivalent for the application.
You can customize the hover text by script, maybe that would be
enough for your needs.
Hey Bob, that's terrific!
Congratulations!
What's the price of the thing over there? Here it still looks like an
expensive toy
:)
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exactly
with 12.3.2
_version = 1203002
gets locked on backbone 1.5
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12.2.3 and 12.3.2 both choke on backbone
simple.htm works fine
12.2.4 and 12.3.4 work fine
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Hello Moon
Can Jmol be embedded into other program?
Oh yes. Please read the website and the wiki
http://jmol.org
The JmolViewer is a development tool kit that can be integrated into other
Java
applications.
http://jmol.sourceforge.net/docs/JmolDevelopersGuide.html
Hi Moon
I'm not a programmer, so I cannot really give you a firm advice.
Being different programming languages, the bets are not good.
But I think I read a post by Bob Hanson, not long ago, about isolation of the
core
functionalties in Jmol (probably related to making the recent Android
Nico, if you want I can revise all links in the website and put any
fixes and commit. Then you can update the site.
·
Dr. Angel Herraez
Dep. Bioquimica y Biologia Molecular, Universidad de Alcala
E-28871 Alcala de Henares (Madrid), Spain
Done and committed.
On 17 Jan 2012 at 20:04, Nicolas Vervelle wrote:
Ok :)
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Thanks for reporting the problem, Alexandru
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Hi,
(JmolApplet 12.2.2)
After having a 'file not found' in Jmol console, I am seeing an error
in my Firefox javascript console that seems to be trying to echo the
Java error.
The original Java error makes sense since the file was not there.
That is not the issue.
Could this be a bug in
Thanks, Bob, that's what I needed to know and I would have expected
so, but certainly my page is not doing anything of the sort -on
purpose at least- and Jmol.js is the standard file.
I will pursue it and share any findings.
You'll have to look on your page or version of Jmol.js. To my
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