Hi Bob
14.2.2_2014.06.29 application, the interface opens in English instead
of Spanish.
The pop-up language shows Spanish ticked, when I click on that the
interface changes to Spanish.
So the switch works, it's just the initial display where the language
is not applied correctly.
I haven't
Precedents, for reference:
29 Jan 2014, 11:55, Bob Hanson wrote:
___JmolVersion=14.1.8_dev_2014.01.29
bug fix: show MENU write MENU load MENU all broken in 12.2
[feature-requests:#213] custom pop-up menus
Status: open
Created: Tue Jan 28, 2014 11:08 AM UTC by Angel Herraez
Last Updated:
Dear Bob,
In 14.1.16 and 14.2.2, issuing a move command works, but any
further moveto or zoom does nothing
load $caffeine;
moveto 1.0 { 916 -393 -75 38.89} 65.75 0.0 0.0 {-0.45 0.19 -0.065}
5.5 {0 0 0} 0 0 0 3 0 0;
move 90 0 0 0 0 0 0 0 5 30; // 90 degrees around X
moveto 1.0 { 916 -393 -75
FYI,
this was broken between 14.1.10 and 14.1.11
In 14.1.16 and 14.2.2, issuing a move command works, but any
further moveto or zoom does nothing
load $caffeine;
moveto 1.0 { 916 -393 -75 38.89} 65.75 0.0 0.0 {-0.45 0.19 -0.065} 5.5 {0 0 0}
0 0 0 3 0 0;
move 90 0 0 0 0 0 0 0 5 30; // 90
Hello Priya
Nothing has changed? That's surprising
I've visited your page and in the source code I can see nothing
related to J(S)mol
Can you please give a better pointer?
--
Want fast and easy access to all the code
Dear Bob,
I am getting this error when running a page in Firefox 30 from local
disk (file:// protocol), in an alert box wehn loading the page:
[Java2Script] Script error: missing ] after element list
../../JSmol/j2s/core/corescript.z.js
[Exception... Access to restricted URI denied
Dear Bob,
After the last update of Jmol, 29th July, I am still having trouble when my
page runs a script with move command and later a moveto or zoomto.
I've prepared a simplified test-demo page at
http://biomodel.uah.es/en/model4/dna/_test_.htm
That's using an older version of Jmol, but the
Bob, are both syntaxes supported?
Jmol.resizeApplet(appletid, w, h)
Jmol.resizeApplet(appletid, [w,h])
I only had the 2nd documented
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Functions#resizeApple
t
--
in 14.3.7_2014.09.08b
chainCaseSensitive
is being ignored and acts as true
That is,
load =1crn
select *:a //0 atoms selected
select *:A // 327 atoms selected
irrespective of the setting of chainCaseSensitive
--
There is also a problem with numeric chain IDs:
load =1LMB;
select *:1; //selects chains 1 and 2
select *:2; // same atoms
select *:3; //selects chains 3 and 4
select *:4; // same atoms
I notice that hover display quotes around the ID, like
[DG]37:2.O3'
so I tried
select *:1
in 14.3.7_2014.09.08b
cartoon
is broken for Calpha-only files
It used to render cartoons, now it just renders trace
load =1LMB
cartoon only // ok for dna, not for protein
--
Want excitement?
Manually upgrade your
sorry, that's not Calpha-only
But the problem is present --now I don't know the reason
--
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce.
Perforce version
9 Sep 2014, 2:58, Robert Hanson wrote:
In addition to that, the chain read from then HELIX record was not
stored the same way, so helixes and sheets were not read for any
chain that was outside the range A - Z.
Partly solved, but with another glitch now present:
in 14.3.7_2014.09.08b
Bob, that sounds fully reasonable to me.
The way I see it, old PDB files used to have just uppercase chain IDs
and in many old scripts we just got used to use lowercase. When some
Upper+Lowercase PDB files started, set chainCaseSensitive appeared so
the user could cater for those and still the
Hi Rolf
This is interesting but not what I can really discuss about, but I'd
contribute one or two hints:
One really nice thing (I've seen it in other tree viewers) would be
the ability for the user to pull a node and have the whole thing
rearrange dynamically. That's a force field and Jmol
It seems that setAppletCss() is not working, tested in JSmol 14.3.10
Case example: the button has red border, but the JSmol object has not:
head
style type=text/css
.grayBox { border:1px solid red; }
/style
/head
body
script type=text/javascript
Jmol.setAppletCss('grayBox');
El 23 Jan 2015 a las 7:02, Robert Hanson escribió:
Who is handling these? Anyone?
jmol-users-boun...@lists.sourceforge.net
I've done it a couple of times, but in others when I logged in, the
problem had already been taken care of (Nico, maybe?)
On the other hand, I suspect I have admin access
I am seeing a problem in using COMPARE() and ROTATE SELECTED with
only recent versions:
My script is of the type
load a.pdb // 10 frames
load append b.pdb // single frame
select protein; trace only; color trace gray;
rotMx = compare({2.1 alpha}, {1.10 alpha});
show rotMx;
select 2.1; color
Hi Rolf
I was about to suggest what Bob is putting forward: if Javascript is faster,
you
might take part of the code out from JmolScript into JavaScript. I believe he
has demo'ed how.
Another idea: I found that in Javascript there is much improvement in loops
when they are decrementing
It seems that the console div is created when either the console command
is executed or the popup menu option is picked.
It is appended after the BODY tag, with this content:
div id=jmolApplet0_console class=jmolConsole style=display: block;
background-color: yellow; width: 600px; height:
Wow, that's very helpful, thank you! So I assume if you can create a
permanent console in Jsmol,
it's possible in Jmol as well.
Java is a different business, the console IS a java window so you cannot fix it
in the page.
Example test: http://biomodel.uah.es/JSmol/test_console.htm?_USE=JAVA
Hi Sam
What you describe is very uncommon.
Please, describe the procedure you have used to load the files.
example:
load files =4KKS =1PD6
Hey! I see now!
The particular 1PD6.pdb is a structure resolved by NMR as so it contains 28
different structures (conformations) -- taht's the reason
Hello Sam, and welcome
(This rather belongs into jmol-users list)
I'm emailing to ask a few questions about JMol. From what I've
found on your emailing archives, it seems like it is possible to load
multiple structures at once, but how exactly would one do that using the
frame
Dear Bob,
http://chemapps.stolaf.edu/jmol/docs/#setcallback
set AnimFrameCallback
says 9 parameters are returned. I only see 8; I think that maybe
isAnimationRunning and animationDirection are merged into one?
14.2.14_2015.06.11
Regards,
Angel
Dear Bob,
I thought you'd like to know that the ligand contacts view, View Pocket in
Jmol in the PDB website seem to be broken. When I click on the link,
nothing happens.
Maybe a consequence of their updates in viewers.
(I've tried to reproduce that nice display manually via the console, and
I am trying to convert the Jmol source code to JSmol using Java2Script.
I've made some changes to it and I want to know how they affect JSmol. I
got the code from here: http://jmol.sourceforge.net/#Obtain%20Jmol
Ah, ok
That's a purely developer-programmer issue, then. It's clear now.
I
Java2Script for it to work, what's the scoop on that?
This is confusing. Do you want to convert Jmol source code?
Or Jmol commands / scripts? These need no conversion, as they work
equally in JSmol.
Please, clarify what your Jmol code is about
·
Dr. Angel Herráez
Biochemistry and Molecular
Dear Bob
I've being working on checkbox groups, to implement the display of partially
selected state --which is a supported feature in html5.
https://sourceforge.net/p/jmol/feature-requests/228/
Can you consider this for inclusion in next release?
I don't know where that should be located in
Yes, it's working through all levels (tested with 3, see
http://biomodel.uah.es/JSmol/test_cbGroup.htm
On 13 Nov 2015 at 16:25, Robert Hanson wrote:
>
> Did you get the sub-group business working?
>
> On Fri, Nov 13, 2015 at 1:46 PM, Angel Herráez < angel.herr...@uah.es> wro
Hello Krishna, and welcome to Jmol community
There are probably several ways you can try for your purposes (although I
am not sure to closely understand your setup). Here are some tips:
1. Do not use zap, as it clears one model before starting to load the next.
Maybe just
load file1.xyz;
Dear developers, in particular Bob and Jonathan,
Over the last weeks I was teaching a course where whe learned to produce
webpages from Jmol Export to Web.
As a consequence, I am starting some revision of the page code generated,
to be more HTML5-compliant and cleaner in terms of tags (e.g.
Ok, Abel
So you are not loading a mol2 file, you are loading data.
Reloading of data might not be possible, or may need a different syntax.
More investigation is needed on this, I cannoy say right now.
What happens if you copy that data into a text file and load it into Jmol?
Bob will know,
Hi Klaus
Go to http://chemapps.stolaf.edu/jmol/docs/ and search for "rotationRadius"
You will see there is "set rotationRadius"
therefore you can try
show rotationRadius
and it works!
Examples of use:
show rotationRadius // rotationRadius = 20.94923
rr = rotationRadius; print rr; //
The documentation under "data" says
http://chemapps.stolaf.edu/jmol/docs/#data
Using load data instead of just data you can load model data with all of the
loading options of the standard LOAD command.
Also, it says that you should probably use model as part of your data label;
this may be the
Hello Abel
We need to narrow the problem
I've just tested with Jmol 14.6.0_2016.05.24, with a pdb file, a mol file and a
mol2 file, and "load" works fine.
e.g.
load =1crn; load "";
load $caffeine; load "";
load
"https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/mol2/csc
load models {0 0 1} filename
is broken in all 14.6.0 releases; it complains the closing brace was not
expected
We are trying to fix a problem in Proteopedia (Jmol 14.4.1) with rendering of
beta strands when the file does not contain SHEET records(note*). I realized
that bug is fixed
Thanks, Bob
As far as I've seen, for whatever reason the EBI PDBe people are doing
changes in the CIF format of those files; in several respects they do not
match their regular CIF files. They remove some fields and others change
names. I talked to them and basically they say that's how it's
We are starting to work on reading mmCIF files from PDBe, for "assemblies".
This means the actual biological unit of the molecule, be it monomer, dimer,
tetramer, etc -- manually checked since there are often several automatically
prepared biological units in PDB
Apparently EBI has been
It seems this previous post (4th April) went unnoticed
> Bob,
>
> This parameter can be shown but not set:
>
> $ print _versionDate
> 14.4.4_2016.03.29 2016-03-29 22:33
> $ show nihResolverFormat
> nihResolverFormat = "http://cactus.nci.nih.gov/chemical/structure/%FILE;
> $ set
Bob,
This parameter can be shown but not set:
$ print _versionDate
14.4.4_2016.03.29 2016-03-29 22:33
$ show nihResolverFormat
nihResolverFormat = "http://cactus.nci.nih.gov/chemical/structure/%FILE;
$ set nihResolverFormat =
"https://cactus.nci.nih.gov/chemical/structure/%FILE;
ERROR en
I just noticed in my local build that Russian (the latest added language) is
not
available in the pop-up menu.
It appears there, though, after I enter this in the console:
set language ru
and it stays in the menu upon more language changes
So I guess there is something that must be changed
Forget that last one -- I found where the language must be added,
src\org\jmol\i18n\Language.java
I am adding Russian since it is over 95% translated
--
Mobile security can be enabling, not merely restricting. Employees
(Just for the record and to finish this thread)
Those changes in the Export to Web interface and the templates it uses for
produced pages were finally committed to the trunk a few days ago.
They are now used in Jmol 14.6.0
> > As a consequence, I am starting some revision of the page code
Hello Klaus
I think that it should be possible to do what you want without using eval(),
which is usually not recommended by javascript gurus.
The variable is indeed an object and not a string, but that is what Jmol
expects.
There may be a problem when the variable has not been defined
Ok, those were my first commits from within Eclipse, so it took me a few trials
and errors. I believe all is well.
That was an update to the Export to Web interface, to better match
descriptions for JSmol.
--
Mobile
Hello Klaus
Yes, the files are now different since JSmol.
It is recommended that you change to the new JSmol Object syntax (see the
Wiki for guidance)
Otherwise, you could possibly still run it the old way. The Java applet files
are inside the "java" folder which is inside the "jsmol.zip"
Bob,
I know you worked on this recently.
I am testing this on "14.6.2_2016.08.28 2016-08-28 07:48"
color gray
color grey
color lightgray
color lightgrey
color darkgray // all ok up to here
color darkgrey // script ERROR: a color or palette name (Jmol, Rasmol) is
required
set measurements 0.25
(any width in angstroms)
is failing in versions below -- it used to work as expected, giving a not s
thick cylinder
14.6.4_2016.10.02
14.6.2_2016.08.28
14.7.0_2016.06.27
14.6.0_2016.06.22 used at Proteopedia
---
El software de antivirus Avast ha analizado este
Dear Bob,
I have noticed two issues with the rendering of the pop-up menu in
JSmol-html5
1. The language submenu is way too long, and may become taller than the
screen, so in some page designs the lower half of the languages may be
unreachable.
2. The names of some languages display
/jmol/jsmol/jsmol/htm
On Sat, Sep 17, 2016 at 10:29 AM, Angel Herráez <angel.herr...@uah.es> wrote:
Ok, thanks
I have later been able to do it from Java applet - so it may be that
On 17 Sep 2016 at 9:53, Robert Hanson wrote:
I don't think write menu was implemented in
Is this a bug?
On https://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
in the console: " write menu ? "
gives this error after requesting the file name:
ERROR en guión: TypeError: er.printStackTrace is not a function
Fine, Bob
The funny thing was that the first string (language name translated to current
name) was correct, the second was wrong (language name in the original
language). If you siwtch to Russian, you can see in the same line one
correct, one wrong.
So I understand this is fixed for next
> The way too long problem is generally solved by dragging the menu higher
on the screen.
I know. But still sometimes it's higher than the screen.
In many pages of mine the JSmol panel is 100% height, locked and cannot
be scrolled down (overflow:none), so it's actually impossible to reach the
Ok, thanks
I have later been able to do it from Java applet - so it may be that
On 17 Sep 2016 at 9:53, Robert Hanson wrote:
I don't think write menu was implemented in JSmol. Will take a look.
--
I like CSS solutions; they are very clean and you do not mess up with the js
code.
> something like "menus that do not contain any menus" --- li with no
> containing ul --- I think
that can be done in jQuery. Can it be done in CSS?
Not actually straightforward, since you cannot apply css to
Hi Jonathan
I've seen this kind of a problem occasionally (my system is configured for
Spanish so the JSmol popup menu opens in Spanish, and has accented
characters), but have not been able to track it down.
I think it may be a bad combination of charsets in the several files involved.
I
> thank you. fixed. Are people still using IDTF?
Yes, hardly anyone, given the amount of information that can be found
online. Still, there is some life -- see [1]
But I am picking again the idea of producing PDFs with 3D models, and IDTF
-> U3D is the only route.
I just found that Power PDF
Dear Bob,
load $aspartate;
write IDTF Asp.idtf
does nothing, reports nothing
Jmol 14.6.4, 2016-10-02 application
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Hi Jeff
That's a little strange. "exit" should do what you wish, at least according to
the documentation (I have no direct experience)
I suggest that you try this:
add
!exit
as the first line of your script files or the first command of your inline
scripts
that are callled from buttons.
Hi Jeff
I've done a little testing.
It seems that the problem is in the "move" commands, that cannot be
interrupted. I found about "set waitForMoveTo" and "moveTo stop", so this
seems to work:
1.
Edit you spt files to change the move commands to equivalent moveTo
commands.
// move 0 0 0 80 0
Hi Jeff
Glad you are finding a solution. The lack of working of "!exit" straight away
is
disturbing.
"move" is considered an obsolete command and that may be the reason
there is no method to interrupt it, but I agree that some things are not easy
to
reproduce with other commands, as you
Hello Klaus
1. Yes, the location of the language files cannot be specified. As far as I
remember, it always looks for them in a 'idioma' folder which is a sibling of
the 'java' folder. I'm not sure what happens when you don't specify the java
folder
2. Some javascript error loading the
On the other hand,
Why http:/_ ? That is not correct
You need either two slashes (and then it must be an absolute server url) or
no http (relative url)
> is a complete unreasonable path. It should be:
> http:/_INCLUDE/JSMOL/idioma/de.po
that is not correct. You need
Dear Bob,
I have noticed that some characters do not display properly in the pop-up
menu, Languages submenu in JSmol-HTML5
Checked in JSmol 14.6.4 and 14.9.1 in two different pages, see snapshot
https://ibb.co/hpdWck
Many foreign characters display well, but not those few in Russian, Chinese
Dear Bob,
We are finding a strange behaviour in JSmol-html5 within Proteopedia:
changing antialiasDisplay does not display any effect until you click on the
JSmol canvas.
Test case: go to
http://proteopedia.org/wiki/index.php/1a2m
open the JSmol console and type
zoom 300
set antialiasDisplay
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