I will look at this, but I certainly have not observed it to date. I assume
you are doing this from an application that has Jmol embedded in it? Are
you sure you are starting a new thread and not using the main execution
thread when executing viewer.scriptWait? This is necessary.
On Tue, 25 Dec
On Tue, 25 Dec 2007 21:20:05 -0500, Golagani, Ravi
[EMAIL PROTECTED] wrote:
Hi,
I'm using the latest release jmol-11.2.14 (applet) in our project. When
an
atom consists PDB Insertion code as '100A' it shows it with some illegal
character in tooltip. I'm passing the correct Insertion code
thank you - please enter as an official request for a bug fix.
Perhaps Egon can find that code in SelectionManager.java and fix it for us.
On Fri, 4 Jan 2008 15:50:11 +, Brian McMahon [EMAIL PROTECTED] wrote:
Hello
If one invokes the Jmol console (at least in 11.4RC1) and clicks the
On Wed, 2 Jan 2008 21:02:59 -0500, Frieda Reichsman [EMAIL PROTECTED]
wrote:
Bob, two part question:
1, Which component files of Jmol will download when a page has an
applet displaying one structure (DNA only), in wireframe only, with
NO buttons or other controls? (Assuming I am using the
looks like a missing semicolon after color selectionHalos none
If you can fix that manually for now, that will make it work.
[[Egon, can you fix this? It's in org/jmol/shapes/Halos.Java
62 public String getShapeState() {
63 return super.getShapeState()
64 + (colixSelection
please enter as a request for a bug fix; in the mean time, please use
color polyhedra opaque :)
On Wed, 2 Jan 2008 19:05:49 +0100, Paul Pillot
[EMAIL PROTECTED] wrote:
Happy new year to all Jmolers !
I think there is something broken in respect with polyhedra
translucency :
polyhedra bonds
Thanks, Rolf. Yes, that's a bug introduced recently. It's the capital
letters.
That's checked in for 11.6.RC9.
On Tue, Aug 19, 2008 at 6:19 AM, Rolf Huehne [EMAIL PROTECTED] wrote:
Hi,
I tested Jmol 11.6.RC8 with our 'JenaLib Jmol Viewer' and noticed the
following problem:
Problem
fixed and, sure, why not...
getProperty pointGroupInfo
print getProperty(pointgroupInfo.principalAxis)
etc.
On Tue, Aug 19, 2008 at 11:17 PM, Dean Johnston [EMAIL PROTECTED]wrote:
Bob,
write pointgroup draw gives the following error (for 11.6.RC8):
Exception in thread QueueThread0
Jeff,
The mistake here is timing. You cannot query an applet while the page is
loading (prior to /body and completion of applet initialization). In some
cases this crashes browsers; in others it just causes an error; in others it
permanently disables the applet communication.
The simple fix is
ever? even if you don't manipulate the model? Please check for Java console
errors.
On Wed, Aug 20, 2008 at 12:29 PM, Thomas Stout [EMAIL PROTECTED]wrote:
It's odd that the question about syncing with pop-up applet windows came up
today just as I noticed the following:
with the applet
: Java
heap space
at org.jmol.g3d.Platform3D.allocateTBuffers(Platform3D.java:89)
I see this behavior on both both WinXP and linux (CentOS) and both a pretty
hefty machines (graphics and RAM-wise)
-Tom
On 8/20/08, Robert Hanson [EMAIL PROTECTED] wrote:
ever? even if you don't
On Wed, Aug 20, 2008 at 11:53 AM, Eric Martz [EMAIL PROTECTED]wrote:
Dear Bob,
In Proteopedia.Org, Jaim Prilusky has implemented a popup button
under each Jmol that opens a new window containing only a Jmol. This
window can be made large and resized at will; resizing has been more
, Robert Hanson [EMAIL PROTECTED] wrote:
fixed and, sure, why not...
getProperty pointGroupInfo
print getProperty(pointgroupInfo.principalAxis)
etc.
On Tue, Aug 19, 2008 at 11:17 PM, Dean Johnston [EMAIL PROTECTED]wrote:
Bob,
write pointgroup draw gives the following error (for 11.6.RC8
thanks -- RC9 is broken for pointgroups. (It can crash jmol when drawing)
On Thu, Aug 21, 2008 at 11:22 AM, Xavier Prat-Resina
[EMAIL PROTECTED]wrote:
Bob,
I finally had time to test the point groups in jmol.
I used a set of structures included in Patchkovskii's code. They are not
real
University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 20, 2008, at 3:43 PM, [EMAIL PROTECTED]:
Message: 4
Date: Wed, 20 Aug 2008 14:42:00 -0500
From: Robert Hanson [EMAIL PROTECTED]
Subject: Re: [Jmol-users] getting info
On Wed, Aug 20, 2008 at 2:22 PM, Robert Hanson [EMAIL PROTECTED] wrote:
There's your answer. Out of memory. How big are these resizes?
height/width? I wonder if a settable maximumWindowSize option might be in
order here.
Bob
On Wed, Aug 20, 2008 at 3:00 PM, Thomas Stout [EMAIL PROTECTED
I guess I don't understand the context here. What is the addJmol command?
Why is it being created as a script tag and not just as
script
addJmol() // whatever that may be
/script
Bob
On Fri, Aug 22, 2008 at 2:22 PM, Matthew Zwier [EMAIL PROTECTED] wrote:
If it's in the HTML page itself,
That's fixed. Thanks. Also, now you can still make double-click measurements
while you have
set picking spin
The double click will stop any current spinning that might be happening.
Bob
On Fri, Aug 22, 2008 at 12:21 PM, rspinney
[EMAIL PROTECTED] wrote:
Set picking SPIN seems to be
Steve,
right -- it's simply a matter of the wiki not finding the path to Jmol.js.
Nico or Angel can help you get that going.
Bob Hanson
On Fri, Aug 22, 2008 at 4:42 PM, Stephen Weppner [EMAIL PROTECTED]wrote:
Hi,
I have installed the JMol Mediawiki extension found at:
I cannot reproduce this problem. Are you sure you have not already defined
mybackground PRIOR to the set fontscaling false command?
set fontscaling only affects echos created after its invocation.
On Mon, Aug 25, 2008 at 5:34 PM, Thomas Stout [EMAIL PROTECTED]wrote:
Interesting.
I have
for the code to
do this, just another pointer in the right direction to move me in the right
direction. Sorry if I'm too much of a bother.
Robert Hanson
Fri, 22 Aug 2008 07:22:24 -0700
oh, yes! You can do all that. Check the Jmol wiki for lots of tips. Commands
include jmolEvaluate (my favorite
;
set echo depth 0;
set echo mybackground 43% 83%;
set echo mybackground image star2.gif;
I am still using the applet of version 11.6RC7 -- perhaps I should download
and test whatever the most current RC version is today.
-Tom
On Tue, Aug 26, 2008 at 8:56 AM, Robert Hanson [EMAIL
thanks for finding that, Angel. It's fixed for 11.6.RC11. Those files should
be available as
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11_5.zip shortly
Bob
On Tue, Aug 26, 2008 at 2:25 PM, Angel Herráez [EMAIL PROTECTED] wrote:
Hello all
I had this script for getting a
It's a bug I need to fix. Don't go back to RC9 -- that's broken for drawing
pointgroups the second time. It's a problem with the caching I added in
RC10. Jmol doesn't recalculate the point group or the draw set if it finds
suitable ones already present. But I forgot to check for that axis number.
be a point group specific thing, because a lower symmetry (C2)
version of my twistane structure works just fine.
BTW, I love the getProperty pointGroupInfo. Thanks Bob!
Dean
On Fri, Aug 22, 2008 at 10:01 AM, Robert Hanson [EMAIL PROTECTED]wrote:
found it -- Nico, let's get RC10 out so Dean can
Right -- name attribute is quite problematical. In some browsers id is
accessible as name, but that's not acceptable. And in some browser
versions the name of an element in a form is under the form name rather than
the document.
Always use id and, as Dean points out, then access it only using
that's what I needed. Fixed. Vertical was off as well.
On Wed, Aug 27, 2008 at 10:56 AM, Angel Herráez [EMAIL PROTECTED]wrote:
On 27 Aug 2008 at 10:57, Dean Johnston wrote:
OK, here is the state for ammonia, with a label of Point Group =
Csub3v/sub at the
bottom left. Without the tags the
echo depth 0;
set echo mybackground 43% 83%;
set echo mybackground image star2.gif;
I am still using the applet of version 11.6RC7 -- perhaps I should download
and test whatever the most current RC version is today.
-Tom
On Tue, Aug 26, 2008 at 8:56 AM, Robert Hanson [EMAIL
I'm working towards my own at this point and I'm afraid looking at yours
will just prevent my learning how to do it myself.
Shame! NEVER say that! The way to learn this is by adapting anything you can
find. That's the great thing about JavaScript. Learn how these code
fragments work by testing
yes, thanks, Paul, that's right. It's an interesting compromise. I had to
abandon the type=file in Jmol Protein Explorer for FireFox3 because of that.
If you can't get the actual path to the file, which I think is actually a
good security feature, you can't later reproduce the state, unless you
. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***
On Aug 27, 2008, at 2:14 PM, Robert Hanson wrote:
I'm working towards my own at this point and I'm afraid looking at yours
will just prevent my learning how to do it myself.
Shame! NEVER
problem.
Dean
On Wed, Aug 27, 2008 at 10:41 AM, Robert Hanson [EMAIL PROTECTED]wrote:
Dean, that fix is checked in -- problem for any case where there is no
principal axis.
On Fri, Aug 22, 2008 at 9:52 PM, Dean Johnston [EMAIL PROTECTED]wrote:
OK, it's working much better, but a few obscure
remove the \ around the load command. It's just:
this.loadString = load ../Jmol/jmol/Models/ + molecule;
On Thu, Aug 28, 2008 at 2:59 PM, Jeff Hansen [EMAIL PROTECTED] wrote:
Thanks for your help Angel. This is getting me very nearly there. To
recap. I am trying to create a web
Steven,
You have the quotes there still. The word branch cannot be in quotes.
Check the documentation. There are several entities atoms might be within,
including
element
chain
group
structure
branch
molecule
model
boundbox
Quotes are used to indicate a sequence, such as RGGGAA, not one of
Jeff, why don't you come over to St. Olaf and I'll show you how this works!
:)
Seriously, hang in there. You are trying to do a lot all at once, and you
will catch on. This is precisely what this list is for. Just keep at it.
jmolScriptWait would not break anything.
jmolScriptWait should only be
Well, I don't know... Please send the file for which this is a problem and
also the state script from
show state
just prior to giving that command. Here's what I see using the application:
load =1crn
select within(branch,{4.N},{4.ca})
326 atoms selected
Are you using the application or the
]
***
On Aug 28, 2008, at 10:47 PM, Robert Hanson wrote:
Jeff, why don't you come over to St. Olaf and I'll show you how this works!
:)
Seriously, hang in there. You are trying to do a lot all at once, and you
will catch on. This is precisely what this list is for. Just keep at it.
jmolScriptWait would
I've gone ahead and added for Jmol 11.6.RC12 the applet param tag
maximumSize. This can be set to a maximum size for which the height and
width are not allowed to exceed when resizing. I think this will be a more
user-friendly option. The way to invoke it would be
jmolInitialize(...)
1. What are the default values and typical values for:
bondTolerance
public final static float DEFAULT_BOND_TOLERANCE = 0.45f;
minBondDistance
//minimum acceptable bonding distance ... from OpenBabel ... mth 2003 05
26
public final static float DEFAULT_MIN_BOND_DISTANCE = 0.4f;
All
I'd like to propose a change to Jmol.js. The change would be an addition.
If the page URL contains JMOLJAR=
then Jmol.js would be instructed to ignore the jmolInitialize() command and
instead use the codebase directory and jar file as defined after that tag.
For example:
Paul, check out this page to see how yours might be different.
http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm
It's using the signed applet and working just fine. Maybe has to be newer
than 11.6.RC8, but I don't think so. It should load files from the PDB using
load = and files
I'm working with them -- they are mostly waiting for 11.6 to be stable. Then
they will go to that.
Bob
On Sat, Aug 30, 2008 at 7:29 AM, Angel Herráez [EMAIL PROTECTED] wrote:
One of the interesting aspects is that I could use
JMOLJAR=
RCSB beta site is using Jmol 11.4. See for example:
http://betastaging.rcsb.org/pdb/static.do?p=explorer/viewers/jmol.jsp?structureId=1O1I
Current version there is 11.4.6, I think.
On Sat, Aug 30, 2008 at 8:08 AM, Robert Hanson [EMAIL PROTECTED] wrote:
I'm working with them
:
Quoting Robert Hanson [EMAIL PROTECTED]:
One of the interesting aspects is that I could use
JMOLJAR=
http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolAppletSigned.jar
for example to go to the PDB website and use MY applet instead of theirs.
Bob,
have you tried that already
Steve, there's probably not much sense in creating a generic bond-equivalent
object like that. But you can do what you say yourself. For example, if a
student is asked to click on a peptide bond, you know what bond it is, so
you can create the link yourself and, like you say, make them transparent
is the bond order; next are the identities of the two atoms and
the bond distance. The last three numbers are the coordinates of the center
of the bond.
That work for you, Steve?
Bob
On Sat, Aug 30, 2008 at 1:11 PM, Robert Hanson [EMAIL PROTECTED] wrote:
Steve, there's probably not much sense
all three are independent:
set atomPicking
set bondPicking
set drawPicking
On Sat, Aug 30, 2008 at 2:49 PM, Angel Herráez [EMAIL PROTECTED] wrote:
On 30 Aug 2008 at 14:20, Robert Hanson wrote:
Jmol 11.6.RC12 now has
set atomPicking [default TRUE]
set bondPicking [default FALSE
Yes, this information comes back as a string in the pickCallback (second
parameter). The third parameter is an atom index:
0+ atom
-2 draw
-3 bond
Also, you can always check the most recent pick information using
var x = jmolEvaluate(_pickInfo)
or
var x = jmolEvaluate(_atomPicked)
You
getProperty can be a very inefficient function. The algorithm is designed to
return the entire property set, then do the selections. So, for example, if
you say:
print getProperty(atomInfo[3])
and there are 3 atoms, then first a vector containing 3 elements is
produced and only after
. On the contrary jmolScriptWaitAsArray() gives me
access denial errors...
Paul
Le 30 août 08 à 15:07, Robert Hanson a écrit :
Paul, check out this page to see how yours might be different.
http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm
It's using the signed applet and working just fine
PROTECTED] wrote:
Quoting Robert Hanson [EMAIL PROTECTED]:
ok. Shucks. That's convincing. OK if it allows same-server jar changes?
Yes, I think so. If the server is compromised then I guess it won't
make much difference anyhow.
Regards,
Rolf
[EMAIL PROTECTED]
***
On Aug 30, 2008, at 11:45 PM, Robert Hanson wrote:
getProperty can be a very inefficient function. The algorithm is designed
to return the entire property set, then do the selections. So, for example,
if you say:
print
OK. Others have comments on this?
Bob
On Mon, Sep 1, 2008 at 9:58 AM, Rolf Huehne [EMAIL PROTECTED] wrote:
Robert Hanson wrote:
One more thought on this: What about an option that allows the
replacement
of the Jar file but first prompts the user for an OK (using JavaScript
prompt
On Wed, Sep 3, 2008 at 12:25 PM, rspinney [EMAIL PROTECTED]
wrote:
I am not sure if these are bugs are not, but I have a couple of problems
with the echo command. First is set echo myecho hidden does not work, set
echo hidden does, i.e. it does not like the echo name being used.
Does seem
I consider the fact that
hide $my*
does not extend to ECHO to be a bug. Jmol 11.6.RC13 will have
hide/display/color/delete $*xxx*
implemented for ECHO
Bob
On Wed, Sep 3, 2008 at 1:14 PM, Robert Hanson [EMAIL PROTECTED] wrote:
On Wed, Sep 3, 2008 at 12:25 PM, rspinney
[EMAIL
It's saying LiveConnect is not working.
On Thu, Sep 4, 2008 at 2:30 PM, Angel Herráez [EMAIL PROTECTED] wrote:
(Well, this reply to Henry's posts has become long, so I'm splitting it
into this Chrome-
related part and another Java 6u10 post)
So I've just installed the new Java 6u10RC
fascinating. So one would simply need to write a U3D file format exporter.
Very good project for someone. But of course, one would lose much of the
richness of the Jmol experience. Still
On Thu, Sep 4, 2008 at 4:58 PM, Wayne Decatur [EMAIL PROTECTED] wrote:
Thought people might be
definitely needs fixing. (1) antialiasdisplay is doubling the image size.
(2) vertical centering is not quite right, I think.
Bob
On Fri, Sep 5, 2008 at 4:25 PM, Eric Martz [EMAIL PROTECTED]wrote:
Hi, Bob,
This does not have to work in 11.6 (final release).
On April 13, 2007, you
set historylevel 2
works fine for me. It should work as you expected.
But history was recording full scripts, not individual commands, so commands
were out of order. This might have thrown you off. That's corrected now.
On Sat, Sep 6, 2008 at 9:12 AM, Eric Martz [EMAIL PROTECTED]wrote:
It
better to fix that.
On Fri, Sep 5, 2008 at 8:18 PM, Eric Martz [EMAIL PROTECTED]wrote:
It appears to me that the javascript command of Jmol does not work in
Safari on Mac OS X.
Examples, typed into the Jmol console:
javascript alert(hi)
or
javascript alert(document.location.href)
These
sorry - missed some of those messages. OK, I'll assume the javascript
command is working ok. As for pause -- that would be a threading issue. But
pause is working fine for me on Mac OS-X.
Bob
On Sat, Sep 6, 2008 at 10:00 AM, Robert Hanson [EMAIL PROTECTED] wrote:
better to fix that.
On Fri
yes, that's a far better solution anyway. The javascript command cannot be
used with the signed applet in any command that also accesses files --
script, load, echo IMAGE. I had to do something like that in Jmol Protein
Explorer as well. You have to be very careful with more complex scripts that
Eric,
That script is way too complex for me to reproduce here, but I did fix the
echo alignment. There were a couple of bugs there, particularly with the
y-offset of centered echos. All should be fixed. I'll see if we can get RC13
out this weekend so you can check it.
Anything else you are
Dear Avenha,
there is absolutely nothing special about cgi output. Hard to say what you
mean by a Jmol java script inside an HTML document. pasted the code to
what? Can you send an example or point us to a page? The main thing is to
have Jmol.js in the right place and have Jar and model files
I don't think you can put that many bytes on a URL line. Better would be to
put the base64 data into a textarea in a form and submit it using
method=post. Even that might have some limitations.
Bob
On Sat, Sep 6, 2008 at 12:19 PM, [EMAIL PROTECTED] wrote:
Hi Bob,
Aha, jmolScriptwait ?
Eric,
No, it just means they are related. That's all.
Nico has released 11.6.RC13, so please check out my bug fixes.
Thanks, Nico!
Bob
On Sat, Sep 6, 2008 at 11:42 AM, Eric Martz [EMAIL PROTECTED]wrote:
In the documentation, the sections on echo and set echo say See
also: hover. At the
On Sun, Sep 7, 2008 at 9:48 AM, Steven R. Spilatro [EMAIL PROTECTED]wrote:
Could the issue be the size of the jmol-derived image?
Yes, I'm pretty sure that's it. The way to test, of course, is to use the
same base64 info from Jmol in an img data: - aware browser. There's a link
under the
then for that I'm not aware of any threading issues. But in general, be
careful that you are not
cycling one thread around and around
JavaScript--Jmol--JavaScript--Jmol--... That could be a potential
problem. It's good to do some setTimeout() calls just to get a new thread
periodically. Otherwise
works for me -- once I figured out I needed to click a radio button. A
default there would be nice.
Most impressive is that by using a base tag and my own signed applet I can
even make it work in MSIE from a version saved to my hard drive.
Good job!
Bob
On Tue, Sep 9, 2008 at 1:34 PM, Steven
Well, if you want, give it a try. You will have to use the latest version of
Jmol -- http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolApplet.jar
Just issue
var x = jmolGetPropertyAsJavaObject(image)
That AsJavaObject ensures that the image created is returned as a byte
array -- the actual
Any chance these are pages that involve more than one applet? In any case,
it's some sort of caching problem with that browser version.
You might get around it by adding a random search to the URL:
test/advanced/ReO3.cif?23023789234
where that number changes each time so that it forces an
http://www.umass.edu/molvis/bme3d/materials/jmoltuts/antibody/contents/contents.htm
Jmol Version 11.3.13 2007-08-28 16:07
really?
Bob
On Mon, Sep 8, 2008 at 10:15 PM, Eric Martz [EMAIL PROTECTED]wrote:
At long last, I have completed a version of the Jmol
Tutorial-Authoring Template (JTAT)
no. not that I know of. Only PDB and CIF support for that. Is there some
sort of MOL2 designation that would suggest otherwise?
On Wed, Sep 10, 2008 at 8:22 AM, Reichsman Frieda [EMAIL PROTECTED] wrote:
Hi Bob et al.,
If a mol2 file is correctly formated, should Jmol be able to recognize
We could set up the mol2 reader to do this. BUT I have to be convinced first
that it's a real standard. What programs write these? Is it just totally
arbitrary what these IDs are? Are the names standard? Try some more unusual
structures, like DNA, RNA, nonstandard amino acids, 1BLU with its FeS4
On Wed, Sep 10, 2008 at 9:33 AM, Steven R. Spilatro
[EMAIL PROTECTED]wrote:
Thanks to everyone for the feedback on the 'Placing Jmol image in
same web page' which I've updated.
Soon Nico will be releasing 11.6.RC14. I think this will be one of our last
releases prior to Jmol 1.6.0.
Something I'm very interested in people trying out is the signed applet. You
can do that at http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm
The cool thing there is that the
[still catching on to Google Mail...]
Soon Nico will be releasing 11.6.RC14. I think this will be one of our last
releases prior to Jmol 1.6.0.
Something I'm very interested in people trying out is the signed applet. You
can do that at http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm
There's help available for the command line, but to see it on a Windows
machine you have to use java -jar jmol.jar -h not just jmol.jar -h
java -jar jmol.jar -h
usage: Jmol
-o,--noconsole no console -- all output to sysout
-q,--quality JPG image quality (1-100;
using
java -jar jmol.jar -g600x600
and you should be good to go.
Bob
On Fri, Sep 12, 2008 at 3:29 PM, Reichsman Frieda [EMAIL PROTECTED] wrote:
On Sep 12, 2008, at 4:12 PM, Robert Hanson wrote:
There's help available for the command line, but to see it on a Windows
machine you have to use
We are almost there! I think I made some work for the translators, but in
general we have an amazing signed applet. Here's the scoop:
Basically the signed applet and the application now allow you to script
user-prompted file input and saving. All you do is use a question mark in
the script:
.
If someone knows how to coerce Java on the Mac to display a file name entry
box, let me know. Othewise I'll have to put up something different for
web-based file entry. I suppose it could be added as a separate text box.
Bob
On Tue, Sep 16, 2008 at 12:42 AM, Robert Hanson [EMAIL PROTECTED] wrote
didn't
add that possibility to the menu.
On Mon, Sep 15, 2008 at 4:26 PM, Robert Hanson [EMAIL PROTECTED] wrote:
OK, I'll check out Mac OS tonight. Not surprised, really.
http://chemapps.stolaf.edu/Users/paul/Documents/Bob
On Mon, Sep 15, 2008 at 3:46 PM, Paul Pillot
[EMAIL
: no more command can be issued...
Paul
Le 16 sept. 08 à 07:51, Robert Hanson a écrit :
Oh, I see now that Java on the Mac doesn't allow entry of filenames by
keyboard typing in file-open dialog boxes. That's unfortunate.
It boggles my mind why Apple hasn't caught on to the fact that maybe
11.4.6, MacOS 10.4.11
Jonathan
On Sep 16, 2008, at 2:37 AM, [EMAIL PROTECTED]
wrote:
Message: 1
Date: Tue, 16 Sep 2008 00:51:03 -0500
From: Robert Hanson [EMAIL PROTECTED]
Subject: Re: [Jmol-users] big step for Jmol 11.6
To: jmol-users@lists.sourceforge.net
Message-ID
On Tue, Sep 16, 2008 at 7:30 AM, Rolf Huehne [EMAIL PROTECTED] wrote:
There is usually no drastic quality difference. It depends of course of
the specific rendering and larger images might also be more problematic.
If file size matters in my experience the quality of GIF images of PDB
Jmol has some very odd bonding radii for unusual anions. Note the numbers:
(8 4) + (-2 + 4), 1320, // O-2
(8 4) + (-1 + 4), 1760, // O-1 // WAY too large?
(14 4) + (-4 + 4), 2710, // Si-4
(14 4) + (-1 + 4), 3840, // Si-1 // same problem here?
(34 4) + (-2 + 4), 1910,
Thanks, I'll take a look at that, but more important things to do now.
On Wed, Sep 17, 2008 at 5:01 AM, Rolf Huehne [EMAIL PROTECTED] wrote:
Robert Hanson wrote:
On Tue, Sep 16, 2008 at 7:30 AM, Rolf Huehne [EMAIL PROTECTED]
wrote:
There is usually no drastic quality difference
good news -- Jmol is working perfectly, including liveConnect, with a recent
fix to Chrome.
Info on this fix and relevant Chrome release:
http://code.google.com/p/chromium/issues/detail?id=580#c30
Bob
On Thu, Sep 4, 2008 at 4:24 PM, Robert Hanson [EMAIL PROTECTED] wrote:
It's saying
, 2008, at 1:00 PM, Robert Hanson wrote:
If that's all you want to do, try this:
load .pdb
set propertydatafield 9
x = load(.mol2)
data property_partialcharge @x
color property_partialcharge
On Sat, Sep 13, 2008 at 8:22 AM, Reichsman Frieda [EMAIL PROTECTED]wrote:
That sounds
?JMOLJAR=./JmolApplet.jar
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?JMOLJAR=./JmolAppletSigned.jar
Bob
On Mon, Sep 1, 2008 at 10:03 AM, Robert Hanson [EMAIL PROTECTED] wrote:
OK. Others have comments on this?
Bob
On Mon, Sep 1, 2008 at 9:58 AM, Rolf Huehne [EMAIL PROTECTED
From the documentation:
*[radius option] Addition of the keyword radius followed by a distance in
angstroms allows definition of the radius of a modified or newly created
bond. If the modify/create option is absent, then modify is assumed; if
the bond type is absent, then bonds of any type are
That's a bug. Fixed for the next version. Workaround is to open the console
and type
write image ?.jpg
Bob
On Sun, Sep 21, 2008 at 7:36 AM, Volker Blum [EMAIL PROTECTED] wrote:
Hi again,
- The Export - image menu as well as the Save current view as an image
button do not function in the
I certainly see your point. Once defaults are in, though, that's pretty much
a done deal.
The idea in this case was that this is the only mechanism for changing the
radii of specific bonds that already exist. So it is conservative -- with
modify as the default you can always undo it; with create
, Robert Hanson wrote:
The way to get partial charge data into .pdb files is to put it in
the temperature field. You can do that with:
{*}.temperature = {*}.partialcharge.all
Which will work on the revised Jmol that I haven't uploaded yet.
Which suggests to me that you might
Sorry, I broke the menu/toolbar buttons for writing images in Jmol
11.6.RC15. The workaround is to open the console and type
write image ?.jpg
This will open up the dialog box.
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If
Final testing appreciated for Jmol 11.6. Anything you can do to try to break
it would be great.
One bug I know about seems to be that the applet stalls if a file load error
occurs. I'm onto that one.
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
(That's the SIGNED applet...)
On Mon, Sep 22, 2008 at 6:14 PM, Robert Hanson [EMAIL PROTECTED] wrote:
One bug I know about seems to be that the applet stalls if a file load
error occurs. I'm onto that one.
Bob
Nice. You can save yourself a little trouble with:
var title = jmolEvaluate('getProperty(fileHeader).split().find(TITLE)')
Also, realize that this goes back and retrieves the file again from its
source. If you know you want to use the file header this way, it's more
efficient to use
set
Dean,
Fun! Yes,
write VAR
is a great way to go. Signed applet or Jmol application will do that.
Bob
On Tue, Sep 23, 2008 at 12:48 PM, Dean Johnston [EMAIL PROTECTED]wrote:
Dear All,
I've been playing around with some of the molecular math features of
Jmol - it's truly amazing how
. However, if I run the un-signed
Applet, it is still reporting version 11.6.RC14 -- is this known and/or
intentional?
Cheers,
Tom
On Mon, Sep 22, 2008 at 4:14 PM, Robert Hanson [EMAIL PROTECTED] wrote:
Final testing appreciated for Jmol 11.6. Anything you can do to try to
break it would be great
1 - 100 of 5320 matches
Mail list logo
