Actually, hold that. Not sure of this result, let me do more testing first. May
be a day or two.
> On Feb 3, 2016, at 10:46 PM, Frieda Reichsman wrote:
>
> Hi Bob,
>
> I tried getting just the negative difference map using
>
> isosurface id ~m00 rmsd -2.5 within 2.5
ber indicates that only the positive part of the surface is desired.
> (See also RMSD, below.)
>
> On Tue, Feb 2, 2016 at 4:45 PM, Frieda Reichsman <mailto:frieda...@mac.com>> wrote:
> Hi Bob,
>
> Is it possible to obtain a difference density map (isosurface) at a differe
Thanks Otis and Angel, I’ll check out both of these options.
Frieda
> On Feb 1, 2016, at 2:16 PM, Otis Rothenberger wrote:
>
> Frieda,
>
> The drag motion that you want may be too complex for this suggestion, but
> I’ll put it out there anyway. It’s a variation of Angel’s non-key-modifier
>
possible to make a map that is negative only?
Thanks,
Frieda
//
Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
USA
sing the mouse button first, then the Ctrl Shift keys, then drag, but this
produces only rotation.
Anyone know how to get this to work on Mac?
Frieda
//////////
Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.mole
Never mind, it’s working now!
Thanks!
> On Jan 30, 2016, at 9:51 AM, Frieda Reichsman wrote:
>
> Sorry, what I am saying is, this command had no effect on the surface display:
>
> isosurface MINSET 10 id ~m40 rmsd 2.0 sign red [x00dd00] within 2.5 {ret}
> insideout
id. The
> RESOLUTION option is only for isosurfaces that are generated de novo by Jmol
> -- vdw, sasurface, molecular, solvent.
>
> Bob
>
>
> On Thu, Jan 28, 2016 at 8:39 PM, Frieda Reichsman <mailto:frieda...@mac.com>> wrote:
> Hi Bob,
>
> Using the
Sorry, what I am saying is, this command had no effect on the surface display:
isosurface MINSET 10 id ~m40 rmsd 2.0 sign red [x00dd00] within 2.5 {ret}
insideout "250u-2m-0.40.ccp4”;
> On Jan 29, 2016, at 12:51 AM, Robert Hanson wrote:
>
> Yes. I just used this:
>
> isosurface minset 1000 "
lution 5.0” in a variety
of different locations within the command, to no effect.
Also - will red become the negative rmsd in the way I’ve set it up? Hard to
tell from the documentation.
Thanks,
Frieda
//////
Frieda Reichsman, PhD
Molecules in Motion
Interactive
rieda
//////
Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
USA
00 +1 413-320-7449
//
--
Site24x7 APM Insight
t numerous
scripts from 10 years ago are still robust. And thank you for your tireless
work on J and JSmol!
All the best,
Frieda
//////
Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmoti
Transparent png now displays correctly (without a black background) thank you!
If the png has a black background, the background remains. So I take it J/Smol
is no longer making first pixel’s color transparent - do I have that right?
Also, the other bug remains in this version (jmol-14.2.14_201
In fact the pngs are not displaying either in this new version. The old version
I was using is 14.3.13_2015.03.16.
> On Jun 10, 2015, at 5:18 PM, Frieda Reichsman <mailto:frieda...@mac.com>> wrote:
>
> Hi Bob,
>
> In this version, the jpg images I was using for the e
Hi Bob,
In this version, the jpg images I was using for the echo images are no longer
displayed. I haven’t checked png fixes yet-- thought you’d want to know about
the jpgs in any case.
Frieda
> On Jun 10, 2015, at 8:11 AM, Robert Hanson wrote:
>
> yes, sorry -- I just realized that it was
Oh - I see now that you said that the applet worked with depth 0, not
JSmol/HTML5. Sorry for the confusion; I have now confirmed your confirmation
that “set echo depth 0" does not address the black background problem in JSmol.
;-)
> On Jun 9, 2015, at 2:21 PM, Frieda Reichsma
Angel, thanks for your response! And for confirming these reports. I hope you
are well.
Unfortunately, the trick you suggest below (setting the echo depth to zero)
does not clear the black background for me - not sure why it would work in one
circumstance (yours :) and not another.
> On Jun
ackground color is white).
Thanks,
Frieda
///////
Frieda Reichsman
Molecules in Motion
Interactive Molecular Structures
http://www.molecu
Thanks Bob, much appreciated.
Angel - thanks also for your suggestion. It had been a while since I needed to
color labels explicitly, and I couldn't recall the command correctly - so I
went back to the Jmol interactive script documentation and found this html tag
method. I couldn’t find the more
attaching a png that can be dropped into Jmol to show the offset issue.
Note that the Cl atom’s label is well to the left of the atom. The label
behaved correctly until the offset 0 0 command was issued.
Jmol version: jmol-14.2.13_2015.03.13
Frieda
////
Forgot to say, I did click the ‘show’ link, and I am in Chrome, Version
35.0.1916.114.
On May 27, 2014, at 5:07 PM, Frieda Reichsman wrote:
> Clicked several times. Saw the single carbon atom. Selected all text. Here’s
> the file.
> Frieda
>
>
>
> On May 27, 2014, at 5
Clicked several times. Saw the single carbon atom. Selected all text. Here’s the file.Frieda
JSmol is an HTML5/Java-switchable version of Jmol. For a zip file containing
all the files in this directory, see
http://chemapps.stolaf.edu/jmol/zip/Jmol.zip. This page demonstrates Jmol using
HTML5, Ja
t;anim frame []
>
> to do that instead..
>
>
>
>
> On Sun, May 18, 2014 at 5:17 PM, Frieda Reichsman wrote:
> Sorry, I’m not getting this. What I’m going for is that all frames of the
> animation should be visible. There should be a delay such that frame 12 is
> shown for 2
shown…
animation frame [12]
frame *
frame delay 2.0
Thanks,
Frieda
On May 18, 2014, at 6:08 PM, Frieda Reichsman wrote:
> Aha, OK, makes sense.
>
> So if I want to pause only at frame 12,
> animation frame [12]
>
> Why do you then say,
> frame *
>
> Is that necess
lay) as visible
>
>
> On Sun, May 18, 2014 at 4:53 PM, Frieda Reichsman wrote:
>
> On May 18, 2014, at 5:52 PM, Robert Hanson wrote:
>
>> Set the desired set of frames for which you want to set the day as visible.
>
> I’m not following that sentence. Must be a ty
l delay:
>
> frame delay 2.0
>
> then run your animation.
>
> Sorry, somehow that did not get documented.
>
> Bob
>
>
>
>
>
> On Fri, May 16, 2014 at 5:26 PM, Frieda Reichsman wrote:
> Hi all,
>
> I am using a series of models as an anima
Thanks, Otis and Angel.
Angel, you have hit the nail on the head with respect to my current needs,
thanks. I will try it today. I had gotten confused by this, in the scripting
doc:
ID “xxx” | … the optional ID keyword introduces an echo ID that is in quotes...
and somehow in my sleed-deprived
Hi Bob et al.,
I would like an echo to appear at the top of the frame during frames 1-10 of an
animation, then a different echo to appear in the same spot for frames 15-25,
and a third for frames 30-35. I’ve been looking at 'set echo' in the script
doc, where I see:
> Echo text can be associate
animation repeats (loops) at one
or two different specific frames.
I can think of some workarounds to make this happen, but I am wondering if
there is a more direct ‘animi’ command that would work here.
Thanks,
Frieda
///////
Frieda Reichsman
Molecules
alues >= 1000 are relative to original point. So you
>> might want
>>
>> Set echo myecho @1
>>
>> Set echo myecho depth 1020
>>
>> 20% of depth in front of atom 1
>>
>> Will get uploaded tomorrow.
>>
>> Sent from my stu
A little more investigation paid off - I think this is it:
set allowMoveAtoms FALSE
Set this parameter TRUE to allow the moving of selected atoms (not just whole
molecules) using ALT-LEFT drag and ALT-SHIFT-LEFT drag.
On May 1, 2014, at 8:12 AM, Frieda Reichsman wrote:
> Hi all,
>
is there another
way to grab the coordinates?
Thanks,
Frieda
///
Frieda Reichsman
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
On Apr 21, 2014, at 6:11 PM, Robert Hanson wrote:
> write @{'anim01/1_anim' + format("%02d",i) + '.png;’}
>
>
> http://chemapps.stolaf.edu/jmol/docs/?ver=14.0&search=format#functionsx=fyfunctions
>
> about a page down in that list
>
Many thanks.
Frieda
On Apr 21, 2014, at 4:05 PM, Brenton Horne wrote:
> Oh and is it possible to hide everything (like the haem molecules, the
> solvents, etc.) except the protein and the ligand? Like atm I'm working on
> COX and NSAIDs binding, is it possible for me to get it such that I can see
> just the prot
thers think.
Frieda
>
> Thanks for your time,
> Brenton
>
>
>
> On Tue, Apr 22, 2014 at 5:50 AM, Frieda Reichsman wrote:
> On Apr 21, 2014, at 3:44 PM, Brenton Horne wrote:
>
>> Hi,
>>
>> I don't know where else to ask this question, but I
On Apr 21, 2014, at 3:44 PM, Brenton Horne wrote:
> Hi,
>
> I don't know where else to ask this question, but I really want to know how I
> can have the macromolecule displayed as ribbons only but the ligand(s) being
> displayed in ball-and-stick format with their implicit hydrogens also
> di
read, e.g.,
write @{'anim01/1_anim' + format("%02d",i) + '.png;’}
Could you add that and/or enlighten me?
Thanks,
Frieda
///////
Frieda Reichsman
Molecules in Motion
Interactive Molecular Structur
On Apr 21, 2014, at 1:14 PM, Robert Hanson wrote:
> I don't see that exact compiler error when I run this in 14.0.13. What I see
> is an execution error:
>
> script ERROR: bad argument count
> line 1 command 1 of function testwrite:
> script "rotate x 1; write file PNG anim01/1_a
+ i + "%; delay 1; refresh;"
> }
> script inline @x
> set hermitelevel 4
> delay 0.1
> }
>
> Bob
>
>
>
> On Mon, Apr 21, 2014 at 9:42 AM, Frieda Reichsman wrote:
> Hi Bob,
>
> The following works for “growing” spacefill w
tells me:
script compiler ERROR: command expected
>>>> for(var i=1 <<<<
$
Sorry to ask more than one thing at a time, but since they both involve for
loops I thought they might be related.
On Apr 21, 2014, at 10:46 AM, Frieda Reichsman wrote:
> Oh
Oh yeah— I’m using Jmol 14.0.13.
On Apr 21, 2014, at 10:42 AM, Frieda Reichsman wrote:
> Hi Bob,
>
> The following works for “growing” spacefill when I use the signed applet, but
> not when I use JSMol:
>
> function off2cpk
> delay 0.1
> set hermiteLevel 0
>
>
televel 4
delay 0.1
end function
Do I need to be doing something differently here?
Frieda
///////
Frieda Reichsman
Molecules in Motion
Interactive Molecular Structures
http://ww
have stopped developing with
> Jmol.js, and the JSmol "JavaScript Object" option is much better, even for
> Java, just in terms of how it fits into web pages and how you put together
> applets on the page. Not that you can't keep using Jmol.js
>
> Bob
>
>
Thanks Angel, I had cleared browser cache and updated Java as well as
restarting my machine. I had no idea that the Java cache was resistant to all
of that... in fact, clearing the Java cache and browser cache again were
necessary, and finally I can see my page in action. Whew!
On Jun 20, 2013
there.
>
>
> On Tue, Jun 18, 2013 at 6:22 AM, Frieda Reichsman wrote:
> In Jmol 13.1.16_a, "set cartoonladder true/false" is not recognized. Bug?
>
>
> On Jun 17, 2013, at 10:00 AM, Robert Hanson wrote:
>
>> The only change in Jmol.js since 2011 wa
t;
> On Mon, Jun 17, 2013 at 8:28 AM, Frieda Reichsman wrote:
> OK, thanks Bob.
>
> On Jun 17, 2013, at 9:15 AM, Robert Hanson wrote:
>
>> Oh, OK. I see that Jmol.js wasn't going into the zip file. See
>> http://chemapps.stolaf.edu/jmol/Jmol.js
>>
>>
OK, thanks Bob.
On Jun 17, 2013, at 9:15 AM, Robert Hanson wrote:
> Oh, OK. I see that Jmol.js wasn't going into the zip file. See
> http://chemapps.stolaf.edu/jmol/Jmol.js
>
>
>
>
> On Sun, Jun 16, 2013 at 9:58 PM, Frieda Reichsman wrote:
> I'm not tryi
You want
>
> http://chemapps.stolaf.edu/jmol/jsmol.zip
>
>
>
>
> On Sun, Jun 16, 2013 at 7:37 PM, Frieda Reichsman wrote:
> I'd be happy to try this out and report back, but neither of those files are
> included in the downloaded folders, either. Where does one ge
; complicated pages. Read the top comment in Jmol2.js.
>
>
> Bob
>
>
>
>
> On Sun, Jun 16, 2013 at 5:14 PM, Frieda Reichsman wrote:
> Thanks Bob, I have downloaded 13.1.15, and 13.1.16_a, but I do not see the
> Jmol.js file in these releases. Where do I find the Jmol
3.0. Sorry for not
> making that clear.
>
> Also, note that there are already some bug fixes for PyMOL PSE file reading
> particularly. See http://chemapps.stolaf.edu/jmol/Jmol-13.zip for the latest.
>
>
> On Sun, Jun 9, 2013 at 2:31 PM, Frieda Reichsman wrote:
>
&g
On Apr 29, 2013, at 2:15 PM, Robert Hanson wrote:
>
> new feature: set cartoonLadder -- default TRUE (standard Jmol rendering of
> nucleic acids), but when FALSE no bases, just "ladders", like PyMOL
Hi Bob,
I'm using the Jmol application, version 13.0.16, and finding that cartoonLadder
is
This is just so lovely, Bob. Truly amazing.
For me, the command line will not work at present. I get an "Error connecting
to server" alert for the chemapps.stolaf.edu.
Nonetheless, kudos for this great work!
Frieda
On Oct 25, 2012, at 5:45 PM, Robert Hanson wrote:
>
>
> On Wed, Oct 24, 2
Just now thought to try "labels hide" and "labels display" which works very
nicely for my purposes.
So no need to solve except for documentation purposes.
On Jul 8, 2012, at 11:12 AM, Frieda Reichsman wrote:
> Hi Bob et al.,
>
> From the documentation,
>
eries of commands
then go to the command line and type
label toggle (atomno=616)
All the atoms of the structure get labeled "toggle (atomno=616)".
Frieda
//////
Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.molecul
Congratulations, Bob! what a wonderful addition!
Frieda
On May 7, 2012, at 6:52 PM, Robert Hanson wrote:
> Jmol 12.3.24 will calculate charges using the MMFF94 model. Thus, you will be
> able to do this:
>
> load caffeine.xyz
> calculate partialcharge
> isosurface vdw map mep
>
> It was an int
On Oct 5, 2011, at 7:57 AM, Frieda Reichsman wrote:
> is likely to work in most any context where this security error occurs.
After sending this I realized that the message no longer contained the original
error report so that the "this error" above may be quite unclear. The erro
he two sites that have my most extensive work
are unavailable.
Thanks,
Frieda
On Sep 16, 2011, at 7:10 AM, Frieda Reichsman wrote:
> Great news that this works.
>
> Bob, it seems to me that the useCommandThread mechanism for setting up
> threads somehow avoids the need for Java
Great news that this works.
Bob, it seems to me that the useCommandThread mechanism for setting up threads
somehow avoids the need for Java to do a reverse DNS lookup, which is the
process that triggers the error. Is that right?
Frieda
On Sep 16, 2011, at 12:52 AM, Paul Pillot wrote:
> We a
1.6.0_27
also breaks with this error, not very surprisingly.
Frieda
//////////
Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.
host name somehow sees
> the server call as to another host which is not allowed for the unsigned
> applet. Angel, do you remember something about that? Really all these pages
> should be using the signed applet, because users should have the ability to
> save files.
>
> Bob
>
> Editing and ensure content is compliant with Accessibility Checking.
> http://p.sf.net/sfu/ephox-dev2dev___
> Jmol-users mail
Hi Reinhold,
Select all, then drag and drop into a text document works for me.
Frieda
On Jun 9, 2011, at 6:11 AM, Reinhold Störmann wrote:
> Having 3 different molecules in one JMol window, and after arranging
> them interactively to give the best representation of what I want to
> show, I stum
Yes, now 12.1.30 is available.
Thanks,
Frieda
On Feb 2, 2011, at 7:52 AM, Robert Hanson wrote:
Hmm, that does appear to be the case. Well, at least the files are
there and updating is possible.
2011/2/2 Angel Herráez
New downloads are available, but I still cannot browse the SVN
Guess I'm
Hi Nico,
Still no ability to get the files onto Sourceforge?
Frieda
On Jan 27, 2011, at 2:44 PM, Nicolas Vervelle wrote:
On Thu, Jan 27, 2011 at 8:30 PM, Egon Willighagen > wrote:
Hi Nico,
On Thu, Jan 27, 2011 at 8:23 PM, Nicolas Vervelle
wrote:
> Since yesterday, I don't manage to ma
ould show up at SourceForge soon.
Bob
On Wed, Jan 26, 2011 at 12:19 AM, Frieda Reichsman
wrote:
Hi All,
I am seeing some strange behaviors with animating a 10-model pdb file
when I turn on spin. At best, very jerky, then stops; at worst,
strange distortion of molecule. I see that there was an iss
Wow, that is scary... you did mean 12.0.29, in fact, that's what your
email said.
Sigh. Long day, sorry.
Frieda
On Jan 26, 2011, at 6:47 PM, Frieda Reichsman wrote:
Hi Bob,
1. Thanks so much for your ever-fast response!
2. Did you by any chance mean 12.0.29? It looks like that was
if what I did fixes
your particular problem. I'm pretty sure it will.
So that should show up at SourceForge soon.
Bob
On Wed, Jan 26, 2011 at 12:19 AM, Frieda Reichsman
wrote:
Hi All,
I am seeing some strange behaviors with animating a 10-model pdb file
when I turn on spin. At b
Thanks Bob, sent this to you off-list - let me know if you need something else.
Frieda
On Jan 26, 2011, at 10:55 AM, Robert Hanson wrote:
> Please use
>
> write "tobob.jmol"
>
> and send me that file.
>
>
> On Wed, Jan 26, 2011 at 12:19 AM, Frieda Reichsman
ideas what is going on here?
Frieda
On Jan 26, 2011, at 1:45 AM, Frieda Reichsman wrote:
> Seems that reducing the hermite level to zero improves this
> considerably, which makes sense. However it is still not a smooth
> animation when spinning, as it is for example here:
> http://pro
:19 AM, Frieda Reichsman wrote:
> Hi All,
>
> I am seeing some strange behaviors with animating a 10-model pdb file
> when I turn on spin. At best, very jerky, then stops; at worst,
> strange distortion of molecule. I see that there was an issue with
> this in 2009 but it was f
this. It works fine in Proteopedia; they are using
11.8.24.
I am seeing this issue in 12.0.27 and 12.0.RC7 on Mac OSX 10.6 in
Safari.
Frieda
-
Frieda Reichsman, PhD
Senior Research Scientist
The Concord Consortium
http://concord.org
25 Love Lane
Concord, MA 01742
Office: 978-405-3228
I have selected the correct set of
atoms prior to applying the surface. This is different from the
previous bug - and worse, I'm afraid. I'll send the files to you
offline.
Frieda
-
Frieda Reichsman, PhD
Senior Research Scientist
The Concord Consortium
http://concord.org
l
generally run at much higher default resolution.
Bob
On Sun, Aug 29, 2010 at 12:46 AM, Frieda Reichsman
wrote:
Hi,
Does the display of an isosurface (the area it covers) vary
depending on what is selected at the time you call the jvxl file? I
don't recall this, but it is true i
d/finalsurface.jvxl" map property_x color translucent -1
colorscheme "user";
if I say "select protein" before it, the surface is truncated in several places
if I say "select :b" the surface is fully intact. Let me know if you want the
files...
Frida
>
>
Hi,
Does the display of an isosurface (the area it covers) vary depending
on what is selected at the time you call the jvxl file? I don't recall
this, but it is true in 12.0.8 and 12.0.10. I expect the surface in a
jvxl file to be the same surface all the time... but perhaps somehow I
hav
Hi Otis,
I'm on a MacBook Pro, 10.6.4, Safari 5.0.1.
On Aug 25, 2010, at 1:21 AM, Otis Rothenberger wrote:
>
> 1) Load (could be a slow load)
> http://chemagic.com/web_molecules/script_page_large.aspx
Actually quite fast - seconds.
> 2) Click The Molecule Editor link.
> 3) In the command field
Yep, that's it! Thanks.
Frieda
On Aug 15, 2010, at 6:53 PM, Robert Hanson wrote:
I think it's just
draw arrow1 width 0.3 /* or whatever */ arrow ...
On Sun, Aug 15, 2010 at 5:48 PM, Frieda Reichsman
wrote:
Hi Jmolers,
I am drawing an arrow like so:
draw arrow1 arrow (27:x.c
les window", the
commands produce the thicker lines seemingly automatically. So is this
a bug?
Thanks,
Frieda
-
Frieda Reichsman, PhD
Senior Research Scientist
The Concord Consortium
http://concord.org
25 Love Lane
Concord, MA 01742
Office: 978-405-3228
Mobile: 413-320-7449
Realizing
Thank you Bob! And for the info on the anisou records as well.
Frieda
On Aug 7, 2010, at 1:21 PM, Robert Hanson wrote:
thanks, Frieda. That will be fixed for 12.0.4 and 12.1.2
On Sat, Aug 7, 2010 at 8:40 AM, Frieda Reichsman
wrote:
Hi,
I am finding in Jmol 12.0.2 that
Select within
Hi,
I am finding in Jmol 12.0.2 that
Select within(helix)
works fine, but
select within(sheet)
freezes Jmol entirely.
Frieda
-
Frieda Reichsman, PhD
Senior Research Scientist
The Concord Consortium
http://concord.org
25 Love Lane
Concord, MA 01742
Realizing the educational potential of
rface
rendering, or calculation of the charges therein?
Thanks,
Frieda
-----
Frieda Reichsman, PhD
Senior Research Scientist
The Concord Consortium
http://concord.org
25 Love Lane
Concord, MA 01742
Realizing the educational potential of techn
Thanks, Paul, but the synchronization of rotations is not appropriate
for these structures.
Frieda
On Apr 1, 2010, at 2:00 AM, paul.pil...@ac-orleans-tours.fr wrote:
> Try the sync script command (see domumentation)
> Paul
>
> - Message d'origine -----
> De: Frie
bering Jmol uses), I am getting a Javascript
alert that Jmol cannot find Applet0. This message appears only on the
first time I click the button. Any ideas?
Frieda
On Mar 31, 2010, at 9:01 PM, Frieda Reichsman wrote:
> Hi Angel,
>
> Thanks - I do want to affect both applets with a si
Hi Angel,
Thanks - I do want to affect both applets with a single jmolScript
call, but I cannot seem to get "all" to work. I am using Jmol 11.8.22.
So, for example, this sends the script to the second applet on the page:
one or all.
> I'm assuming you use Jmol.js.
>
> jmolScript() takes as its
Hi, can someone please remind me of how to tell a button to send its
script to more than one Jmol applet, and/or to all Jmol applets on a
page? I know this is documented somewhere...
Thanks,
Frieda
-
Frieda Reichsman, PhD
Senior Research Scientist
The Concord Consortium
http
I am seeing a similar bug in Jmol 11.8.11 and in Jmol 11.8.7, where
the moveto commands result in a smooth movement to a seemingly final
position, but then a small jump.
In addition, it looks like there is a more serious bug in 11.8.11. In
Jmol 11.8.7, a specific moveto command works as expe
On Jun 30, 2009, at 6:47 PM, Dan Connolly wrote:
> Now I wonder why the First Glance in Jmol scripts work.
Hi Dan,
Likely because FGiJ uses an old applet version, before the bug was
introduced.
Frieda
-
Frieda Reichsman, PhD
Senior Research Scientist
The Concord Consortium
h
" flag off after it gets
an update message. Reloading the browser seems to clear it, and it
actually causes no problem with Jmol.
Bob
On Mon, Jun 15, 2009 at 6:38 AM, Frieda Reichsman
wrote:
Hi Eran and Eric,
Do you remember this problem in Firefox/windows some time back? I
just
;t
detect any other liveconnect calls before loading the PDB file and
script from our server.
As explanation for the difference between InternetExplorer and
Firefox I
found the suggestion that the more stringent default security
policy of
Firefox is responsible for it.
Regards,
Rolf
Bes
before loading the PDB file and
script from our server.
As explanation for the difference between InternetExplorer and
Firefox I
found the suggestion that the more stringent default security
policy of
Firefox is responsible for it.
Regards,
Rolf
Best regards,
Eran
On Mon, Apr 21, 2008 at
Have you tried a screen capture program such as Jing, Captivate, SnapZ
Pro, or Camtasia?
Frieda
On Apr 18, 2009, at 12:32 PM, Ralf Stephan wrote:
> Hello,
> let's say I have two orientations and want to write 50
> intermediate frames as image files:
>
> ---From:
> moveto 0.0 { -142 866 480 107.
Beta
4. Link does not work; applet does not download.
On the other hand, I have an old G4 iBook running 10.4.11 and Safari
3.2.1 on which the link works, albeit a little slow.
Phil Bays
On Apr 18, 2009, at 12:15 PM, Frieda Reichsman wrote:
The page does not work on my machine running
The page does not work on my machine running Safari 3.2.1 - not a
beta. The applet never finishes loading.
Frieda
On Apr 17, 2009, at 8:58 PM, Philip Bays wrote:
This page works fine on the Mac using Firefox, but not using the
latest beta of Safari. Is that a problem with java in this ver
ture, then
convert that to partial charge.
Thanks,
Frieda
///////
Frieda Reichsman
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesin
, add a print command within your loop:
>
> print "x=" + x + " y=" + y;
>
> Regards,
> Rolf
-
Frieda Reichsman, PhD
Senior Research Scientist
The Concord Consortium
http://concord.org
25 Love Lane
Concord, MA 01742
--
Works - fantastic! Thanks.
On Nov 20, 2008, at 11:21 AM, Rolf Huehne wrote:
> Frieda Reichsman wrote:
>> On Nov 20, 2008, at 9:27 AM, Robert Hanson wrote:
>>
>>> I can see you are having great fun, Frieda,
>>
>> Yes, I sure am! Hope to have something to sho
On Wed, Nov 19, 2008 at 6:26 PM, Frieda Reichsman wrote:
> How would I then see the calculated values for x and y coordinates?
> Jmol's output does not show the result of the calculations.
On Nov 20, 2008, at 9:27 AM, Robert Hanson wrote:
> function moveEcho
> for ( var
gen)}
The result is a sphere. I realize I need to add a height parameter, of
some kind, to get a cylinder but I can't seem to figure out which
parameter it is in the documentation...
Also, just curious, could I get the diameter to be in Angstroms
instead of pixels?
-Frieda
-
Frieda R
end for
end function
On Wed, Nov 19, 2008 at 2:52 PM, Frieda Reichsman
<[EMAIL PROTECTED]> wrote:
Hi,
I am trying to move an echo diagonally across the Jmol applet using a
function (I have created and positioned the echo at (0, 450) before
calling the function). I want the echo to sto
cool- works great, thanks.
On Nov 19, 2008, at 4:01 PM, Robert Hanson wrote:
function moveEcho
for ( var i=0; i<250; i = i + 2 )
set echo myecho @i @{450-i}
delay 0.1
end for
end function
On Wed, Nov 19, 2008 at 2:52 PM, Frieda Reichsman
<[EMAIL PROTECTED]> wrote
Thanks - sorry I missed that, by not looking at the Jena3D... subject
emails!
On Nov 19, 2008, at 2:09 PM, Rolf Huehne wrote:
> Frieda Reichsman wrote:
>> Hi, The scripting documentation is down, was there any mirror set up?
>
> Yes, I set up a mirror at the Jena3D server:
>
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