Hi All --
I am *just *getting started with JMol, so I apologize if this is blatently
obvious, but I've run into a bit of strange behavior with scripting the
applet. Is there something particularly special about the load
command? I am calling out to a script file to load several PDB files, but
differentiate between double, single or back-tick quotes and
doesn't nest them)
Many, many thanks for these insights!
-Tom
On Wed, Mar 26, 2008 at 12:29 PM, Bob Hanson [EMAIL PROTECTED] wrote:
Thomas Stout wrote:
Thanks very much -- this is getting /more/ confusing! If I add set
I've been doing (more) development of a web page using jmol thank you
again for all of the guidance of a couple weeks ago - it's been very
helpful!
I've run into two more oddities, which I am sure derive from my lack of
in-depth knowledge.
1) Is there a limit to the length of a script file
This seems to have gone into the bit bucket the first time I sent it
-Tom
-- Forwarded message --
From: Thomas Stout [EMAIL PROTECTED]
Date: Sat, Apr 5, 2008 at 2:00 PM
Subject: script file names (again) and persistence?
To: jmol-users@lists.sourceforge.net
I've been doing
On my linux box (RHEL, WS 4) running Firefox 2.0.0.4/Java 1.6.0_01 (yes,
old) all of the green links work just fine
Also, 1) the front page is 1EVE with the correct view.
2) I avoid Windows when I can.
3A) all the green links work on randomly loaded structure pages
BTW, the site is
OK - thanks!
-Tom
On Tue, Apr 8, 2008 at 7:11 AM, Bob Hanson [EMAIL PROTECTED] wrote:
Thomas Stout wrote:
I've been doing (more) development of a web page using jmol thank
you again for all of the guidance of a couple weeks ago - it's been
very helpful!
I've run into two more
OK - thanks!
-Tom
On Tue, Apr 8, 2008 at 7:11 AM, Bob Hanson [EMAIL PROTECTED] wrote:
Thomas Stout wrote:
I've been doing (more) development of a web page using jmol thank
you again for all of the guidance of a couple weeks ago - it's been
very helpful!
I've run into two more
I too am very supportive of adding this functionality! For macromolecules
however, I would like to comment though that the number of
ultra-high-resolution (sub 1.0-1.4Angstrom) structures is continuing to
increase rapidly. This is due to both better crystals and much more
powerful synchrotron
properly so that the
unit cell parameters and reciprocal axes can be determined. Correct?
Bob
Thomas Stout wrote:
I too am very supportive of adding this functionality! For
macromolecules however, I would like to comment though that the number
of ultra-high-resolution (sub 1.0-1.4Angstrom
Hmmm.is anyone else using interactive measurements? I've just added
links to a web page to turn on and off the measurements mode (so that
someone could interactively measure distances/angles/torsions of interest
and then turn it off again). Distance and Torsions work just fine, but I
find
,
Tom
On Sat, Apr 19, 2008 at 4:58 AM, Bob Hanson [EMAIL PROTECTED] wrote:
Tom, I think it's your links. The command is
set pickingStyle MEASURE
not
set pickingStyle MEASURE ON
Bob
Thomas Stout wrote:
Hmmm.is anyone else using interactive measurements? I've just
added links
, Apr 19, 2008 at 12:10 PM, Bob Hanson [EMAIL PROTECTED] wrote:
I don't think so. It is measuring angles from the measure reports. And
when I try these commands they work great. Try those commands from the
Jmol console; I'm guessing something is still wrong with your JavaScript.
Thomas Stout
measureCompleted: [3, 2097, 2100, 2099, 118.2 °]
Script completed
-Tom
On Sat, Apr 19, 2008 at 12:24 PM, Thomas Stout [EMAIL PROTECTED]
wrote:
OK - thanks -- I've probably been distracted by the fact that the Distance
and Torsion measurements are working fine that the Angle appears
Sorry to burst in on this thread, but I found it interesting and then the
specification caught my eye:
what does cavity3 mean? I don't find that in the documentation for the
isosurface command (
http://chemapps.stolaf.edu/jmol/docs/?ver=11.6#isosurface). According to
this, cavity should take
//
On May 20, 2008, at 4:34 PM, Thomas Stout wrote:
Sorry to burst in on this thread, but I found it interesting and then the
specification caught my eye:
what does cavity3 mean? I don't find that in the documentation for the
isosurface command (
http
Is there a way that I'm not seeing (I'm sure there must be) to test the size
(in number of atoms) of the current selection?
I've tried:
select ligand;
natoms = selected.size;
This sets natoms to 0, while:
select {:Z};
natoms = {:Z}.size;
sets natoms to the proper atomcount of chain Z. center
well, what do you know.yes, that works. sometimes the obvious is just
too obvious.
Thanks!
-Tom
On Mon, Jul 14, 2008 at 4:32 PM, Angel Herráez [EMAIL PROTECTED] wrote:
Tom, without testing it, but following literally your message, I'd say you
should try
natoms = {selected}.size;
Hi everyone --
I have a script that iterates over a range of residues that is defined by
choosing the min and max residue numbers. When testing out version
11.5.49 in order to take advantage of some of the great new additions, I
find that the line in my script with max is throwing
Thanks for the quick fix Bob! I'll try it out as soon as I can get the new
files...
-Tom
On Fri, Jul 25, 2008 at 4:40 PM, Bob Hanson [EMAIL PROTECTED] wrote:
yes. ARGH! I know exactly what I did Thanks for spotting that. I
will have an update available later this evening.
Bob
Thomas
max is working just fine again.
Many thanks, again!
-Tom
On Fri, Jul 25, 2008 at 6:32 PM, Bob Hanson [EMAIL PROTECTED] wrote:
they are available now. http://chemapps.stolaf.edu/jmol/docs/examples-11/
Thomas Stout wrote:
Thanks for the quick fix Bob! I'll try it out as soon as I
Here's something like what I meant that I found on Google SketchUp
(attached shapes.gif)
-Tom
On Sat, Jul 26, 2008 at 1:16 PM, Thomas Stout [EMAIL PROTECTED]
wrote:
Very nice. I especially like the new version of the rotate button --
it's more indicative of 3-d rotation. I'm of mixed
Oh, those are very good! I quite like that set
Kalzium is a periodic table viewer, so perhaps not that confusing? On the
idea of adding a J to the kalzium icon, perhaps it could be the J from
the Java logo?
-Tom
On Sun, Jul 27, 2008 at 1:15 PM, Angel Herráez [EMAIL PROTECTED] wrote:
Well, we have deployed an internal web page that feeds data to Jmol applets
from a Flex app*, which is rendered to HTML as a Flash movie, so I think
the answer to your question is yes, although we have not attempted to embed
Jmol within the Flash component itself.
-Tom
* It reads our
:-)
On 28 Jul 2008 at 13:54, Thomas Stout wrote:
Oh, those are very good! I quite like that set
Kalzium is a periodic table viewer, so perhaps not that confusing? On
the idea of adding a J
to the kalzium icon, perhaps it could be the J from the Java logo?
Not from Java, but from
Hi All --
Well, I've stumbled over this long enough I need to ask for help! I have
a case where I want to step through the chains of a selection (many PDB
files have more than one identical protein-ligand complex per
crystallographic asymmetric unit and use the identical atom names and
residue
responding. It's quite odd: the console still works.
On Fri, Aug 1, 2008 at 3:37 AM, Rolf Huehne [EMAIL PROTECTED] wrote:
Thomas Stout wrote:
Hi All --
Well, I've stumbled over this long enough I need to ask for help! I
have
a case where I want to step through the chains
for me
I think I don't entirely understand the use of parentheses () and brackets
{} .(when needed, when not)
Many, many thanks for your continued willingness to help!
-Tom
On Tue, Aug 5, 2008 at 9:20 AM, Rolf Huehne [EMAIL PROTECTED] wrote:
Thomas Stout wrote:
Has anyone ever made
When running Jmol 11.5.37, the following script (color_models.spt) works
fine:
n_models = getProperty(modelInfo,modelCount);
clist=array(green,palevioletred,lightblue,coral,yellow,cyan,\
dodgerblue,aqua,salmon,greenyellow,lavender,\
/08, Bob Hanson [EMAIL PROTECTED] wrote:
I'm pretty sure I found that and fixed it last week. Please try 11.6.RC2
Thomas Stout wrote:
When running Jmol 11.5.37, the following script (color_models.spt)
works fine:
n_models = getProperty(modelInfo,modelCount);
clist=array(green
Terrific - looking forward to it!
Thanks Bob,
Tom
On Sun, Aug 10, 2008 at 12:14 AM, Bob Hanson [EMAIL PROTECTED] wrote:
I found it. That's fixed for 11.6RC4
Thomas Stout wrote:
Hi Bob --
It looks like 11.6RC2 behaves the same way. I had bigger problems
with 11.6RC3, so I can't
)
at sun.plugin.com.DispatchImpl.invoke(Unknown Source)
On 8/10/08, Thomas Stout [EMAIL PROTECTED] wrote:
Terrific - looking forward to it!
Thanks Bob,
Tom
On Sun, Aug 10, 2008 at 12:14 AM, Bob Hanson [EMAIL PROTECTED] wrote:
I found it. That's fixed for 11.6RC4
Thomas Stout wrote:
Hi Bob --
It looks like
Hi All --
I've been mucking about with zoom today and wondered this: is it expected
behavior that the 100% level for zoom should be held constant for a loaded
model? What I mean is this: when a structure is loaded, the 100% level is
calculated by Jmol to be the factor at which all atoms are
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 (version 11.6RC7) creating pop-up windows with the contents
of an applet in a web page works just fine, but when re-sizing that pop-up
window, the structure
bar) -- is there a means
of specifying the size of the *popup* window and not allowing it to be
resized once created??
-Tom
On Wed, Aug 20, 2008 at 10:49 AM, Rolf Huehne [EMAIL PROTECTED]wrote:
Thomas Stout wrote:
It's odd that the question about syncing with pop-up applet windows came
up
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 (version 11.6RC7) creating pop-up
, Aug 20, 2008 at 1:00 PM, Thomas Stout [EMAIL PROTECTED]wrote:
Yes, the display fails just on re-sizing the window (no model
manipulation). Without re-sizing the window, one can manipulate the model
and do anything one wishes with Jmol with complete stability.
Curiously, the popup window
, Thomas Stout [EMAIL PROTECTED]wrote:
Exception in thread AWT-EventQueue-3 java.lang.OutOfMemoryError: 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
Interesting.
I have found today that set antialiasDisplay ON forces scaling of images
even when set fontscaling false is set.
Expected or no? I was surprised it took me a while to narrow it down to
this one setting
-Tom
Here are some commands for testing:
set antialiasDisplay ON;
created after its invocation.
On Mon, Aug 25, 2008 at 5:34 PM, Thomas Stout [EMAIL PROTECTED]wrote:
Interesting.
I have found today that set antialiasDisplay ON forces scaling of images
even when set fontscaling false is set.
Expected or no? I was surprised it took me a while
true;
set antialiasImages true;
end function;
_setState;
On Wed, Aug 27, 2008 at 5:53 AM, Robert Hanson [EMAIL PROTECTED] wrote:
yes, absolutely you must use the latest version if you are using any RC at
all.
On Tue, Aug 26, 2008 at 3:03 PM, Thomas Stout [EMAIL PROTECTED]wrote:
I have
Thanks Angel --
Yes, it definitely turned out to be a memory issue. My inexperience is
another! I was stumped since the Jmol graphic stopped responding, but Jmol
itself was still running and doing stuff -- I could still enter commands
into the console and get appropriate responses. Now I know
Hi All ---
I was just working on adding a toggle stereo button to my web page driving
the Jmol 11.6RC10 applet (separate issue...possible?), when I noticed that
the status of stereo doesn't seem to propagate to a new pop-up applet
window. I've reproduced this on Bob Hanson's new page:
I do not have an iPhone, but have seen Molecules in action. It certainly
looks like an implementation of RASMOL to me. It's pretty buggy though
too...bonds don't display properly...
But the performance is, indeed, impressive
-Tom
On Thu, Sep 4, 2008 at 10:52 AM, Rzepa, Henry [EMAIL
Wow!:)
-Tom
On Sun, Sep 14, 2008 at 10:53 PM, Robert Hanson [EMAIL PROTECTED] wrote:
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
I sure hope that we have all missed something: I never realized how often I
use those pages every single day, until they were suddenly gone! Does
anyone have a copy anywhere?
-Tom
On Tue, Sep 16, 2008 at 7:28 AM, Frieda Reichsman [EMAIL PROTECTED] wrote:
Hi Bob,
I have not seen a response
can!
-Tom
On Tue, Sep 16, 2008 at 11:40 AM, Thomas Stout [EMAIL PROTECTED]wrote:
I sure hope that we have all missed something: I never realized how often I
use those pages every single day, until they were suddenly gone! Does
anyone have a copy anywhere?
-Tom
On Tue, Sep 16, 2008
Actually, on re-reading this: I see that I made a typo. What I've been
trying is actually:
jmolScript(echo [EMAIL PROTECTED]);
but Jmol is echoing that literally @variable and not the contents of that
variable.
Thanks,
Tom
On Fri, Sep 19, 2008 at 2:50 PM, Thomas Stout [EMAIL PROTECTED]wrote
Thanks Angel -- I have, but Jmol merely echos null or newline or
something to the screen. I know it's echoing *something* because it paints
over text that is there from an earlier echoif I give a javascript level
alert then I get the proper text in the pop-up window, but it's not going
to
Here, then -- with my thanks for all the help -- is a working method to pull
the TITLE lines from a PDB file and echo it to the bottom of the Jmol
Applet window:
var headerInfo = jmolGetPropertyAsString(fileHeader);
var cutUp = headerInfo.split(\n);
Good suggestion..done!
http://wiki.jmol.org/index.php/Recycling_Corner#Echoing_PDB_.22Title.22_to_the_Applet_window
On Mon, Sep 22, 2008 at 2:19 PM, Angel Herráez [EMAIL PROTECTED] wrote:
On 22 Sep 2008 at 13:50, Thomas Stout wrote:
Here, then -- with my thanks for all the help
().find(TITLE).split()
for (var i = 1; i = titleLines.size;i = i + 1)
titleLines[i] = (titleLines[i])[11][0].trim()
end for
return titleLines.join(|)
end function
set echo bottom left
echo @{getheader()}
Something like that
Bob
On Mon, Sep 22, 2008 at 3:50 PM, Thomas
are required to
differentiate taking the last line of lines 3-11:
(titleLines[3][11])[0]
and taking the 11th through the last character of line 3:
(titleLines[3])[11][0]
which is what we want here.
On Tue, Sep 23, 2008 at 11:43 AM, Thomas Stout [EMAIL PROTECTED]wrote:
It looks to me
for what it's worth: I have never seen that using FF 3 on WinXP or linux
... I don't have a modern Mac, so have not been running Jmol there...
-Tom
On Wed, Sep 24, 2008 at 10:03 AM, rob yang [EMAIL PROTECTED] wrote:
--
Final testing appreciated for Jmol
it. The release files are fine.
Bob
On Wed, Sep 24, 2008 at 12:16 PM, Thomas Stout [EMAIL PROTECTED]wrote:
One oddity that I've just noticed: I downloaded 11.6.RC16 (several times
in the last 24 hours) and find that if I run the stand alone or load the
signed applet, they report version 11.6.RC16
the signed Applet now
-Tom
PS - No, I did NOT clear the java cache -- I have no idea how to do that
under linux!!
On Thu, Sep 25, 2008 at 1:35 AM, Angel Herraez [EMAIL PROTECTED] wrote:
El 24 Sep 2008 a las 17:35, Thomas Stout escribió:
Oh, I restarted everything - including the computer
One thought about the wiki not loading: I have the same problem for any
link to the wiki that uses the port number.
For example:
http://wiki.jmol.org:81/index.php/Solving_Java_Problems#Java_cache
will never load for me due to the :81 and our local firewall denying
access. If I cut-and-paste the
Great! Thanks very much -- that's very useful.
-Tom
(google is amazing!)
On Thu, Sep 25, 2008 at 8:15 AM, Angel Herraez [EMAIL PROTECTED] wrote:
Just found this (well, not me, Google of course):
Clearing Java cache on Linux, Mac, Windows:
Does it need to be a single object? Could you:
draw myIDa {point1}{point2}
draw myIDb {point2}{point3}
etc?
-Tom
On Sat, Oct 4, 2008 at 5:25 AM, Angel Herráez [EMAIL PROTECTED] wrote:
One can draw a line using
draw myID {point} {point}
and, if I want more than 3 nodes,
I could play it just fine (only tried VLC media player - the swiss army
knife of video players) and the resolution is fine. However, I found the
frame rate to be much too fast to be sensible - atoms were flying around
faster than I could discern! When you encode in VideoMach, can you set a
I am not knowledgeable about the algorithms that are out there (perhaps
someone like Warren DeLano and others might chime in), but I'd like to throw
in my 2 cents (currently approaching the true value of my opinion with the
state of the US dollar!).
I'd rather see Jmol do *something *in this
clouds, etc)
Yes/No?
-Tom
On Tue, Nov 4, 2008 at 2:59 PM, Robert Hanson [EMAIL PROTECTED] wrote:
On Tue, Nov 4, 2008 at 2:23 PM, Thomas Stout [EMAIL PROTECTED]wrote:
The basic premise was: if two appropriate heteroatoms are spatially
located within a set range of separations (1.8-3.4A
I'd have to go dig in the literature for a referenceit's just my
personal guideline(s). I'll see what I can find -- most of that literature
is pretty old
-Tom
On Tue, Nov 4, 2008 at 3:23 PM, Robert Hanson [EMAIL PROTECTED] wrote:
Possibly. Is that documented or discussed somewhere
bonds. If you need more, then it's just a
matter of defining what angle requirements one might want.
Bob
On Tue, Nov 4, 2008 at 7:49 PM, Thomas Stout [EMAIL PROTECTED]wrote:
It looks nice! -- is the angle adjustable? I tried setting it to other
values (even extreme values) and didn't see
Hi Bob --
I think this is pretty slick especially nice for hard-core users (those
who are using the command language and needing to type), but I also think
that it would be distracting for casual users So, I would vote for
making it off by default and leaving it to the knowledgeable user(s)
As more of an implementor and end-user than a developer I would
agree that yes, this would be strongly welcomed! CCSDs ReLiBase does
this, but again that is far from user friendly or open source (and
ReLiBase+ is exorbitantly priced)
Good luck,
Tom
On Apr 2, 2009, at 7:23 AM, Chris
AFAIK OT/OT1/OT2 are no longer standard but are still freqently
generated by legacy software (XPLOR comes to mind as a primary source
of OTs versus O/OXT). So, you shouldn't be finding any in the PDB, but
you're still apt to run into them in local .pdb files...
-Tom
On May 11, 2009, at
It'd be neat if it could be tied to the size of the bounding box of
the loading molecule...
-Tom
On Jun 12, 2009, at 3:45 PM, Greeves, Nick
ngree...@liverpool.ac.uk wrote:
While displaying polymer chains, we have been wondering if it is
possible to change the shape and size of the
The only equivalent that I am aware of is an implementation of PyMOL
called AxPyMOL that allows one to embed a PyMOL session file within M$
PowerPoint. While freeware, AxPYMOL uses ActiveX, so it is constrained to M$
Windows.
All those caveats aside, it does work and is pretty nice to have a 3D
PyMOL has incorporated ffmpeg into it for doing just this (FreeMOL) --
Perhaps Warren DeLano could offer some advice on this? Even if a
third-party freeware were not bundled directly into Jmol, I think that a
built-in script to record the frames as JPGs or PNGs and then run them
through ffmpeg
How about the facebook style effect, where a drop-down menu selector appears
when one mouses-over the frank/logo?
-Tom
On Mon, Oct 19, 2009 at 12:58 PM, Jeff Hansen jhan...@depauw.edu wrote:
Angel,
I agree with you. I like to use the same background color for my Jmol
applets too. To me
I am sorry to pass along this rather shocking news regarding Warren:
Dear CCP4 Community:
I write today with very sad news about Dr. Warren Lyford DeLano.
I was informed by his family today that Warren suddenly passed
away at home on Tuesday morning, November 3rd.
While at Yale, Warren made
PM, Thomas Stout thomasjst...@gmail.comwrote:
I am sorry to pass along this rather shocking news regarding Warren:
Dear CCP4 Community:
I write today with very sad news about Dr. Warren Lyford DeLano.
I was informed by his family today that Warren suddenly passed
away at home on Tuesday
This is great -- really lovely! (When is Jmol coming to the iPhone?!) :)
One oddity that I noticed: when I induce a rotation via a swipe, it
continues (as expected) until my screensaver comes on --- when the display
is re-awakened, the display is static. Not an issue, as far as I am
I believe that I have just stumbled into either an oversight, a bug or --
most likely -- my not keeping up with version changes...
Anyway, I recently decided that it was time to consider upgrading a
(private) site that I maintain from Jmol version 11.6RC16 (signed) to the
current version. I
they're looking at and locating themselves in space -- this is a fantastic
feature. I also think it makes Jmol look really polished
Thanks Bob!
-Tom
On Mon, Dec 14, 2009 at 2:05 PM, Robert Hanson hans...@stolaf.edu wrote:
On Mon, Dec 14, 2009 at 12:55 PM, Thomas Stout thomasjst
Hi again --
The combination of zshade translucent surfaces is working great in 11.9.11
-- thanks Bob!
I've just stumbled into one more oddity: after putting the display into
side-by-side stereo, the entire right-hand panel becomes the right-most
few-percent space for zooming. That may well be
PM, Robert Hanson hans...@stolaf.edu wrote:
OH, funny! OK
On Tue, Dec 15, 2009 at 3:55 PM, Thomas Stout thomasjst...@gmail.comwrote:
Hi again --
The combination of zshade translucent surfaces is working great in
11.9.11 -- thanks Bob!
I've just stumbled into one more oddity: after
While the plotting functionality may not be directly molecular-centric, I
don't see how it detracts from Jmol. If the program were to become
bloat-ware then yes, of course, that's a problem. For the moment it seems
to be constrained within the bounds of scientific functionalities that many
of us
Hi All --
I am currently trying to re-work an old, rather long script and continually
getting lost in if/else/endif loops -- Are there any language aware
editors/IDEs out there that you recommend for jmolscript/javascript?
I tend to just use vi on a linux box, but could move to a WinOS
is going to help with JavaScript. Although if you
go to the standard JavaScript syntax:
if (..) {
...
} else {
}
Jmol now supports that. And it's possible that some IDE will at
least tell you where your braces are unmatched.
On Mon, Dec 21, 2009 at 5:54 PM, Thomas Stout
I'm hoping fresh eyes can spot my trouble here. I have a loop that cycles
through a series of specific residues and selects out the one with the
largest number of atoms. Under prior versions of Jmol (11.6.RC16), I could
get away with the following syntax:
if {(resno=bigres)}.size 6
I'm
$ if ({resno bigres}.size 3) {print {resno bigres}.size}
45
On Tue, Dec 22, 2009 at 5:24 PM, Thomas Stout thomasjst...@gmail.comwrote:
I'm hoping fresh eyes can spot my trouble here. I have a loop that cycles
through a series of specific residues and selects out the one with the
largest number
Hi again --
One more observation for the is that the way it's supposed to work?
file
I've found in Jmol 11.9.11 that set zshade on doesn't actually apply until
*after* there are coordinates loaded. If I bring up the applet apply my
standard settings (I have an initialization script) and
, zoom, and
orientation are all reset upon file loading. You can set a defaultLoadScript
to run if you want to do this sort of thing automatically.
Bob
On Wed, Dec 23, 2009 at 12:57 PM, Thomas Stout thomasjst...@gmail.comwrote:
Hi again --
One more observation for the is that the way it's
That's an NMR structure so does not have a unit cell. Makes one
wonder if it/they should have a CRYST1 card at all!
-Tom
Sent from a tiny virtual keyboard.
On Dec 24, 2009, at 11:27 PM, jaime.prilu...@weizmann.ac.il wrote:
Jmol (11.5.35 and 11.8.9) can't open PDB 3irj,
reporting this
...@uwosh.edu wrote:
On Jan 4, 2010, at 2:55 PM, jmol-users-requ...@lists.sourceforge.net
wrote:
Date: Mon, 4 Jan 2010 12:55:50 -0800
From: Thomas Stout thomasjst...@gmail.com
Subject: Re: [Jmol-users] GUI javascript color picker widget for Jmol,
please look at and vote on inclusion
Very exciting! This would be of enormous value (at least to me the
protein crystallography community). I should think the PDB Proteopedia
would be quite interested as well...
-Tom
On Wed, Jan 13, 2010 at 8:59 AM, Eric Martz martze...@yahoo.com wrote:
I am again making an effort to render
, Proteopedia will be very
interested when we succeed!
-Eric
At 1/13/10, Thomas Stout wrote:
Very exciting! This would be of enormous value (at least to me
the protein crystallography community). I should think the PDB
Proteopedia would be quite interested as well...
-Tom
On Wed, Jan 13
Thank you for that detailed explanation of quaternions, Bob! This is the
first time I've actually been able to picture how to utilize them in a
general way. (guess I just needed a different explanation)
-Tom
On Wed, Feb 3, 2010 at 7:09 AM, Robert Hanson hans...@stolaf.edu wrote:
Otis,
;\
Cool, huh?
:)
Bob
On Wed, Feb 3, 2010 at 12:58 PM, Thomas Stout thomasjst...@gmail.comwrote:
Thank you for that detailed explanation of quaternions, Bob! This is the
first time I've actually been able to picture how to utilize them in a
general way. (guess I just needed
Hi All --
Before I embark on re-inventing yet another wheel, I thought I would ask:
has anyone already created a script for choosing an optimal orientation in
which to display a given molecule? I am thinking in terms of minimizing the
overlap of atoms along the vector of view (z axis), i.e., the
not tested it on molecules
such as intermetallics or NaCl, but don't expect any difference.
Cheers,
Tom
On Sat, Feb 13, 2010 at 3:04 AM, Rolf Huehne rhue...@fli-leibniz.de wrote:
Thomas Stout schrieb:
Hi All --
Before I embark on re-inventing yet another wheel, I thought I would
ask: has
selection, should the user wish to focus on a different selection of
atoms
-Tom
On Tue, Feb 16, 2010 at 1:20 PM, Rolf Huehne rhue...@fli-leibniz.de wrote:
r...@ellerbach.com schrieb:
On Tue, 16 Feb 2010 12:04:32 -0800, Thomas Stout thomasjst...@gmail.com
wrote:
To follow up on my
But electron density maps can be on arbitrary scales, so the value 1.0 may
very well be meaningless (except in the particular case where normalization
has made 1.0=1e-/A**3), and will certainly produce wildly different results
from dataset to dataset depending on the provenance of each particular
Is there a convenient way of distinguishing molecules when there is more
than one in the asymmetric unit? In this case, I am not referring to
macromolecules or PDB files, which have the handy chain ID, but rather
small organic molecules loaded from cif files. I'm looking to
(automatically)
Thanks Angel --
I thought that might do the trick, but perhaps I am implementing it wrong.
I thought this might work:
measure RANGE 1.8 3.2 (within molecule) (not within molecule);
but that generates neither measurements nor errors. I think the symmetry
part here is a red-herring. Attached is
that was the best ad hoc visual fit to what I
was seeing in the electron microscopy literature. So I'm wondering now if
different fields have different standards.
Bob
On Mon, Feb 22, 2010 at 1:38 AM, Thomas Stout thomasjst...@gmail.comwrote:
I will try and track down the actual algorithm used - CCP4
And just to clarify my understanding: there is no concept of GROUP for
non-PDB/mmCIF files, correct?
I am currently battling a similar logic problem I think what I need to do
is write my own group(index) variable to count up the number of discrete
molecules in a coordinate file. So, for
OOPS - just found this in my Drafts folder from last week
---
Thanks Angel - that was certainly one of my problems! I now realize
that I need a slightly more complicated approach. For the general case
of N molecules in the asymmetric unit, is there a
++ ) {
x = {molecule=i}
print molecule + i + is + x
}
On Mon, Feb 22, 2010 at 3:46 PM, Thomas Stout thomasjst...@gmail.comwrote:
OOPS - just found this in my Drafts folder from last week
---
Thanks Angel - that was certainly one of my problems! I
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