On Mon, July 18, 2011 11:34 am, Robert Hanson wrote:
You should be able to get the correct molecular view even without any {xxx
xxx xxx}, but maybe only if you use the latest build. Would you please
try
that? http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
Bob,
Would it make
On [2011-Jul-14] Robert Hanson hans...@stolaf.edu wrote:
OK, I got it. In generating models, Jmol was not establishing this
connection:
C4 C6 2_855 1.393(3)
[snip]
I'll take a look at this and get back to you. I'm a bit surprised that
Jmol can't handle it directly, but here's how you
On Fri, July 15, 2011 12:52 pm, s...@publcif.co.uk wrote:
[snip]
So what is the generic command that'll load a molecule and display all
of
those (complete) molecules that have an atom within a unit cell?
Rich
load {444 666 1}; display within(molecule, cell=555)
might be worth a try?
On Fri, July 15, 2011 1:02 pm, r...@ellerbach.com wrote:
On Fri, July 15, 2011 12:52 pm, s...@publcif.co.uk wrote:
[snip]
So what is the generic command that'll load a molecule and display all
of
those (complete) molecules that have an atom within a unit cell?
Rich
load {444 666 1};
On Tue, April 26, 2011 4:13 pm, Eric Martz wrote:
I recently noticed that a colleague, using a Mac with Snow Leopard OS
10.6, has Java 1.6.0_24. In contrast, the java running Jmol on my Mac
with (plain old) Leopard OS 10.5 is version 1.5.0_28, despite my
having run all Apple Updates.
If you
Yeah, I know. I was sure you'd say that. :-)
Unfortunately it isn't a machine I have any control over. But I will send
the suggestion.
Rich
On Fri, April 15, 2011 9:02 am, Robert Hanson wrote:
Yeiks! 11.2! upgrade!
On Fri, Apr 15, 2011 at 7:40 AM, r...@ellerbach.com wrote:
Thanks Bob.
I
On Wed, November 24, 2010 10:17 am, Alexander Rose wrote:
Manipulating the pdb file before creating the surface with PyMOL does not
work because the PyMOL obj has no relation to the pdb coordinates.
Isn't this something pymol should do? Maybe suggest a bug-fix/enhancement
on the pymol list?
Understood Bob. I think having a parameter for it would be good and I
think the default should be:
multipleBondSpacing = 0.35
multipleBondCylinderThickness = 0.75 (or however you want to code it)
Rich
On [2010-Sep-10] Robert Hanson hans...@stolaf.edu wrote:
This isn't thickness, it's distance
On Fri, September 10, 2010 9:19 am, Robert Hanson wrote:
that can be experimented with at
http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm?topic=11
I think this could be a new default. Let's talk about it.
On Fri, Sep 10, 2010 at 7:31 AM, Robert Hanson hans...@stolaf.edu wrote:
Bob,
My choice of words is leading to some confusion.
In the current implememtation as the model is rotated the double bond
rotates so the user sees two sticks in almost all orientations. This
requires rotating the bond cylinders as the molecule rotates. Sometimes
the aliasing of edges of the
Jmol Application 12.1.10 on MacOSX 10.5.8 with FF 3.6.7 or X11
If I'm rotating a molecule in Jmol and switch over to FF or X11 and type
text or scroll the page and then click back into Jmol the leftmouse button
no longer rotates the molecule but either translates it or zooms it. It
appears that
Why is Jmol 12.0 called Jmol-11.zip?
Rich
Uploaded version is at
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
--
This SF.net email is sponsored by Sprint
What will you do first with EVO, the
Robert Hanson wrote:
Jmol is not attempting to write a perfect PDB file, especially when
the data are not originally PDB data. I'll look into the occupancy
issue. I think that should be proper if the file has occupancy data.
Since the PDB-format is such a fundamentally broken one it is
Otis Rothenberger wrote:
Bob,
This is the cat's meow. Thanks for the help. I'm still stuck with a
server side approach (AJAX very frustrating!), but the Jmol load
completed approach seems to work. Cholestane is below. What a slick
way to communicate 3D models via email:
Yep, fixed.
Rich
Robert Hanson wrote:
Mac-side bug fixed. Please do check this out:
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=135
Bob
--
___
I agree with Angel. I think Jmol should be a professional-level display
tool and there should be an educational-level tool for the molecule
manipulation functions. The focus/needs of the two groups are different
enough that one program is never going to satisfy the two groups and
the
nada
Rich
Robert Hanson wrote:
so you don't even see a structure?
On Thu, May 20, 2010 at 7:07 PM, Philip Bays pb...@saintmarys.edu
mailto:pb...@saintmarys.edu wrote:
Bob:
I click on the red text in the description which transfers the
command to the command area under the
Running OSX 10.5.8.
Downloaded jmol-12.0.RC12-full.tar.gz and double clicked on the jmol.jar
file. Error to console is:
Exception in thread main
May 18 14:57:39 xrayMP [0x0-0x40040].com.apple.JarLauncher[771]:
java.lang.UnsupportedClassVersionError: Bad version number in .class file
May 18
Robert Hanson wrote:
Yes, the issue is definitely the Java version.We changed to 1.5
recently. Actually, from what I could tell, we were using 1.5
functionality already for several months. It looks like Eric is
probably using Java 1.4.
Eric, if that's the case, first thing to do is check
On Fri, April 9, 2010 12:16 pm, Otis Rothenberger wrote:
Downside: It's a helper application. Upside: ACD generously makes
ChemSketch a free download for private, student, educational use.
Isn't ChemSketch a MSWindows-only product?
Rich
On Mon, 15 Mar 2010 11:29:40 -0500, Robert Hanson hans...@stolaf.edu
[snip]
The operation Jmol is performing is definitely an alignment of sorts; I
can
certainly be careful not to claim it is structural alignment if that
term
is now synonymous with something more involved.
of sorts
It
On Mon, 15 Mar 2010 13:48:19 -0500, Robert Hanson hans...@stolaf.edu
wrote:
[snip]
Be that as it may, I'm also quite happy to change the name to anything
reasonable. Since it's not just doing (at this point) a standard
matrix-based RMSD minimization operation (which is what you want to call
On Mon, 15 Mar 2010 14:33:08 -0500, Robert Hanson hans...@stolaf.edu
wrote:
Spacial doesn't really describe it.
The method goes like this:
--Identify pairs of matched residues (as opposed to atoms).
So not of general use but limited to the special cases of nucleic acids
and proteins.
On Tue, 9 Mar 2010 17:22:39 +0100, Egon Willighagen
egon.willigha...@gmail.com wrote:
On Mon, Mar 8, 2010 at 2:57 PM, Robert Hanson hans...@stolaf.edu
wrote:
That's ridiculous. Sorry, but to try to go retro on this is just too
strange.
:)
I agree; don't shoot the messenger.
Especially
I kinda agree with Bob. I certainly wouldn't want Jmol to be able to
produce something of the quality of the image in that first link Egon
quoted :-) But, if Jmol is to be a tool to produce hard-copy images for
publications then an argument could be made for a really good-looking ORTEP
style image
On Tue, 16 Feb 2010 12:04:32 -0800, Thomas Stout thomasjst...@gmail.com
wrote:
To follow up on my question from last week concerning
auto-orientation,
Rolf Huehne very graciously pointed me in the direction of a solution
that
he had already crafted for JenaLib. He uses the dimensions of the
The sigma is the esd (estimated standard deviation) for the value of the
electron density at any grid point. So if the electron density calculations
provide an esd of 1.2 electrons per cubic angstrom the 1 sigma contour
lines would be at 1.2, the 2 sigma lines at 2.4, 3 sigma at 3.6 etc.
Rich
On
On Tue, 19 Jan 2010 14:03:32 -0600, Robert Hanson hans...@stolaf.edu
wrote:
Is that in the file somewhere? What I have is
dmin dmax dmean (density min max mean)
rms
Now, I DON'T think the rms is really rms -- I think it's rms
deviation,
but I could be wrong about that. What seems to
Robert Hanson wrote:
Keep talking, Rich. I don't quite have it.
I have a file of numbers. An isosurface is produced not by contouring
but by finding the surface that intersects that cube of numbers at a
specific cutoff value.
dmin dmax dmean (density min max mean)
rms
How do you decide on how pyramidal (or not) to make a N Bob? What about
hydroxyl H atoms when there is the potential for intramolecular H-bonding?
Rich
On Fri, 15 Jan 2010 11:01:22 -0600, Robert Hanson hans...@stolaf.edu
wrote:
OK, that's in. See Jmol 11.9.19 ---
On Thu, 14 Jan 2010 18:54:46 +0100, Angel Herráez angel.herr...@uah.es
wrote:
El 14 Jan 2010 a las 11:24, Robert Hanson escribió:
A swipe means you drag and the motion stops at the exact moment
that the mouse is released.
So the key is whether you release the button (swipe) or not (drag).
As interesting as it is to plot stuff I really don't see the purpose of
putting time and effort into making Jmol a generic 3D plotting program.
Maybe if its abilities and interface were perfected for plotting molecules
(large and small) then there might be some impetus to create Jplot (or
On Tue, September 22, 2009 3:30 pm, Robert Hanson wrote:
multiple bonds -- I guess this depends upon your definition of ideally.
Others feel that ideally the bonds should rotate so that there is never
a
question as to their order. In addition, this introduces the ambiguity in
cases such as
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 { -142 866 480 107.35} 100.0 0.0 0.0 {61.260506 38.7915
44.659} 50.97134 {0.0 0.0 0.0} 8.481314 102.86942 50.0;
---To:
moveto 2.0 { -46 -870 492
This is a good suggestion Chris. For Ian's problem (since it is a
well-defined in-house setup) the preprocessing could change the ? of an
atom name to disordered (no need to stick with one character).
Rich
On Wed, April 15, 2009 9:05 am, Chris Foley wrote:
Again, this won't solve the ? problem
On Tue, April 14, 2009 3:02 pm, tho...@ccdc.cam.ac.uk wrote:
Hello,
I'm sure there's a really easy way to do this but as a new Jmol scripter
I'm struggling to see how! I need to write a Jmol script to select all
atoms with names ending in '?'. My input file is a CIF and the presence of
a
tho...@ccdc.cam.ac.uk wrote:
Hi Rich,
My input file is a CIF and the presence
of
a trailing question mark in the atom name indicates a disordered atom,
e.g. 'C33?'.
Is this construct a legal CIF atom_site_label Ian? As far as I am aware
the CIF dictionary doesn't allow for that
Have the atom names stayed unique through the various remediation cycles
of the PDB? If so use the CIF files with the names rather than the .pdb
format files.
Rich
--
___
Fred Ziegler wrote:
Jmol-ers:
I still use OSX 10.4.11 (Tiger) on my Macs because it has OS9
(classic) which allows me to use CambridgeSoft's Chem3DPro to create
minimized .mol files for Jmol display. CambridgeSoft no longer makes
Chem3DPro for OSX but it does for Windows. Short of using
With Bob's implementation of quaternions in Jmol it is *extremely* easy to
let Jmol create an image sequence between two user-defined views. This
sequence can then be converted into a movie using the standard tools. I
did this recently (with Bob's help to get the syntax right) using the
On Thu, November 6, 2008 12:01 pm, David Leader wrote:
However I still might see if there is a student up to integrating the
C code. My colleague tells me that this is quite sophisticated. For
example it calculates the H atoms and deals with the uncertainty in
serines and threonines, by
On Sun, May 4, 2008 9:30 pm, Bob Hanson wrote:
Rich, the popup menu is entirely cunstomizable. You can save whatever
modifications you want to a file and then modify it to make it do
whatever you want it to do. So it sounds to me like you should perhaps
consider that as an option and then
Thanks Bob. I understand that that there are some builtin settings for
the application that you want to rely on for a consistent lookfeel so
that is the way it is currently set.
One of my points is that the available preference settings within the app
do not let a user (or a distributor)
On Fri, May 2, 2008 1:24 pm, Angel Herráez wrote:
On 1 May 2008 at 16:03, [EMAIL PROTECTED] wrote:
From a usability perspective most of what is in the right-button menu
should be in the application menus (and sub menus). The pop-up menu
should
be limited to those things that are relevant to
I've had a look at both 11.4.2 and 11.5.33 and I don't think the default
setup of the application is appropriate for new/casual users of chemical
crystallography information.
When fed a CIF the application puts up a unit cell box with one molecule
with the center of rotation not coincident with
On Thu, April 17, 2008 10:46 am, Bob Hanson wrote:
Note that I am defining temperature as
(U11 + U22 + U33)/3.0 * 100
If this is not correct, please let me know. (I can't find where I read
that, and I don't know if I remember it correctly.)
David Watkin prefers:
Uequiv = (U1*U2*U3)**1/3
On Wed, April 16, 2008 6:32 am, Brian McMahon wrote:
Bob
snip
I doubt that it's Jmol's job to distinguish between main residue and
small moiety, so I would suggest allowing an optional colour scheme
that maps ellipsoid colour to maximum/minimum main axis ADP ratio
that runs something like
On Mon, April 14, 2008 9:28 am, Bob Hanson wrote:
Brian, I would love to get this into Jmol. I think we can do a fabulous
job of it, but I need to understand how thermal ellipsoids are
designated in common file formats and how one would suggest depicting
them (with the quarter-segment left
On Mon, January 29, 2007 6:16 pm, Francesco Pietra wrote:
Let me say that a package dealing with molecules that
does not place hydrogens correctly is of no use
professionally.
If Jmol was a MM program or even a molecular-editor you might have reason
to have such a view. But, Jmol is a
Philip, Bob,
It is an unfortunate fact of life that some (many?) CIF parsers rely to
some degree on an assumed ordering of dataitems in the CIF. Even the
cif-checking software that does structure checking at the IUCr breaks in
this regard! The only way to not have this problem is if the CIF is
On Tue, October 3, 2006 12:40 pm, Bob Hanson wrote:
Ah, I see. If they do not cross cell boundaries, you could
select cell=566 and
for example. Or, if not, and they are all connected as a single organic
molecule, you could:
select within(molecule,cell=566 and symop = 1)
site is
On Fri, September 8, 2006 2:12 pm, G. Jones wrote:
PDB is fine, I don't know the format of cif files but if I did, or if you
know a link where I can find it then that would be fine to.
CIF files are very easy to write since they are free-format in a dataname
datavalue style with not very many
On Wed, September 6, 2006 8:32 am, Bob Hanson wrote:
Jmol users:
Please test the new documentation pop-up examples.
Everything seemed to go OK with FF 1.5.0.6 on OSX 10.3.9
Rich
-
Using Tomcat but need to do more? Need
On Tue, September 5, 2006 4:35 pm, Bob Hanson wrote:
In response to requests for Jmol to be able to visualize a wider range
of crystallographic data sets, with the help of Peter and Judith
Murray-Rust and Syd Hall, I've made a preliminary implementation of
space group name analysis in Jmol
On Tue, August 29, 2006 4:47 am, Alan Hewat wrote:
[snip]
But otherwise it would indeed be interesting to have a Jmol script to
apply symmetry operations ie:br
bSelect (Basis);br
Symmetry (x, 1/2-y, 1/2+z)brbr
Select (Basis)/b would mean select all atoms if it is a file that does
not
On Tue, August 29, 2006 8:15 am, Alan Hewat wrote:
html
body
It seems that Jmol-11 does not load CIF files containing any blank lines.
But blank lines are not flagged as errors by ENCIFER
a href=http://www.ccdc.cam.ac.uk/free_services/encifer/;
eudora=autourl
On Tue, August 29, 2006 11:18 am, Bob Hanson wrote:
Alan Hewat wrote:
It seems that Jmol-11 does not load CIF files containing any blank
lines. But blank lines are not flagged as errors by ENCIFER
http://www.ccdc.cam.ac.uk/free_services/encifer/ and should simply be
ignored by the Jmol
On Tue, August 29, 2006 11:49 am, Alan Hewat wrote:
Well a line starting with a hash such as #Jmolscript: will get carried as
a comment by any CIF parser (I hope) so that should be CIF OK.
The problem is that it is up to the individual parser. Parsers are also
allowed to rearrange dataitems
On Tue, August 29, 2006 2:29 pm, Bob Hanson wrote:
must be a different URL
Yep, Bull forgot the enclosing directory. See:
http://www.people.virginia.edu/~wrp/bioch503/bioch503_l3.html
Rich
-
Using Tomcat but need to do
This new version of FF doesn't seem to want to display the Jmol applet
(v10.00) as reliably as the previous versions did (FF 1.5.0.3 and
earlier). Quite often the spot for the applet just stays as an empty
block. Multiple reloads will sometimes get it to display. Safari works
just fine under the
On Tue, June 13, 2006 8:43 am, Bob Hanson wrote:
rich, do you know how to get a Java console output? We need to see that
to see what error is occurring.
No errors reported Bob. It just sits there with an unfilled space for the
applet. In the bottom FF window info bar it says:
Applet
On Tue, June 13, 2006 9:04 am, [EMAIL PROTECTED] wrote:
On Tue, June 13, 2006 8:43 am, Bob Hanson wrote:
rich, do you know how to get a Java console output? We need to see that
to see what error is occurring.
No errors reported Bob. It just sits there with an unfilled space for the
applet.
On Tue, June 13, 2006 10:58 am, Bob Hanson wrote:
Rich, you sure you are looking at the Java console log? (In one of your
Mac directories? logs or log or something like that?)
I checked both the javascript log and the java log. The interesting thing
in the java log is what is not there. After
On Wed, June 7, 2006 1:54 pm, Steven R. Spilatro wrote:
Angel,
1) XP with Service pack 2
2) no compression file installed, other than that which comes with windows
3) the extension is .zip, unless .jar is added in the save as
window as previously described.
What happens if you use FireFox
On Mon, May 22, 2006 5:36 am, Angel Herraez said:
I would say the spinning could retain its status, at least in respect to
spin x , y , z.
I don't see why the spin should be an applet state as opposed to a
molecule state.
I can see setting some things as an applet (or rendering) state that
On Tue, May 9, 2006 4:17 pm, Bob Hanson said:
right, that's my point. It seems unnatural to me as well. That's why I
was surprised and initially thought it was a bug. Personally I can't
imagine it, either, unless
Wouldn't it be more natural to have a model specifier? Do x to model
n, or to
On Mon, April 17, 2006 5:40 am, Egon Willighagen said:
As long as the informat is split up
over several data substructures, and one has to get those bits of
information
together, it does not really matter wether it is PDB, mmCIF or XML syntax.
This is true. CIF is an information exchange
On Tue, April 4, 2006 10:58 am, Bob Hanson said:
I've found one bug in the CIF reader. I believe that if the second
character of the atom.type_symbol field is capitalized, it should be
uncapitalized before checking to see if it is an atom symbol.
Any symbol may be used as the atom type and
On Tue, April 4, 2006 1:34 pm, Bob Hanson said:
Any symbol may be used as the atom type and that symbol (case
included)
is then forever associated with that atom type defined. So I don't think
it is a good idea to assume you can change case to make comparisons or
assignments.
true, but in
On Tue, March 28, 2006 5:24 am, Miguel said:
Several educators have told me that it is a mistake for Jmol to read 2D
structures ... because of the potential confusion caused by representing
these structures as flat.
I'm not sure mistake is the right way to characterize it. But it would
be good
On Tue, March 28, 2006 8:54 am, Miguel said:
If I recall correctly, I suggested only allowing x/y rotation to one of
these people. If I recall correctly, he responded by saying that even x/y
rotation was flawed, because 2D molecular models were supposed to be
presented in a standard
On Wed, February 8, 2006 8:58 am, Frieda Reichsman said:
Firefox 1.5 crashed the first time I tried it, after I used several
different links to report info. I will re-test and get back to you
later.
I didn't get any crashes using FF1.5 on OSX10.3.9 but I do get a lot of
Whether you top-post or bottom-post please trim the quoted material to
*just* what is necessary. Leaving entire multi-person posts intact after a
line or two of top-post reply is really quite annoying.
Rich
---
This SF.net email is sponsored
On Thu, February 2, 2006 10:20 am, Bob Hanson said:
I disagree. From a user perspective, single and double are just
rendering issues of wireframe.
Wireframe should be allowed to respect or not respect the underlying
connect type. If atoms are connected using a double bond then that *is*
the
I'd like to see this file expanded to have, even a brief, description of
each of the files in the distribution.
Rich
---
This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
for problems? Stop! Download the new AJAX
On Thu, February 2, 2006 2:12 pm, [EMAIL PROTECTED] said:
De: [EMAIL PROTECTED]
I'd like to see this file expanded to have, even a brief, description of
each of the files in the distribution.
Would you be willing to write the descriptions ?
Oh, I would have already if I knew what they all
On Wed, February 1, 2006 9:47 am, Miguel said:
I was visited by a rep from a book publisher the other day, who gave
me a booklet with details of the forthcoming 6th edition of Stryer's
Biochemistry (Berg et al.), the premier textbook for teaching
undergraduate biochemistry. I quote from a
Further to the discussion of xhtml and html that was on this list a while
ago I ran across this website that discusses the disadvantage of using
xhtml in any except the most well-constrained environments.
http://www.hixie.ch/advocacy/xhtml
Rich
On Tue, October 25, 2005 7:49 am, Miguel said:
Please comment on the following proposal:
* Jmol will support the 'HG11' version
* The Jmol pdbReader code will convert atom names that
match the following format:
digit H alpha digit - H alpha digit digit
Justification:
* No
On Thu, October 6, 2005 11:33 am, Miguel said:
This is a good task for a novice who wants to contribute. It is a
self-contained, well-defined task that would provide the opportunity to
gain some experience with Java, CVS, open source development, and Jmol.
Some possible ideas:
* Francois
On Tue, August 30, 2005 12:01 pm, Miguel said:
When displaying distance measurements ...
Q: Does anyone feel the need to have more than one digit to the right of
the decimal point when measuring in Angstroms? (or 2 digits with
nanometers)
[snip]
I made an executive decision to reduce the
On Tue, August 30, 2005 12:22 pm, Miguel said:
I was told that:
- the Royal Chemical Society mandates that everything be done in
nanometers
For molecular structures the standard SI unit would be pm.
- many publications no longer accept angstroms
Not that I am aware of. All the journals
On Tue, August 30, 2005 1:29 pm, Egon Willighagen said:
I remember a discussion on this on the list. But cannot find it with
Google.
Last August.
Conclusion indeed was that angstrom where to be phased out.
Not quite. Angstrom measurements are deprecated in all aspects other than
On Mon, July 18, 2005 4:26 pm, Miguel said:
... educate me ... :-)
OK, you asked :-)
More years ago than I want to consider I was doing some research and came
across a paper by J.T. Rule titled Stereoscopic Drawings (J.O.S.A.,
1938) in which he discusses the underlying inadequacies of using
On Mon, June 20, 2005 6:00 pm, Miguel said:
I'm trying to make a jmol page using cgi rather than static html.
Other people have this running successfully.
Yep.
I have the jmol directories where they should be.
On Wed, April 13, 2005 1:51 pm, Joost Van Durme said:
Hi,
I want to use html checkboxes to toggle eg. ribbons on or off. So, when
checked, ribbons are on, when unchecked, ribbons are off.
I'm writing the html page in plain html after loading the applet with
applet.../applet. This is the most
On Wed, April 6, 2005 9:12 am, timothy driscoll said:
hi Rich,
I'm assuming that you mean atom colors according to the default color by
element scheme. Jmol uses a variant of the CPK scheme. if you have
access to the source, you can find the values in
On Wed, April 6, 2005 12:59 pm, [EMAIL PROTECTED] said:
De: [EMAIL PROTECTED]
Thanks Tim! Unfortunately I'm behind a corporate fire-wall that won't
permit CVS access so I'm not able to just grab the source anytime I want
to :-(
You can still use the viewCVS interface of sourceforge (it is
On Wed, April 6, 2005 12:12 pm, Miguel said:
No, you are right.
It is difficult to browse through the source code unless you know what you
are looking for.
Oh good, it's no fun looking stupid on a public forum :-)
Rich
---
SF email is
Is there any provision for defining via javascript what is in the applet's
pop-up menu? For my web pages I'd like to simplify things a bit and
redefine others.
Rich
---
This SF.net email is sponsored by: 2005 Windows Mobile Application Contest
On Tue, March 22, 2005 10:37 am, timothy driscoll said:
Eric suggested that the atom click also return, in some fashion, distance
and angle data. for example, the distance would be the distance from the
clicked atom to the previously clicked atom; the angle would include the
previous two
On Fri, March 11, 2005 1:06 pm, Bob Hanson said:
The problem is in the RES file decoder not recognizing EU1 as europium.
The shelx atom name is an arbitrary string that matches a corresponding
string in its scattering-factor definitions. To be perfectly general the
reader would need to parse the
On Wed, March 2, 2005 12:48 pm, timothy driscoll said:
On 2005-03-02 (11:13) Bob Hanson wrote:
I think it's way better that it supports the HTML instead of just
the=20 applet itself. In fact, I don't know exactly what the applet
itself=20 would mean. I definitely would need that LiveConnect
On Mon, February 28, 2005 11:56 am, Bob Hanson said:
[snip]
HOWEVER, it would be nice -- I'll bet Henry Rzepa knows how to do this
-- if when Java is not there they at least get a GIF or something that
points them to how to proceed. Would that be object code? For example,
jmol.js could be
On Mon, February 28, 2005 12:34 pm, timothy driscoll said:
if they are working correctly, the compatibility checks should not add any
overhead to Jmol operations as long as the system passes the checks.
Maybe not to operations but there would be some overhead to do the checks
in the first
On Wed, February 9, 2005 9:27 am, timothy driscoll said:
On 2005-02-08 (14:35) S. Frank Yan wrote:
Hi,
I was wondering if there is a way in Jmol to select those hydrogen
atoms that are bonded to nitrogen atoms. I could do this by
distance; however, it might be better to say something like
jmol
Warren, send me the RGB values for C,N,O,H,S and I will implement
set defaultColors pymol
Very nice!
Now if Waren would implement an equivalet to set colors Jmol I could get
rid of my colors file and make my make_a_png script independent of
everything except the coordinates file :)
Rich
Safari works correctly when I use jmolApplet(480,load /testmol.pdb); but
if I read the pdb contents into a string (properly constructed, it works
in FireFox) and use:
jmolApplet(480);
jmolLoadInline($pdb);
the I get a crash in Safari:
AppletRegistry.checkIn(jmolApplet0)
2005-01-06 10:48:44.747
98 matches
Mail list logo
