Hi there! I will send this to the lammps and the jmol list, because any
solution will probably involve either of the programs :)
I have problems when reading a lammps xyz trajectory with jmol :(
It's a system consisting of LJ particles and a metal, in different parts of
the box, obviously
;)
Greetings, Pim
On Mon, Jan 18, 2010 at 5:36 PM, Robert Hanson hans...@stolaf.edu wrote:
That would be crucial for sure. Not necessary, though to load as a
trajectory if you only want a few models. Just load the file normally.
On Mon, Jan 18, 2010 at 9:35 AM, pim schravendijk pimli
Thanks! That works perfectly!
greetings, Pim
On Tue, Jun 23, 2009 at 7:18 PM, Robert Hanson hans...@stolaf.edu wrote:
Hi, Pim,
On Tue, Jun 23, 2009 at 8:38 AM, pim schravendijk pimli...@googlemail.com
wrote:
hi!
Now the printing part:
For frames that are counted as x.y, load
parameters? How do they
indicate to do this?
Bob
On Tue, Jun 23, 2009 at 4:12 AM, pim schravendijk
pimli...@googlemail.comwrote:
if you really really really would need to perform operations on all
the frames, you could also split the xyz before reading them in jmol:
Say, if you have 1 atoms
+ }) }
because that will evaluate the string ({0}) at run time, and that will be
turned into a bitset.
On Wed, Jun 17, 2009 at 5:24 AM, pim schravendijk
pimli...@googlemail.comwrote:
Hi!
it seems that the scriptevaluator does not recognize my bitset as a
bitset when I try to put a variable
Hi all,
I would like to disable the automatic calculation of bonds on startup. This
is needed for viewing large metal structures.
There is an option in edit-properties-Bonds and then Don't Compute
Bonds.
However: It doesn't seem to do anything. I tried setting autoBonds in
Hi there again!
2 minor oddities I found when opening a simple script with jmol commands in
11.4.1:
..1.. when writing to povray in a script, it is bothered by relative paths
in the output filename:
In other contexts, relative paths work, for example, this works:
$ write JPG ./out.jpg
type=JPG;
. Maybe Bob can
elaborate?
Frieda
On Nov 7, 2007, at 1:46 PM, pim schravendijk wrote:
You should set:
hermitelevel =5;
in your jmol script. That will make your trace look much better in jmol!
And povray just copies that. So actually it was already looking irregular in
jmol, just less
of no_shadow
elements in both. So I did not try removing them from mine.
On Nov 7, 2007, at 1:08 PM, pim schravendijk wrote:
I have no idea about the lack of smoothness, but the fact that no shadows
are present might be understandable. There are by default no shadows in the
povray output for jmol
I have no idea about the lack of smoothness, but the fact that no shadows
are present might be understandable. There are by default no shadows in the
povray output for jmol. They can be turned on by removing the no_shadow
elements in the povray script. I will make this more easy to do, and maybe
Test of the resize script:
Most models there automatically resize fine.
BUT: watermo, bdno, and t2 seem to crash (black screen, mouse still
works) when I increase the size above a certain point (or too fast).
Memory usage at the point of crash is still under 64 MB. Reloading the
page doesn't
Strangely enough I didn't manage to start the Java console.
I followed the instructions here:
http://www.java.com/en/download/help/521200.xml
but no console started. Has anyone experience with this? Maybe I need
to make sure java quits and then restarts.
At my second try watermo didn't crash
So many options, I'm getting confused :) Just for completeness: in
which cases should one call variables via @variable?
On 10/14/07, Frieda Reichsman [EMAIL PROTECTED] wrote:
Thanks, Bob - does the trick, and makes more tricks possible.
Frieda
--
Greetings, Pim
http://www.molmod.com
I couldn't use Jmol to open a 185 MB multiframe xyz file. I increased
the memory available for java (via -Xms and -Xmx) to 1 GB, but this
didn't help. The file opens in vmd without problems, using 5 % memory
on a 1 GB system. That is about 50 MB, java allocates 64 MB on default
(one can see that
On 10/5/07, Bob Hanson [EMAIL PROTECTED] wrote:
load myfile 3
loads just the third frame. Haven't considered
load myfile 3-4
But it's certainly worth looking at. Only problem here is that it would
require some retooling of all the multifile readers. Not so bad, really,
but a task.
Ah
After I have read Bob's recent explanation on bond orders in Jmol
OK, here is a total generalization of partial bonds. With this (11.3.28)
you can draw any type of partial whatever up to 5 bonds. Works in
bondOrder and connect, both:
Did you get the latest CVS already? Your version
On 9/29/07, Latévi Max LAWSON DAKU [EMAIL PROTECTED] wrote:
Dear all,
I cannot figure out wether it is possible to
have a povray renderering of a whole Jmol
scene that contains polyhedra and other
drawn objects. I have had no success so far.
Does support exist for doing such a thing ?
Oh, and could you (or someone else) update this fixes to the
wiki.jmol.org page as well? Since you are apparently the last person
who followed the instructions of that page you probably know best how
to put it :)
On 9/26/07, Shiller, Paul J. [EMAIL PROTECTED] wrote:
The following fix was sent to
I'm sorry, I have no experience with MOPAC, but just a few hints:
Jmol should be able to read mopout and graphf files:
http://wiki.jmol.org/index.php/File_formats#MOPAC
http://openmopac.net/manual/graph.html
You will probably need the mo or isosurface command
I've just been playing around with the molecular workbench 3D modeler,
which has a completely different menu structure, but it's no effort at
all to work with this new menu set. Actually I am glad they didn't
leave the jmol interface and put everything under 'macros' for
example, it would have
Excellent looping (I didn't like the looping before much), and pretty
straightforward to understand, but why the goto? For all fortran
addicts? :)
I didn't install the new release yet, will jmol still interpret
javascript in load files? Can the languages be mixed?
On 9/16/07, Bob Hanson [EMAIL
In Jmol, you can use the SMILE notation to select (sub)groups of
connected atoms, e.g.:
select substructure(C(O)C)
That's the reason there is a SMILES package in Jmol.
On 8/21/07, Li Yang [EMAIL PROTECTED] wrote:
Has anyone try view SMILES molecules in Jmol? Are there any examples
and
That is an impressive program! But as far as I can see, the builder in
that suite is also using the Jmol interface. Porting the building
capacity to Jmol shouldn't be too much of a problem then, should it?
On 9/4/07, Bob Hanson [EMAIL PROTECTED] wrote:
no plans for this as part of Jmol itself.
Couldn't you just add the string ;color isosurface red to the end of
the command that is send to jmol? That way it still send one _line of
text_, but due to the semicolon that can be multiple commands. I can't
imagine something like that is not possible in javascript. Otherwise
show the part of
I just tried, when I select a new molecule on the left it opens with
the original settings. Then I change it, select the other molecule,
and go back again, and all changes are lost, back to default as well.
So, the applet seems to have the behavior you want, at least here.
Using firefox on linux,
I would be pretty happy with these features as well, and would like to add:
- the possibility to switch between the unit cell and filled
supercell representation (only adding copies of those atoms that are
filling the unit cell).
- the possibility to create periodic copies of the unit cells /
On 7/4/07, Eric Martz [EMAIL PROTECTED] wrote:
save early and often comes to mind. Especially, save before you go
elsewhere to do some research even though you haven't finished your edit!
-Eric
I also noticed the logging out, is this a new feature or was it always
like this? I was saving
Also check the information on:
http://wiki.jmol.org/index.php/Jmol_Applet
and
http://wiki.jmol.org/index.php/Files_Description
On 6/26/07, Angel Herraez [EMAIL PROTECTED] wrote:
Hello, David
Are there any tutorials currently available for inserting the applet into a
webpage?
Not very
I think that Bob puts the documentation online the moment a
functionality is in the newest code. Actually, all software
documentation should be like this, don't you think?
Therefore, try to get the prerelease (at 11.1.48 now so still to old)
or get the code via SVN and build it, that should
On 6/13/07, Angel Herraez [EMAIL PROTECTED] wrote:
I understood that iPhone uses plain MacOSX, so how is Java prevented
from working? Do they block installation? What happens with other plugins,
like Flash? Can't the browser be supplemented?
If it is true that he puts MacOSX in mobile phone,
At 17:12 05/06/2007, [EMAIL PROTECTED] wrote:
I was wondering if any of you could recommend a program that would allow me
to create the molecules so that I could load them into Jmol.
The dundee Prodrg server lets you draw a molecule in an applet, then
do some configuration optimization on it.
Wouldn't a program like this deserve a publication? rasmol had some,
back in the days ( http://www.umass.edu/microbio/rasmol/rasbib.htm ).
The flexibility of in-webpage jmol, the new density map algorithm by
Bob Hanson, etc. this is all pretty advanced and new stuff.
On 6/4/07, David Leader
Dear Jmol people,
As a jmol user, I am highly impressed of all the new features that
jmol has gotten in the last year, it's becoming an amazingly versatile
program.
BUT, I just noticed that I really lost track of all the features that
have been implemented and are still being implemented. There
Hi again!
All the main info is there, especially the very good /doc/ page at
stolaf. The biggest problem is that the rest of the website is very
dispersed. The sourceforge page is hard to change, being old-style
html :) so the wiki must be the way to go then. I will see if I can do
something
34 matches
Mail list logo
