On Sat, Jul 14, 2012 at 5:44 AM, Andreas Truszkowski <[email protected]>wrote:
> Hi together,
>
> I am new to JMol and I want to use it to visualize results from a
> Molecular Fragment Dynamics simulation. The idea is to handle the fragments
> as atoms thus I have to define my own elements.
>
> 1) Is it possible to define your own elements with their own names, colors
> , size(radius/volume), ... using the JMol scripting abilities.
>
yes. If by "element" you mean "element of the periodic table" or
"structural element" the answer is still yes.
color iron red
{_Fe}.color = "red"
{_Fe}.radius = 2.4
volume = 5
{_Fe}.radius = volume**(1/3)
@myelement atomno < 30
{myelement}.radius = 2
> 2) I want to use the XYZ-File format to code my fragment data. May I load
> several XYZ-Files in a single JMol view.
>
If you are creating data on the fly, the best thing to use is the LOAD DATA
script command. Do not use loadStringInline. It's not queued, and it's not
thread-safe. Try to do everything with the .script() method in JmolViewer.
load data "mydata"
3
test
C 3 3 4
O 3 2 1
C 3 4 2
end "mydata"
load data "append mydata"
3
test
C 10 3 4
O 10 2 1
C 10 4 2
end "append mydata"
This creates two models. You can display or hide them independently.
HOWEVER...
I suggest taking a look for "trajectory" in the documentation. With
molecular dynamics calculations you can be better off using load
TRAJECTORY, as it is much more memory-friendly. Doesn't allow displaying
two at a time, though.
> 3) When I use the attached class to access a JMol panel and the
> JmolSimpleViewer openStringInline method. I cant see any rendered atoms
> although the output console writes that atoms have been created:
> The Resolver thinks Xyz
> reading 9000 atoms
> ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
> 1 model in this collection. Use getProperty "modelInfo" or getProperty
> "auxiliaryInfo" to inspect them.
> Default Van der Waals type for model set to Babel
> 9000 atoms created
>
> Many thanks in advance.
>
>
Oh, I think they are there, but they are not connected and not visible for
some reason. Try
select *
or
spacefill 3.0
to see if you can find them.
> Kind regards,
> Andreas
>
>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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