Hi,
@Robert: Thank you very much for your detailed answer.
One problem is still open. I will display molecular fragement data
consisting of fragments like methane, water, benze, .... and I only have
the coordinates of this fragments. Hence I use the XYZ file format to
describe my data. But how can I define my own symbols (including color,
size(radius/volume)) to avoid the following error messages:
'Et' is not a recognized symbol
'H2O' is not a recognized symbol
Kind regards,
Andreas
Am 14.07.2012 18:22, schrieb Robert Hanson:
On Sat, Jul 14, 2012 at 5:44 AM, Andreas Truszkowski
<[email protected] <mailto:[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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