Dear all,
How can I export the fractional coordinates of one specif frame having loaded
in Jmol a structure with several model?
I am asking that question because I experienced the following drawbacks:
Ok if I type var xyzCoord = {1.1}.label(" %16.9[xyz]"); print xyzCoord i get
Fe 0.355299979 0.355300009 0.355300009
Fe1 0.144699976 0.144699991 0.144699991
Fe1 0.644700050 0.644700050 0.644700050
Fe 0.855300009 0.855300069 0.855300069
O 0.555899978 0.944100022 0.250000030
O 0.249999970 0.555899978 0.944100022
O 0.944100022 0.250000060 0.555900037
O 0.444100022 0.055900037 0.750000060
O 0.750000000 0.444100022 0.055900037
O 0.055899978 0.750000000 0.444099993
When I do like var xyzCoord = {1.2}.label(" %16.9[xyz]"); print xyzCoord i get
Fe 0.355299979 0.355300009 0.355300009
Fe1 0.144699976 0.144699991 0.144699991
Fe1 0.644700050 0.644700050 0.644700050
Fe 0.855300009 0.855300069 0.855300069
O 0.555899978 0.944100022 0.250000030
O 0.249999970 0.555899978 0.944100022
O 0.944100022 0.250000060 0.555900037
O 0.444100022 0.055900037 0.750000060
O 0.750000000 0.444100022 0.055900037
O 0.055899978 0.750000000 0.444099993
Fe 0.355299652 0.355299652 0.355299652
Fe1 0.144700378 0.144700363 0.144700378
Fe1 0.644700468 0.644700408 0.644700408
Fe 0.855299592 0.855299652 0.855299592
O 0.555843592 0.944156408 0.249999940
O 0.249999970 0.555843532 0.944156349
O 0.944156468 0.249999881 0.555843532
O 0.444156408 0.055843621 0.749999881
O 0.750000000 0.444156408 0.055843621
O 0.055843592 0.749999940 0.444156379
which includes the second frame but also the first. Now if I type var xyzCoord
= {1.3}.label(" %16.9[xyz]"); print xyzCoord
I get 1, 2 and 3 and so on .
How can I make jmol printing just the coordinates which belongs to the second
frame or the third when i type {1.2}.label(" %16.9[xyz]") or {1.3}.label("
%16.9[xyz]")?
2) I cannot find in the script guide how to get the number of atoms of a
certain frame. For instance I have a MgO cell with 4Mg and 4O atoms how can I
know that the structure has 4 Mg and 4O?
Thanks, Piero.
--
Please consider the environment before printing this e-mail.
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
e-mail: pc...@kent.ac.uk
mobile: +44 (0) 7772-9756456
-----------------------------------------------------------
________________________________
From: Robert Hanson [hans...@stolaf.edu]
Sent: Thursday, September 02, 2010 6:40 AM
To: P.Canepa
Subject: Re: how export in fractional coordinates
Piero, let's work on communicating more clearly.
I can't process little tiny messages like that. If you are still having
problems with not being able to separate the two models, you need to send me
the file (again if necessary -- no attachments in any of these messages in this
thread) and explain exactly what you are having a problem with and what you are
expecting to accomplish.
It sounds like you are developing some interesting things, and I'm happy to
help you, but this particular thread is not working.
The best thing to do is to send me .jmol files that you create using
write xxxx.jmol
and then tell me exactly what commands you are having trouble with.
Also, for things like this that are simply "how do you use Jmol" questions, I
would appreciate it if you would address those to
jmol-users@lists.sourceforge.net<mailto:jmol-users@lists.sourceforge.net>, not
hans...@stolaf.edu<mailto:hans...@stolaf.edu>. That way others can help you at
least as well as I can, and in the process more people will learn.
Thanks,
Bob
On Wed, Sep 1, 2010 at 8:22 AM, P.Canepa
<pc...@kent.ac.uk<mailto:pc...@kent.ac.uk>> wrote:
there it is
--
Please consider the environment before printing this e-mail.
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
e-mail: pc...@kent.ac.uk<mailto:pc...@kent.ac.uk>
mobile: +44 (0) 7772-9756456
-----------------------------------------------------------
________________________________________
From: Robert Hanson [hans...@stolaf.edu<mailto:hans...@stolaf.edu>]
Sent: Wednesday, September 01, 2010 2:08 PM
To: P.Canepa
Subject: Re: how export in fractional coordinates
On Wed, Sep 1, 2010 at 7:32 AM, P.Canepa
<pc...@kent.ac.uk<mailto:pc...@kent.ac.uk><mailto:pc...@kent.ac.uk<mailto:pc...@kent.ac.uk>>>
wrote:
Please consider the environment before printing this e-mail.
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
e-mail:
pc...@kent.ac.uk<mailto:pc...@kent.ac.uk><mailto:pc...@kent.ac.uk<mailto:pc...@kent.ac.uk>>
mobile: +44 (0) 7772-9756456
-----------------------------------------------------------
________________________________________
From: Robert Hanson
[hans...@stolaf.edu<mailto:hans...@stolaf.edu><mailto:hans...@stolaf.edu<mailto:hans...@stolaf.edu>>]
What happens when you say
print {1.1}
print {1.2}
print {*}[0].model
?
Send me the file. That should work fine.
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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