Hi,
I am fairly new to using Jmol and find it great tool for showing
undergrad students 3D images of crystal structure.
I have found that when I load a cif file of quartz using the following
command:
load /*file*/ quartz.cif {3 3 3};
I do not get the correct structure. Jmol seems to put
Hi people, i tried to use my page
http://pinostriccoli.altervista.org/?page_id=873 with JME sending the
code to JMOL. When drawing a simple cyclohexane, i have a planar ring
with the C6H12 formula. When i put a substituent on the ring, it becomes
as a cyclohexan should be in chair
On Fri, Oct 22, 2010 at 12:16 PM, Rzepa, Henry h.rz...@imperial.ac.uk wrote:
http://www.theregister.co.uk/2010/10/21/apple_threatens_to_kill_java_on_the_mac/
As of the release of Java for Mac OS X 10.6 Update 3, the version of Java
that is ported by Apple, and that ships with Mac OS X, is
At 11:24 +0100 22/10/10, Egon Willighagen wrote:
On Fri, Oct 22, 2010 at 12:16 PM, Rzepa, Henry h.rz...@imperial.ac.uk wrote:
http://www.theregister.co.uk/2010/10/21/apple_threatens_to_kill_java_on_the_mac/
As of the release of Java for Mac OS X 10.6 Update 3, the version of Java
that is
On Fri, Oct 22, 2010 at 12:33 PM, Rzepa, Henry h.rz...@imperial.ac.uk wrote:
http://lists.apple.com/archives/Java-dev/2010/Oct/msg00248.html
That expresses future aspirations, rather than testable reality. There is
nothing for
OS X at http://openjdk.java.net/
You can find instructions
Hi Pino,
Your problem is the following:
jmolLoadInlineScript( gid('editor').molFile()...
If you change .molFile to .jmeFile() it should load properly:
jmolLoadInlineScript( gid('editor').jmeFile()...
The minimize function in Jmol is very useful, but sometimes is gets
stuck in energy
Thanks Otis, it works good now ... really thanks. Pino
Il 22/10/2010 15.39, Otis Rothenberger ha scritto:
Hi Pino,
Your problem is the following:
jmolLoadInlineScript( gid('editor').molFile()...
If you change .molFile to .jmeFile() it should load properly:
jmolLoadInlineScript(
This is interesting and intriguing... What is the reason why Jmol
minimizes correctly the model coming from JME string but not the MOL
string?
As I said, I'm quite confident this is only a cyclohexane problem.
--
Nokia
Ha, ha
I think I remember that Bob implemented something to get
preferentially the chair conformation when the JME string was loaded
(and to automatically add hydrogens and run minimize). That is JME-
input-specific, and so does not apply to MOLdata.
But try and see what happens when you draw
Hi Angel and Pino,
Bob can speak to this better than I can, but as we worked on the use of
Jmol with JME, Bob made some specific 3D fixes - e.g.
cyclohexane/substituted cyclohexanes/alkynes. One sure route to these
fixes is the jme file load route. Although it's not in the documentation
that
Thanks, Otis. You're right.
There is some doc about the filters, particularly for JME strings, in
http://wiki.jmol.org/index.php/File_formats/Chemical_Structure#JME
I don't think I collated this info for MOLfiles.
That's right ... it works.
I've just tried the Pino's page and the raw way from the jme example page.
I didn't know was possible to load the .jme file directly in jmol, they are
loaded
immediately in 3D with all the sobstituent and with the right number of
bond.
I think it is quite amazing and
Hi all, today i tried and installed Jmol in Joomla. It's work and i hope
it will work in next days jmetojmol so i can use joomla for websites. It
takes always a bit of time with java. The real problem, at least for me,
is that in many templates php and html are written together ...
Julian, it's a bug in the CIF reader. A fixed version is at
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
Bob
ps; The basic problem, for the record, was this: There are two CIF terms
that introduce symmetry operators: _space_group_symop_operation_xyz, and
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