Hi Bob,
That's excellent - thanks very much for looking into it. I'll give the
'\?' a go soon. When will this be included in a publicly available
build, and which build(s) will it go into?
Thanks again,
Ian
Robert Hanson wrote:
OK, the \? is in and has been tested with CIF files. Jmol
Hi Bob,
Thanks for your message.
1) DO NOT poll the applet with a setTimeout(). This will occasionally
crash the applet and could cause one of the strangest bugs in Firefox
-- while polling, if you type in the address line, your text comes out
sdrawkcab. No kidding. I kid you not.
That's
Ian,
You are very welcome. It was just a few lines of code.
You can get the file now --
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
Should be released later this week as Jmol 11.7.34.
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
OK, two threads of discussion here.
1) DO NOT poll the applet with a setTimeout(). This will occasionally crash
the applet and could cause one of the strangest bugs in Firefox -- while
polling, if you type in the address line, your text comes out sdrawkcab. No
kidding. I kid you not.
2) You need
OK, the \? is in and has been tested with CIF files. Jmol doesn't allow * at
the beginning of atom names, and some PDB atom names already have * in them,
so \* is not an option. But what you can do is match specific numbers of
characters, and make that wide enough to encompass all reasonable
I'm neither a _javascript_ programmer nor a proficient Jmol scripter but
would these options be workable with those technologies:
1. Is there a way to check if Jmol is ready (either in _javascript_ or
Jmol)? Do somehting like this:
while(! isJmolReady()) {
wait for 0.1s
}
Call the Jmol
Hi Chris,
Thanks for your suggestions.
I'm not too sure about your suggestion 1 - perhaps a Jmol expert will
know how to check if Jmol has finished loading the molecule?
However, your suggestion 2 has got me somewhere. I modified my
javascript so that if 'jmolGetPropertyAsArray(atomInfo,
Hi Angel,
Angel Herráez wrote:
In my experience, the only safe solution is to have Jmol call the
javascript, and to include that call in the jmolApplet() call itself.
So, it could be something like
jmolApplet(300, 'load myFile.cif; javascript parseAtoms(); ')
I tried what you suggested
I'm not too sure about your suggestion 1 - perhaps a Jmol expert will
know how to check if Jmol has finished loading the molecule?
I would say that is exactly what the LoadStructCallback function
does. That's the best choice in my opinion.
Cannot imagine why it is not working.
Sounds good. Glad I could help. :)
Chris
Ian Thomas wrote:
Hi Chris,
Thanks for your suggestions.
I'm not too sure about your suggestion 1 - perhaps a Jmol expert will
know how to check if Jmol has finished loading the molecule?
However, your suggestion 2 has got me somewhere. I
Again, this won't solve the ? problem but it may be a way of avoiding
the issue. A simple script to change all ? characters in atom names to
$ (or whatever character might be legal in CIF files and convenient in
Jmol scripts) would be an easy solution. If you don't want to alter your
CIF
Rich, what you can do to select 'C33?' is
select C33? and not C33
If you also have C330 or C331 then you will have to exclude those
explicitly:
select C33? and not (C33,C330,C331)
Bob Hanson
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
Hi Bob,
Thanks for your message.
Your suggestions would be great if I knew a priori what the atom labels
up to the '?' were, but I don't. I need a wildcard filter that selects
all atoms whose names end with (or even just contain) a literal '?'.
Before I had this problem, as a new Jmol user I
This is a good suggestion Chris. For Ian's problem (since it is a
well-defined in-house setup) the preprocessing could change the ? of an
atom name to disordered (no need to stick with one character).
Rich
On Wed, April 15, 2009 9:05 am, Chris Foley wrote:
Again, this won't solve the ? problem
Thanks. :)
Similar to Bob's suggestion, how about:
select C33? and not
(C33,C330,C331,C332,C333,C334,C335,C336,C337,C338,C339)
Are letters allowed?
select C33? and not
(C33,C330,C331,C332,C333,C334,C335,C336,C337,C338,C339,C33a,C33b...)
Clumsy but easily generated.
As a suggestion
Hello,
I'm sure there's a really easy way to do this but as a new Jmol scripter
I'm struggling to see how! I need to write a Jmol script to select all
atoms with names ending in '?'. My input file is a CIF and the presence of
a trailing question mark in the atom name indicates a disordered atom,
Hello Ian
I'm sorry to say that I have no experience with CIF files. That ? character is
quite a bad
choice.
I had a similar problem once with PDB files having * in their atom IDs, and
solved it using
? as the wildcard. Not usable for you ;.(
Regarding your javascript method, the problem of
On Tue, April 14, 2009 3:02 pm, tho...@ccdc.cam.ac.uk wrote:
Hello,
I'm sure there's a really easy way to do this but as a new Jmol scripter
I'm struggling to see how! I need to write a Jmol script to select all
atoms with names ending in '?'. My input file is a CIF and the presence of
a
Hi Rich,
My input file is a CIF and the presence
of
a trailing question mark in the atom name indicates a disordered atom,
e.g. 'C33?'.
Is this construct a legal CIF atom_site_label Ian? As far as I am aware
the CIF dictionary doesn't allow for that type of label. Or is this just
for
tho...@ccdc.cam.ac.uk wrote:
Hi Rich,
My input file is a CIF and the presence
of
a trailing question mark in the atom name indicates a disordered atom,
e.g. 'C33?'.
Is this construct a legal CIF atom_site_label Ian? As far as I am aware
the CIF dictionary doesn't allow for that
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