I'm looking for the equivalent to "getProperty ligandInfo" that will return the
complete list of names in HET or HETAM
definitely:
boolean isHetero = line.startsWith("HETATM");
On Fri, Jan 24, 2014 at 6:16 PM, Robert Hanson
mailto:hans...@stolaf.edu>> wrote:
select hetero
?
On Wed, Jan
http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.8_2014.01.24.zip
bug fix: y = ([3])[1][1] should be [3] not 3
bug fix: break n nonfunctional
bug fix: format() and label() functions limited to 4 arguments; should be
unlimited
bug fix: errors in paths to js code in web export templates.
currently up
I don't see the Jmol application as much more than a development tool. The
target environment for Jmol is a web page.
On Fri, Jan 24, 2014 at 11:18 PM, Ron Mignery wrote:
> I use the application, not the applet. Can I use the javascipt command
> there? The documentation describes the javascript
It is not the name of the added atom that is reduced. ALL side chain atoms
in all chains are reduced. For example, load 1PQA in the application, add a
single hydrogen to a water anywhere, exit the model kit and hover on any
sidechain atom anywhere. What was CB is now C, OG is now O, etc.
On Fri, 2
I use the application, not the applet. Can I use the javascipt command
there? The documentation describes the javascript command as applet only.
On Fri, 24 Jan 2014 at 5:08 PM, Robert Hanson wrote
>I would just use the javascript command to introduce your own audio
>components.
>On Wed, Jan 22
Definitely not PDB format. Why do people do this?
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
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, Le
Documentation for SMILES and SMARTS and Jmol bioSMILES/bioSMARTS are at
http://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/smiles/package.html
I'll be the first to admit that is obscure! And I see the change of code
location in SourceForge broke that link in the documentation.
I agree completely. Good catch!
$ show @{ ([3,4,5])[1][1] }
[3]
is correct. array[i][j] should always return an array, provided i <= the
length of the array.
This behavior is suggested by the documentation, and that it would return
just the number 3 is
unexpected.
Fixed for Jmol 14.0/1.8
Bob
definitely:
boolean isHetero = line.startsWith("HETATM");
On Fri, Jan 24, 2014 at 6:16 PM, Robert Hanson wrote:
> select hetero
> ?
>
>
> On Wed, Jan 22, 2014 at 12:16 PM, Jaime Prilusky <
> jaime.prilu...@weizmann.ac.il> wrote:
>
>> Thank you Angel for the explanation. Still looking for
select hetero
?
On Wed, Jan 22, 2014 at 12:16 PM, Jaime Prilusky <
jaime.prilu...@weizmann.ac.il> wrote:
> Thank you Angel for the explanation. Still looking for a solution.
>
> Jaim
> On Jan 22, 2014, at 5:00 PM, Angel Herráez wrote:
>
> > I'm guessing, but ATP may be recognized as "nucleic" b
This is fixed. May get a release today; more likely tomorrow.
On Fri, Jan 24, 2014 at 5:21 PM, Robert Hanson wrote:
> stranger than that... will fix
>
>
> On Wed, Jan 22, 2014 at 12:58 PM, Ron Mignery wrote:
>
>> Is break n broken in Jmol 14.0.4?
>>
>> function xxx {
>> for (i=0;i<4;i+
Where is the need for window.open() or window.location coming from in the
first place? Jmol has a WRITE command that would let you do that, I think.
Why not just use
write file "xxx.pdb"
That's much cleaner.
On Fri, Jan 24, 2014 at 12:13 PM, Roberto Mosca wrote:
> Ok, sorry, I could fix th
stranger than that... will fix
On Wed, Jan 22, 2014 at 12:58 PM, Ron Mignery wrote:
> Is break n broken in Jmol 14.0.4?
>
> function xxx {
> for (i=0;i<4;i++) {
> for (j=0;j<4;j++) {
> print i
> break 0
> }
> }
> }
>
> xxx
> 0 \
> 1 \ ok
> 2 /
> 3 /
>
> fun
Yes, that is correct. When a function is being used in a math expression,
all delays are disabled. Otherwise the script would hang in the middle of a
mathematics expression, and while that might be possible in Java, that
would be totally impossible to recover from in the asynchronous environment
of
Makes sense. There's no way to know the atom name.
On Wed, Jan 22, 2014 at 1:06 PM, Ron Mignery wrote:
> The atomName of all polypeptide side-chain atoms is reduced to just the
> element name when an atom is added anywhere with the model kit in Jmol
> 14.0.4.
> *example:*CB=>C
>
>
>
> -
I would just use the javascript command to introduce your own audio
components.
On Wed, Jan 22, 2014 at 1:27 PM, Ron Mignery wrote:
> Could a play command similar to the Java play function be
> added to scripting? This would allow clicks and beeps or even entire
> narrations to be added to Jm
I'd say congratulations are in order for just getting the protein there! :)
My guess is that you will see some sort of JavaScript error in the
JavaScript console. What happens when you debug this with the developer
console open or with the debugger running?
Debugging jQuery can be a real challen
I've had no problem with local files on a Windows PC using Firefox or
Chrome with appropriate settings. You can just set your security settings
back to "Medium" to be able to use older applets if you need to. No need to
change any security settings for the newer applets.
On Thu, Jan 23, 2014 at 7
Hi Margaret
It's working correctly for me in
13.28
14.0.7
14.1.6
May be your pdb file be altered?
Try with direct retrieval from the PDB:
load =4kjg.pdb;
Select *:a;
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CenturyLink Cloud: The Leader in Enterprise Cloud
Must have been a fluke; it works when I run a script.
Margaret
From: Franzen, Margaret
Sent: Friday, January 24, 2014 1:40 PM
To: 'jmol-users@lists.sourceforge.net'
Subject: select specified chain
Using Jmol 14.0.4 and 4kjg.pdb; trying to select all the atoms in chain a (or
b); 0 atoms are disp
Using Jmol 14.0.4 and 4kjg.pdb; trying to select all the atoms in chain a (or
b); 0 atoms are displayed
I've tried:
Select *a
Select *:a
Select chain='a'
Select chain="a"
I have no problems selecting in other pdb files...
Any suggestions?
Margaret Franzen
---
Ok, sorry, I could fix the problem by using window.open() instead of
setting window.location.
In any case, anyone can help me in understanding what happens?
Thanks in advance! :)
Roberto
On Fri, Jan 24, 2014 at 6:01 PM, Roberto Mosca wrote:
> Dear all,
>
> I am experiencing a strange problem
Dear all,
I am experiencing a strange problem with JSmol. I have a JSmol applet on my
page and a link to download the PDB file.
The link works by setting "window.location" to a php page that forces the
download of the PDB file (via headers like "Content-Disposition:
attachment; filename=...") wit
Hi to everyone !!
I tried to realize a kind of dialog window using Jquery Simplemodal in
which I would like to create a simple Jmol interface showing the proteins
and with some buttons for different actions. It is not the first time that
I implement an interface using Jmol/JSmol and everything was
car...@cerm.unifi.it
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