I can confirm John's observation, using a different 2D mol file.
load myMol.mol works
load myMol.zip give extra bonds (between close atoms)
This seems to be due to Jmol autobonding being applied in zipped files. If I
issue
set autobond off
before loading the zip file, then it renders
Do Jmol create a new thread for each script or is there a queue and one
thread executing each script on at a time?
Or in other words: If my GUI thread starts starts a Jmol script and after
that start another Jmol script, can I be sure that they are executed and
finishes in that order? That is:
there is a queue that handles all scripts. There are a few ways around it
with a Java application embedding Jmol, but any call to JmolViewer.script()
uses the queue.
On Mon, Apr 6, 2009 at 6:57 AM, Jonathan Alvarsson
jonathan.alvars...@gmail.com wrote:
Do Jmol create a new thread for each
I'll need to see those files. I suspect something is happening to the 2d mol
file when you are processing it; I'm not seeing the same problem with NIST
data. For example, I take the 2d file for cholesterol, put it in a zip file,
load the zip file, and it all works fine
Bob
On Sun, Apr 5,
Jairav,
Yes, that's right -- use the PDB format and designate your atoms as either
CA or P. In fact, you can even use the element symbol field (columns 78 and
79) to designate an element for coloring purposes
if you want independently of whether the atom name is CA or P
Also, then you can use
Aidar,
[switching to Jmol Developers list]
I'm really glad you are working with this. No one has updated this for some
time, and I'm not surprised it may be causing some difficulty for you.
1) Which version of Jmol are you using?
2) If you can, use a Jmol.jar file that was build with
Thanks for the reply. I will try it out with phosphorus atoms.
if you take a look at this image
http://www.umassmed.edu/faculty/graphics/182/DekkerFig2new.gif
In the way you see above, I'm trying to find a simple way to make a straight
line (which represents the gene) and pull together the
yes, that should work like a charm. Have fun with this!
On Mon, Apr 6, 2009 at 12:02 PM, Jairav Desai
jairavdesai2...@u.northwestern.edu wrote:
Thanks for the reply. I will try it out with phosphorus atoms.
if you take a look at this image
Feature Requests item #2738121, was opened at 2009-04-06 19:33
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I just want to confirm, so if I use the pdb format, I don't need to specify
these xyz coordinates? i can just specify the bonds?
2009/4/6 Robert Hanson hans...@stolaf.edu
yes, that should work like a charm. Have fun with this!
On Mon, Apr 6, 2009 at 12:02 PM, Jairav Desai
Feature Requests item #2738121, was opened at 2009-04-06 19:33
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What you don't need to specify are the bonds -- Jmol will connect them
sequentially.
On Mon, Apr 6, 2009 at 2:42 PM, Robert Hanson hans...@stolaf.edu wrote:
well, you definitely need some x,y,z coordinates. Look up the PDB format to
see what all is involved. Example abound.
On Mon, Apr 6,
Feature Requests item #2738121, was opened at 2009-04-06 12:33
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Date: Mon, 06 Apr 2009 12:29:00 +0200
From: Angel Herr?ez angel.herr...@uah.es
Subject: Re: [Jmol-developers] Incorrectly Drawn Bonds in Zipped 2d.mol
files
This seems to be due to Jmol autobonding being applied in zipped files. If
I issue set autobond off
before loading the zip file,
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