Bob,
I had missed the capability of writing a data file as a zip file (xxx.jmol). I
suppose that after doing the compare command on two protein molecules that you
could write a xxx.jmol file rather than a xxx.pdb file? When I do this
operation, I use 'load' and 'load append' putting the
If the history file does not exist, HistoryFIle.getWindowPosition was
returning a null value for window position, throwing the exception. I don't
know why we haven't seen this before, unless we just haven't had any new
Jmol users lately or it's something I messed up very recently. Seems to me
we
That site is back up. I've also uploaded the documentation to sourceForge.
(which I was having trouble doing before)
On Thu, Aug 19, 2010 at 10:53 PM, Robert Hanson hans...@stolaf.edu wrote:
Thank you, Paul, for contacting us about this error. Looks like we had a
bug that only appears for
Karl, the .jmol file is simply a ZIP file. The WRITE command is configured
to automatically get the type of file from common extensions -- .GIF, .PNG,
.SPT, .WRL, etc., and .JMOL. But it's just a ZIP file. It contains:
- a manifest file that tells Jmol which file the autoload script is in.
- a
Hi,
is there a particular reason, why zShade Uses the value of the SLAB and DEPTH
settings to determine the point of no effect and full effect? I find it quite
limitating when I use zShade and slab/depth with slab on.
Alex
Hi,
I'm trying to get some nice settings for viewing specific parts of (large)
proteins. When you view a protein at a level of atomic detail (ball and stick)
and you dive into the protein it happens that atoms and bonds that obstruct the
view on the parts you want to focus, because they are in
Great idea! Exactly. The standard view is like looking through a telescope.
Still have atoms between you and the focal point. What you want is to be
there with no telescope. This is called
set navigationMode
:)
Bob
On Fri, Aug 20, 2010 at 1:01 PM, Alexander Rose alexander.r...@weirdbyte.de
Hmm. Darn. I guess I didn't think about that because I so rarely use that
combination The idea was to have the model fade out at the depth
setting, since there isn't anything to see beyond that, anyway. I suppose
what we need is zSlab and zDepth. Is thay your suggestion?
Bob
On Fri, Aug 20,
Hello,
I use Jmol as an applet for my protein-DNA database. I would like to
know how can I set the anaglyph view (red-cyan) so as to see the
structures in color. Or if the developer team has not already
developed I would like to know whether they will in the future or not.
Thank you very much
Hi Bob,
I'm interested in saving all the isosurface data in a given Jmol state as a
jvxl file. The idea is to not only save the Jmol state for later recall, but
also save all necessary isosurfaces so that when the state is recalled the user
does not have to wait for surface calculation.
I can
On Fri, Aug 20, 2010 at 6:56 PM, Eran Hodis eran.ho...@weizmann.ac.ilwrote:
Hi Bob,
I'm interested in saving all the isosurface data in a given Jmol state as a
jvxl file. The idea is to not only save the Jmol state for later recall, but
also save all necessary isosurfaces so that when the
Just added to Jmol 12.1.8:
print getProperty(shapeInfo.isosurface.ID)
isosurface1
s2
surface3
That is, if a property happens to be a list of associative arrays (a very
common thing), then whereas normally you would think you would have to do
this:
print
Oh, cool!
print getproperty(modelinfo.models.name)
[list of names]
print getproperty(modelinfo.models.modelProperties.frequency)
[list of frequencies]
Why didn't I think of this before??
Bob
On Fri, Aug 20, 2010 at 9:37 PM, Robert Hanson hans...@stolaf.edu wrote:
Just added to Jmol 12.1.8:
Three cheers for Phil! So good to see that this is all it is, so at least it
is an identified and easily fixable problem. If we wanted to, we could even
have the applet notify people of this issue if we wanted to. That might be a
bit of a hack, I suppose.
Bob
--
Robert M. Hanson
Professor of
[sorry about the delay -- I was at a conference, and this got buried]
cubic and square angstroms. You probably already figured that out
Bob Hanson
On Wed, Aug 4, 2010 at 10:32 AM, Victor Rosas Garcia rosas.vic...@gmail.com
wrote:
Hello everybody,
When using isosurface molecular volume
fixed. It will roll over with
0001
0002
like that. Come to think of it, we could even read those back in properly as
1 10001 Hmm.
On Tue, Aug 3, 2010 at 12:12 PM, Alexander Rose alexander.r...@weirdbyte.de
wrote:
Hi,
Jmol does a fine job reading pdb files with more then
not going to be changed, I think.
On Mon, Aug 2, 2010 at 10:15 AM, Paul Pillot
paul.pil...@ac-orleans-tours.fr wrote:
I've realized that the show sequence command doesn't report the insertion
codes, whereas the show residue command does.
I don't know if it is the expected behavior (for
well, that didn't work! I just uncovered this message in my inbox. Sorry
about that. It was a busy spring
In case you are still interested, the list of innovations for the last year
can be found at
http://chemapps.stolaf.edu/jmol/docs/examples-12/new12.htm
I'd love to hear as well what
Look what I just found -- Has it really been 6 YEARS?
Bob
-- Forwarded message --
From: jmol-users-requ...@lists.sourceforge.net
Date: Sat, Aug 28, 2004 at 11:15 AM
Subject: Welcome to the Jmol-users mailing list
To: hans...@stolaf.edu
Welcome to the
I do wish I hadn't missed this one Sorry Daniel -- it went under my
radar. This is what we just fixed. Oy, April!
On Thu, Apr 8, 2010 at 9:42 AM, Daniel Lundin daniel.lun...@molbio.su.sewrote:
Hi,
I am using rotateSelected and translateSelected to superpose two protein
molecules. My code
Sergio -- this message got lost. Very sorry. Remind me how alpha
transparency is SUPPOSED to work in relation to Pov-ray if you are still
interested. There was a problem with alpha translucency and I had to turn it
off. But if you need it, we might be able to try something.
2010/4/19 Sérgio
On Tue, Jul 13, 2010 at 1:34 PM, Shore, Jay jay.sh...@sdstate.edu wrote:
Any suggestions as to where I should look in the code to try
to remove this effect?
no idea. It's important it does it this way, actually. What were you
thinking would be better?
Thanks,
Jay
On 7/12/10 11:33
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