Is there an option for drawing water as crosses instead of spheres?
There is stars. I think you could use it for what you want.
If I remember correctly, Eric uses it in FirstGlance in Jmol.
Is there an option to 'set autobond OFF' only for water?
Don't think so, but maybe you can use
I don't use Pymol, but that doesn't sound bad -as long as it is not
difficult to implement.
By the way, I've recently known about an initiative to set a system
that translates between script languages: Pymol, Rasmol, Jmol are the
first targets. The idea is that you can use the scripting
El 1 Jun 2010 a las 7:37, jaime.prilu...@weizmann.ac.il escribió:
It seems that this only works on alpha helices, no effect on beta sheets.
What Bob meant is that he could expand the existing command so that
it affects beta sheets too.
I have no opinion about whether this should be done or
According to Angel Herráez angel.herr...@uah.es:
connect (water)(water) delete
Great, thanks. This works perfect.
Jaim
--
Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il
Head Bioinformatics|
RD Bioinformatics and Data Management |
Department of
Hello,
I'm trying to show the shrink-wrapped surface of a ligand in Jmol
-- but it appears that isosurface will simply render the portion of
the complete (i.e. all loaded models) solvent-accessible
surface. For a partially buried ligand, this breaks the surface
noticeably. geoSurface seems
If programs that remove the arrow heads from the helix cylinders also remove
the heads from the sheet boxes, then Jmol should do that, too. What does
Pymol do?
2010/6/1 Angel Herráez angel.herr...@uah.es
El 1 Jun 2010 a las 7:37, jaime.prilu...@weizmann.ac.il escribió:
It seems that this
First I've heard of it, though the last thing Warren and I were working on
before his unfortunate demise last fall was exactly this. We were not
optimistic that a general solution could be had. I hope they don't just try
to do this totally on their own -- it requires some substantial
understanding
Check the documentation regarding the isosurface command and the options
SELECT and IGNORE. Some combination of those two will do exactly what you
want. If you use SASURFACE and you want the same scale as geosurface or dots
or spacefill, be sure to use SASURFACE 0.
Some reason not to just use
On Mon, May 31, 2010 at 9:52 PM, Otis Rothenberger
osrot...@chemagic.com wrote:
Bob,
OK, I got it:
1. The url has to be encoded.
2. Which I tried before I wrote using ASP.NET UrlEncode
3) Hand entry of CCC%23C below works.
4) ASP.NET must be choking on # with Server.UrlEncode()
The # has
tisk tisk! Never use setTimeout to do the Jmol load. Use a call FROM Jmol
indicating it has loaded to trigger your AJAX call or whatever.
On Mon, May 31, 2010 at 6:02 PM, Otis Rothenberger osrot...@chemagic.comwrote:
Bob,
Right now I pass it from a server variable to a hidden field on the
Jmol 12.0.RC16 adds full support for SMARTS bond logic:
select smarts(A-,=;@A)
select all bonded non-aromatic atoms (AA)
that are connected by single or double bonds (-,=)
in rings(;@)
I believe I have a well-articulated schema for Jmol 3D-SMARTS. This can be
found at
At 2010-06-01 09:24, you wrote:
From: Robert Hanson hans...@stolaf.edu
Subject: Re: [Jmol-users] surface representations of atom selections
Check the documentation regarding the isosurface command and the
options SELECT and IGNORE. Some combination of those two will do
exactly what you want. If
Sure. That's better than geosurface. Geosurface should only be used with
full molecules, not partial surfaces, as it's rather ragged on the inside.
On Tue, Jun 1, 2010 at 8:53 AM, Roni Gordon roni.gor...@utoronto.ca wrote:
At 2010-06-01 09:24, you wrote:
From: Robert Hanson hans...@stolaf.edu
On Tue, Jun 1, 2010 at 9:03 AM, Otis Rothenberger osrot...@chemagic.comwrote:
Bob,
You may have told me before, but I forget. How do you signal JavaScript
that the Jmol applet is loaded? I've tried putting a Jmol javascript command
into the Jmol load script, but MSIE seems to ignore this.
Wayne, would you like to suggest a set of defaults that would work? Maybe in
consultation with your colleagues at U Mass?
Bob
On Tue, Jun 1, 2010 at 1:45 PM, Wayne Decatur wdeca...@yahoo.com wrote:
Hi Bob,
Anything that lowers the hurdle to bringing users view high quality visuals
when they
I made a change in the most recent development version of Jmol, but before
we consider it for Jmol 12.0, I'd like input:
Problem: JmolApplet.jar and JmolAppletSigned.jar are getting VERY large (2
Mb)
Problem: approximately 30% of the size of the applet is translations.
Comment: It seems
My opinion:
1. I agree that we must stress the recommendation to use the split applet
files. I'll take a look
at the Wiki page to reinforce this.
2. I don't agree about removing the translations from the monolithic applet. If
someone
decides to use it for some reason (e.g. for local testing
Bob,
This is the cat's meow. Thanks for the help. I'm still stuck with a
server side approach (AJAX very frustrating!), but the Jmol load
completed approach seems to work. Cholestane is below. What a slick way
to communicate 3D models via email:
Hi guys : The following code snippet is attempting to display a pdb file in
jmol, by getting it from the http location .
However, it bugs out on me, complaining that the file is not found at
'localhost:/http://www.rcsb.org/pdb/files/1I78.pdb1.gz'
jmolInitialize(jmol/,true);
Otis Rothenberger wrote:
Bob,
This is the cat's meow. Thanks for the help. I'm still stuck with a
server side approach (AJAX very frustrating!), but the Jmol load
completed approach seems to work. Cholestane is below. What a slick
way to communicate 3D models via email:
Same for me with Mac Mail.
***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***
On Jun 1, 2010, at 10:10 PM, rgb wrote:
21 matches
Mail list logo
