According to "Robert Hanson" <[EMAIL PROTECTED]>:
> simple typo. Will be corrected in next versions of 11.6 and 11.7 -- need
> this sooner?
Bob,
There's no need to hurry.
We can keep testing and developing on older Jmol versions
until the new comes out.
Thanks again,
Jaim
--
Dr Jaime Prilusky
According to "=?ISO-8859-1?Q?Angel_Herr=E1ez?=" <[EMAIL PROTECTED]>:
> I've done some test, and this looks like a bug.
> My DX file loads Ok in 11.2.14, 11.4.6, 11.5.6, but not in 11.6.4
Angel,
Thanks for a prompt reply.
Jaim
--
Dr Jaime Prilusky | [EMAIL PROTECTED]
Head of
simple typo. Will be corrected in next versions of 11.6 and 11.7 -- need
this sooner?
On Mon, Nov 10, 2008 at 6:10 PM, Robert Hanson <[EMAIL PROTECTED]> wrote:
> OK, I'll look at that tonight.
>
>
> On Mon, Nov 10, 2008 at 5:09 PM, Angel Herráez <[EMAIL PROTECTED]>wrote:
>
>> On 10 Nov 2008 at 15
Are you sure you're just not setting the range to your liking?
On Mon, Nov 10, 2008 at 6:21 PM, Frieda Reichsman <[EMAIL PROTECTED]> wrote:
> Any chance this would be a realistic feature request? For secondary school
> teaching purposes we use the simpler, bwr color scheme that students are
> alr
Any chance this would be a realistic feature request? For secondary
school teaching purposes we use the simpler, bwr color scheme that
students are already familiar with. It can be difficult for some
students to have to shift gears to another scheme. And showing areas
that are hydrophobic i
ah -- ok, I see. Well, that sounds terrific. I'd be interested just in
peeking at the C code, then, in that case. Just to see what sort of
considerations you made. Who knows. It might be an almost trivial addition
to Jmol.
Bob
On Mon, Nov 10, 2008 at 11:36 AM, David Leader <[EMAIL PROTECTED]>wro
no, sorry. I'd love to know what Chime was calculating; I'm guessing it was
pretty minimal processing and not something that was truly realistic. But I
could be wrong. That's the problem with a proprietary code such as Chime --
you never know if what you see really means anything.
Bob Hanson
On M
OK, I'll look at that tonight.
On Mon, Nov 10, 2008 at 5:09 PM, Angel Herráez <[EMAIL PROTECTED]> wrote:
> On 10 Nov 2008 at 15:42, Robert Hanson wrote:
>
> >
> > I'll need a sample file
>
> The dx is 11 MB. I've packed it together with the original pdb file in
> http://biomodel.uah.es/angel/liso
no, I don't think so.
On Mon, Nov 10, 2008 at 5:46 PM, Frieda Reichsman <[EMAIL PROTECTED]> wrote:
> Hi Bob,
>
> Is there a mechanism, with the rwb or bwr colorshemes, for widening
> the white areas between the red and blue? Many published EP surfaces
> show large neutral regions; I have not figu
Hi Bob,
Is there a mechanism, with the rwb or bwr colorshemes, for widening
the white areas between the red and blue? Many published EP surfaces
show large neutral regions; I have not figured out how to get Jmol to
do this in rwb. These regions are green in the more extended color set.
Than
OK, I will see about contacting them.
On Nov 10, 2008, at 5:28 PM, Robert Hanson wrote:
OK, those files contain basically the same information as an
isosurface -- vertex list, vertex color, vertex value (several!),
and triangles list. That's all you need to do just about anything in
Jmol w
On 10 Nov 2008 at 15:42, Robert Hanson wrote:
>
> I'll need a sample file
The dx is 11 MB. I've packed it together with the original pdb file in
http://biomodel.uah.es/angel/lisozima.zip
-
This SF.Net email is sponsored b
I know this was brought up many months ago From what I could gather from
a search of the archives is that this is apparently hard to do. In
Chime, it is nice to show those small molecules and compare their water
solubility. It was not clear if anyone had taken on the task. Has anyone
worked on
OK, those files contain basically the same information as an isosurface --
vertex list, vertex color, vertex value (several!), and triangles list.
That's all you need to do just about anything in Jmol with a surface. Can't
create a JVXL file. But if this data really is isosurface data, then it
migh
I'll need a sample file
On Mon, Nov 10, 2008 at 3:15 PM, Angel Herráez <[EMAIL PROTECTED]> wrote:
> Hi Jaime
>
> Have you checked
> http://wiki.jmol.org:81/index.php/File_formats#Open_DX
> ?
> There is some info and 3 links there
>
>
> I've done some test, and this looks like a bug.
>
> My DX fi
Hi Jaime
Have you checked
http://wiki.jmol.org:81/index.php/File_formats#Open_DX
?
There is some info and 3 links there
I've done some test, and this looks like a bug.
My DX file loads Ok in 11.2.14, 11.4.6, 11.5.6, but not in 11.6.4
After
load "lisozima.pdb";
isosurface "lisozima.pqr.potent
Hi,
Do you have an example on how to load/display data from
a .dxf (DX) file on Jmol 11.5.51 ?
This is what I have (and it's not working)
jmolInitialize('/wiki/extensions/Jmol');
jmolApplet(400, 'isoSurface file "/wiki/support/g_slide1.dx"');
Java Console reports:
data file type was de
I am sending the efvet file under separate cover as it is 2.4 MB.
(Apparently it is in xml format, whereas I had thought that efvet
referred to the format) It is from a single protein chain of the pdb
file 1LMB (efvet files also can contain information for multiple
chains). Here is what the
Bob wrote:
It might be interesting to see how the HBplus program works. I see
http://www.csb.yale.edu/userguides/datamanip/hbplus/algorithm.txt
but that suggests there is no energy calculation here, just a set of
angle/distance rules.
HOWEVER -- NOTE!!! The HBPlus program itself is not public
we had a machine failure on chemapps.stolaf.edu -- that site is temporarily
unavailable.
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it
Sounds very interesting. What's more, Jmol could display the data as JVXL
files possibly and compress the data immensely.
Do you have some of these files, Frieda?
On Mon, Nov 10, 2008 at 9:48 AM, Frieda Reichsman <[EMAIL PROTECTED]> wrote:
> Hi Bob,
>
> eF-site ( http://ef-site.hgc.jp/eF-site/ )
Hi Bob,
eF-site ( http://ef-site.hgc.jp/eF-site/ ) is a database for molecular
surfaces, coloring by electrostatic potential. Seems like the entire
contents of the pdb is available - a great resource. The MEP data can
be obtained in an "efvet" file, described here:
http://ef-site.hgc.jp/eF-s
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