On 30/01/2008, Nicolas Vervelle <[EMAIL PROTECTED]> wrote:
> Noel O'Boyle a écrit :
> > (1) The link to the wiki on the front page of Jmol is broken
> >
> What link ?
> It's working for me (http://wiki.jmol.org)
Yes, that's the link. It's working no
(1) The link to the wiki on the front page of Jmol is broken
(2) Why isn't there something on the front page saying "Jmol book now
available"? It seems like the Jmol book is a secret. I think that
having a book available is a big vote in favour of any project,
especially an open source one, and ca
I've been seeing the exact same thing on WindowsXP/Firefox2.0/Java1.6.
The memory used creeps up after each reload, and then I need to
restart.
Noel
> From: Craig T Martin <[EMAIL PROTECTED]>
> Subject: Re: [Jmol-users] Jmol-users Digest, Vol 19, Issue 21
> To: jmol-users@lists.sourceforge.net
>
I've just updated to the latest prerelease 11.3.55 to use _slabPlane
(which is working fine).
However, mapping property_data onto an isosurface appears to be
broken. The simplest test is to use methane and the following code:
property_d = array(5,1,1,1,1) # C, H, H, H, H
isosurface sasurface 0 MA
> From: Bob Hanson <[EMAIL PROTECTED]>
> Subject: Re: [Jmol-users] General queries about slabs, arrays and
> mapping
> To: jmol-users@lists.sourceforge.net
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Noel,
>
> slab:
>
> Jmol 11.3.55 cl
Dear all,
I've been having a lot of success with Jmol now that I've gotten over
the inital activation energy. Before I write a blog post recording
what I've done and posting some pictures, I thought I might ask a
raise a few questions about random things that I came up against.
(1) Slabs appear t
> Hi,
>
> I'm a novice with Jmol and am trying to help a website migrate from
> chime plugin to Jmol. We've implemented a side-by-side molecule
> comparison using two Jmol applet instances and a drop-down menu of
> molecules using Jmol.js. Nothing fancy, but it's causing *lots* of
> browsers to cra
Thanks for all the suggestions...
Noel
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I am just starting to use Jmol and I would really appreciate some help...
I have a protein file, and I have a ligand file. Task 1 is to select
only those protein atoms within 6Ang of the ligand. Task 2 is to
display only these selected atoms. Task 3 is to draw the isosurface of
the selected atoms.
The answer is Yes - if you read the documentation a second time you
would have found the MAP option.
Noel
On 07/12/2007, Noel O'Boyle <[EMAIL PROTECTED]> wrote:
> Dear Jmol team,
>
> I would like to draw a VdW or Solvent Accessible Surface in the active
> site of a protein
Dear Jmol team,
I would like to draw a VdW or Solvent Accessible Surface in the active
site of a protein and colour it based on some property of the atoms
used to build the surface.
Is this possible with Jmol?
The most common use case is to colour the surface red for proton
donors, and blue for
Dear all,
I am drawing the SOLVENT isosurface around a protein, and used the MAP
keyword to colour using a cube file which consists of a grid over the
active site with values for the 'depth' from the protein 'surface'
(i.e. deep within the active site, the SOLVENT isosurface should be
blue, and cl
Hello again,
Miguel said:
>My only concern about adding explicit support for your NMR shift is that
>I
>assume that there are lots of atom properties and that each person is
>going to want to add his/her own property or two. I fear that will be a
>nightmare ...
No - there's no need for that! I'm j
plans to include
this in the program? (I want to interface gausssum.sourceforge.net with
Jmol in this way).
Regards,
Noel O'Boyle
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