>> 2. set connect false/save (and initscript parameter)
>>
>> For complex structures RasMol and Chime usually ignore CONECT records
>> in .pdb files and use their own internal algorithms to determine
>> bonds. This means that structures with 'unusual' bond lengths, e.g.
>> ionic and metal lattices
Using JavaScript:
Almost all attributes can be set through the scripting language. There
currently are no 'getter' methods.
Using Java:
All attributes are available for getting and setting
Not sure what you mean by 'display settings'.
Sorry, that wasn't clear enough. The Jmol applet version I use
At 06:07 04/11/2003 -0500, timothy driscoll wrote:
at 11:22 am EDT on (Tuesday) 4 November 2003 Sebastian Lisken said:
> Hi again, the recent discussion I joined was about .pdb files and
> the "set connect" script command. Miguel said that when there is
> bond information in a file, Jmol should st
> Just one issue - getter and setter method for the applets
> display settings would be good.
It is not clear to me what level you are referring to ... JavaScript code
using the standard applet or Java code embedded into a 'custom' applet.
Using JavaScript:
Almost all attributes can be set throug
[Egon points out that CML2 could be better]
If there's a variant of CML where I could specify bonds
even if don't know bond orders, my particular requirements
would be met. Assuming, as Miguel is pointing out, that
Jmol would stick to that information as soon as it appears
in the CML file. Pointer
On Tuesday 04 November 2003 14:55, Sebastian Lisken wrote:
> > It looks like proper CML1... (and it is valid according to the CML1 DTD)
> > So, it should work, but it is not... bonds are not read, so Jmol thinks
> > the file does not have bonds... this is a bug in the CMLReader...
>
> It's adapted
It looks like proper CML1... (and it is valid according to the CML1 DTD)
So, it should work, but it is not... bonds are not read, so Jmol thinks the
file does not have bonds... this is a bug in the CMLReader...
It's adapted from some CML that the old version of the applet
did read, and now I seem
> Hi again, the recent discussion I joined was about .pdb files and the
> "set connect" script command. Miguel said that when there is bond
> information in a file, Jmol should stick to it, and I wonder if this
> would apply to all formats.
Jmol is a visualization program, not a calculations progra
On Tuesday 04 November 2003 11:22, Sebastian Lisken wrote:
> Hi again, the recent discussion I joined was about .pdb files and
> the "set connect" script command. Miguel said that when there is
> bond information in a file, Jmol should stick to it, and I wonder
> if this would apply to all formats.
at 11:22 am EDT on (Tuesday) 4 November 2003 Sebastian Lisken said:
> Hi again, the recent discussion I joined was about .pdb files and
> the "set connect" script command. Miguel said that when there is
> bond information in a file, Jmol should stick to it, and I wonder
> if this would apply to al
Hi again, the recent discussion I joined was about .pdb files and
the "set connect" script command. Miguel said that when there is
bond information in a file, Jmol should stick to it, and I wonder
if this would apply to all formats. Back in the days of CaGe
development, the suggestion was made to i
-Original Message-
From: PHILLIP W BARAK [mailto:[EMAIL PROTECTED]
Sent: 29 October 2003 17:23
To: Miguel
Cc: [EMAIL PROTECTED]; Geoff Rowland;
[EMAIL PROTECTED]; [EMAIL PROTECTED]
Subject: Re: [Jmol-users] JmolApplet Wish List[AV Scanned]
- Original Message -
From: Miguel
> My message mainly was about not forgetting my requirements,
> when I saw that others may have similar ones.
> ...
> Just wanted to point out that relying and possibly
> improving the applet's "smartness" in terms of bonds and
> positions may not be all that users want.
You are absolutely right.
Hi again - apologies if my email came over as a complaint. I
was very happy with Jmol and with the support I got from people,
including Egon, at the time. I did submit changes to Jmol to the
list, and interest was expressed, and when I say that these
changes got lost I meant that development of the
On Wednesday 29 October 2003 21:17, Miguel wrote:
> > It is a while ago, and I am no longer working on that project,
> > but you might remember me asking something similar in 2000.
>
> I only started working on Jmol code in 2003.
I should know, but I can't remember... Jmol is not the only thing I
On Wednesday 29 October 2003 22:41, PHILLIP W BARAK wrote:
> > Jmol v8 has very limited support for PDB files... it reads only
> > the atomic
> > coordinates and the unit cell parameters, and symmetry operations
> > are not yet
> > supported... I am not sure what you mean with tiling, but what
> >
- Original Message -
From: "E.L. Willighagen (Egon)" <[EMAIL PROTECTED]>
Date: Wednesday, October 29, 2003 1:15 pm
> > > Phillip Barak of the University of Wisconsin USA recently sent me
> > > a link
> > > that shows some excellent web pages with inorganic molecules. You
> > > shouldtake
> Miguel wrote:
> [Praise for JMol's bonding algorithm, and a request for
> molecules not rendered properly]
I apologize ... I certainly didn't mean to come across as 'praising' the
Jmol bonding algorithm.
I tried to make clear that the bonding criteria are taken from OpenBabel.
The 'praise' I g
Miguel wrote:
[Praise for JMol's bonding algorithm, and a request for
molecules not rendered properly]
It is a while ago, and I am no longer working on that project,
but you might remember me asking something similar in 2000.
Out of sentimentality, I'm still lurking. I used an old version
of the JM
On Wednesday 29 October 2003 18:23, PHILLIP W BARAK wrote:
> > > Just discovered, downloaded and spent a few hours playing with
> > > Jmol-8/JmolApplet-8 and the ?sneak preview? of Jmol-10. ABSOLUTELY
> > > BRILLIANT!
> >
> > Glad that you like Jmol
> >
> > > The materials I have been working on ha
- Original Message -
From: Miguel <[EMAIL PROTECTED]>
Date: Wednesday, October 29, 2003 9:19 am
Subject: Re: [Jmol-users] JmolApplet Wish List
> > Just discovered, downloaded and spent a few hours playing with
> > Jmol-8/JmolApplet-8 and the ?sneak preview? of J
> Just discovered, downloaded and spent a few hours playing with
> Jmol-8/JmolApplet-8 and the sneak preview of Jmol-10. ABSOLUTELY
> BRILLIANT!
Glad that you like Jmol
> The materials I have been working on have been mainly targeted at
> pre-university level (AS and A2 level in UK edu-speak) an
Hi,
Just discovered, downloaded and spent a few hours playing with
Jmol-8/JmolApplet-8 and the ‘sneak preview’ of Jmol-10. ABSOLUTELY
BRILLIANT!
I have been tinkering with web-based educational materials using Chime for
several years but have been totally frustrated by inconsistent behaviour
with
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