The word "autobond" does not occur in the Jmol script manual.
Please add "set autobond on|off" to your list for the next manual update, Bob.
Thanks, -Eric
At 1/25/06, you wrote:
Hi Francois
What you need is to deactivate autobonding.
On a previos post
http://sourceforge.net/mailarchive/messag
>> Correct. If no connectivity information is presented then Jmol will
>> calculate connectivity.
>
> OK
>
>> > but I would expect Jmol to follow the connectivities
>> > if the list of connections is provided in the CML file
>> > (and not to add new ones).
>> >
>> > Am I wrong ?
>>
>> You are corre
Quoting [EMAIL PROTECTED]:
> In fact, his example contains bond informations:
>
>
>
>
> Apparently, Jmol doesn't understand them.
>
> For what I understand from the code of CMLReader, the reader expects to ha=
> ve the atom ids in the atomRefs attribute, not the atom numbers.
My mist
Quoting Miguel <[EMAIL PROTECTED]>:
Oh oh, I am not sure you understood exactly what I wanted to say ;-)
I _do_ have a list a connectivities in the CML file...
Please see:
http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-56/tripos2.mol2.cml
> > I can understand that Jmol calculates its own
De: "Miguel" <[EMAIL PROTECTED]>
>
>Francois indicated that his CML files have no connectivity information. If
>he uses 'set autobond off' then he will have only atoms, with no bonds at
>all.
In fact, his example contains bond informations:
Apparently, Jmol doesn't understand them.
>
> Hi Francois
>
> What you need is to deactivate autobonding.
>
> On a previos post
> http://sourceforge.net/mailarchive/message.php?msg_id=12416924
> Miguel sayed:
> Jmol prerelease 10.00.21 is now available
> It includes support for:
> 2. "set autobond off" can be used before loading any f
Francois wrote:
> This means that the CML files do countain the
> connectivities between the atoms.
[snip]
> I can understand that Jmol calculates its own
> connectivities based on atom
> distances in the absence of connectivity information,
Correct. If no connectivity information is presented th
Hi Francois
What you need is to deactivate autobonding.
On a previos post
http://sourceforge.net/mailarchive/message.php?msg_id=12416924
Miguel sayed:
Jmol prerelease 10.00.21 is now available
It includes support for:
2. "set autobond off" can be used before loading any file type to prevent
Dear All,
I use Jmol to visualize CML files within HTML pages. These CML files are
generated from Tripos mol2 files. This means that the CML files do countain the
connectivities between the atoms.
If you look at
http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-56/info.html
The second molecul
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