Re: [Jmol-users] CML visualization in Jmol

2006-01-25 Thread Miguel
>> 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

Re: [Jmol-users] CML visualization in Jmol

2006-01-25 Thread FyD
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

Re: [Jmol-users] CML visualization in Jmol

2006-01-25 Thread FyD
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

Re: [Jmol-users] CML visualization in Jmol

2006-01-25 Thread nvervell
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.

RE: [Jmol-users] CML visualization in Jmol

2006-01-25 Thread Miguel
> > 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

Re: [Jmol-users] CML visualization in Jmol

2006-01-25 Thread Miguel
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

RE: [Jmol-users] CML visualization in Jmol

2006-01-25 Thread Herráez Sánchez Angel
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

[Jmol-users] CML visualization in Jmol

2006-01-25 Thread FyD
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