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