Could the connect_mode setting be better documented? The current documentation doesn't say much about what that setting does.

nick


On Fri, Mar 12, 2010 at 12:08, Jason Vertrees <jason.vertrees@schrodinger.com> wrote:
Nicolas,

Try:

set connect_mode, 2
load yourXYZ.xyz, discrete=1

-- Jason

On Fri, Mar 12, 2010 at 1:50 PM, Nicolas Bock <nicolasbock@gmail.com> wrote:
> Please find attached an example xyz file.
>
> nick
>
>
> On Fri, Mar 12, 2010 at 11:20, Nicolas Bock <nicolasbock@gmail.com> wrote:
>>
>> When I load an xyz file with several frames (for example the result of an
>> MD simulation) I find that pymol calculates and sets the bonds only using
>> the initial frame. For frames > 1 the bonds are not recalculated. The only
>> "work around" I found is to load(..., multiplex=1) which loads the frames
>> into separate objects. But now I can not play the MD trajectory as a movie.
>>
>> I would like to suggest that this feature be added to pymol so that MD
>> trajectories can be played with proper bonding for all frames.
>>
>> Thanks
>>
>> nick
>>
>
>
> ------------------------------------------------------------------------------
> Download Intel&#174; Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>



--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jason.Vertrees@schrodinger.com
(o) +1 (603) 374-7120