regarding CONECT records and whether to use them, try:

set connect_mode, 1
load youfile.pdb

See also:
http://www.pymolwiki.org/index.php/Connect_mode
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10413.html

Cheers,
   Thomas

Nat Echols wrote, On 05/23/12 20:01:
> On Wed, May 23, 2012 at 10:20 AM, Rituparna Sengupta <rsengu...@wisc.edu> 
> wrote:
>> Sorry about the lack of description in the previous post.
>> The chemicals show incorrect bond connections. Some of the rings go missing. 
>> In all, the structure changes and just by looking at it, its possible to 
>> tell that the structure is not right. I didn't see much details though, 
>> except that the atom connections seem to be wrong.
> 
> A screenshot would be helpful here, but my guess is that PyMOL's
> automatic detection of bond's didn't work for your input structure.
> This can happen for non-standard chemistries or distorted geometries;
> the most frequent artifact is more bonds than are appropriate.  The
> reason it happens is that instead of applying some chemically sensible
> rules and/or prior knowledge to determine bonding (which would be
> relatively slow), PyMOL simply bonds every atom pair within some
> radius (probably excluding certain obvious cases, although I'm not
> sure).  This is very fast, simple, and easily confused.
> 
> I thought perhaps PyMOL can understand CONECT records in the PDB file
> - adding these might fix your problem, although I'm not sure how to
> generate them.  Alternately, you can use the 'bond' and 'unbond'
> commands, but this can be non-trivial to do on a large scale.
> 
> -Nat

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

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