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 ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ 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
