Re: [PyMOL] weird visualization of a peptide structure

[DeLano S. <de...@de...>]

Annalisa,
 
If bonds are not explicitly provided in the input file, then PyMOL infers
bonding based on distance.  Are the input coordinates valid?  It looks like
the atoms may be too close together in space...
 
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:su...@de...
 


  _____  

From: annalisa bordogna [mailto:ann...@gm...] 
Sent: Thursday, December 18, 2008 6:40 AM
To: pym...@li...
Subject: [PyMOL] weird visualization of a peptide structure


Hi all,
I have a little problem with the visualization of a peptide conformation: as
you can see from the picture I enclose, the structure appears as if every
atom is bound to every neighbour atom. What (and how) can I set in PyMOL, to
visualize a correct structure?

Thank you very much for your help.
Best regards,
Annalisa

-------------------------------------------------------
Annalisa Bordogna
Ph.D. Student
Università degli Studi di Milano - Bicocca
Milano, IT