[Chimera-users] problems in opening PDB file

Eric Pettersen pett at cgl.ucsf.edu
Tue Mar 24 08:47:45 PDT 2020

Hi Laura,
	The “loop bond” message specifically means that your PDB file has a CONECT or LINK record that says that an atom is bonded to itself!  So my advice would be to edit your PDB file and remove all CONECT and LINK records and let Chimera figure out the bonds on its own.


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Mar 24, 2020, at 2:05 AM, Laura Rotilio <laura.rotilio at iusspavia.it> wrote:
> Goodmorning, 
> I'm writing because I'm trying to open my pdb file but this error came out "Attempt to form loop bond". 
> I tried to have a look at the _init_.py file in the line 1109 and I found this message: 
> molList = pdbio.readPDBfile(file, errOut=errLog)
> I can't understand this message and I don't know how to eventually modify my pdb file in order to be able to open it. 
> Thanks in advance for helping me, 
> Laura Rotilio
> -- 
> Laura Rotilio, Ph.D. Student
> Structural Biology Lab., Prof. A. Mattevi
> Dept. Biology and Biotechnology "L. Spallanzani"
> University of Pavia
> Via Ferrata 9, 27100 Pavia
> Italy
> Tel. +39-0382-985525 <tel:%2B39-0382-985525>/985534
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