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

Eric Pettersen
UCSF Computer Graphics Lab


On Mar 24, 2020, at 2:05 AM, Laura Rotilio <laura.rotilio@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. +39-0382-985525/985534

Fax +39-0382-528496

Web www.unipv.it/biocry

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