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
Dear Laura, maybe you can have a look at your pdb file by using a text editor to check if the pdb contains some unusual portion (like missing residues). As far I know Chimera tries to reconstruct missing residues but sometimes there could be something wrong. Best regards Marco Il 24/03/2020 10:05, Laura Rotilio ha scritto:
-- Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette
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
participants (3)
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Eric Pettersen -
Laura Rotilio -
Marco Sette