Dear all, I have an error appearing in phenix. I think it is a problem of my pdb file. I do not know how to change it. Error: residue.id_str(suppress_segid=false):segid is not unique: pdbres=ATP C 1 "segid= "O" Does anyone can help me?? Where is the mistake and how to solve it ?? Kind regards, Ivan -- Ivan Ivanov, PhD PostDoctoral fellow at EMBL, European Molecular Biology Laboratory, Structural biology of RNA-protein complexes, Dr. Stephen Cusack, EMBL 71, avenue des Martyrs CS 90181 38042 Grenoble Cedex 9 T: +33 (0)4 76 20 7630 T(lab): +33 (0)4 76 20 7014 Email: [email protected] Url: http://www.embl.fr
Hi Ivan, could you please send me PDB file that causes problem? Thanks, Pavel On 10/16/14 7:36 AM, Ivan IVANOV wrote:
Dear all,
I have an error appearing in phenix. I think it is a problem of my pdb file. I do not know how to change it. Error: residue.id_str(suppress_segid=false):segid is not unique: pdbres=ATP C 1 "segid= "O" Does anyone can help me?? Where is the mistake and how to solve it ?? Kind regards, Ivan
On Thu, Oct 16, 2014 at 7:36 AM, Ivan IVANOV
I have an error appearing in phenix. I think it is a problem of my pdb file. I do not know how to change it. Error: residue.id_str(suppress_segid=false):segid is not unique: pdbres=ATP C 1 "segid= "O" Does anyone can help me?? Where is the mistake and how to solve it ??
This means that within a single "residue" (I guess an ATP ligand?), the unofficial segID field (columns 72-76, I think) that is sometimes use as an alternative to chain ID has multiple values for the different atoms. This tends to break other code so it's checked when the file is read in. There are several ways to fix this, but probably the easiest is to run phenix.pdbtools and tell it to clear the segID - on the command line this would be: phenix.pdbtools model.pdb clear_segid=True and in the GUI it should be pretty obvious which box to check. -Nat
participants (3)
-
Ivan IVANOV -
Nathaniel Echols -
Pavel Afonine