Dear Mahendra, The columns are in the wrong place. Everything from residue number to the right should be moved over one space to the left. Here is a line from your file followed by a corrected line: ATOM 1 N SER B 2010 -15.714 -29.836 129.274 1.00 0.00 ATOM 1 N SER B2010 -15.714 -29.836 129.274 1.00 0.00 … in other words, chain ID is supposed to be in column 22, residue number is in columns 23-26, etc. See the "atomic coordinates" section in our Intro to PDB Format: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.htm...> I attached a corrected file as an example. Maybe you could report this issue to the NORMAD-REF authors. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 14, 2014, at 6:54 AM, Mahendra B Thapa <thapamb@mail.uc.edu> wrote:
Dear Chimera users,
I can't open the pdb file (one of them is attached) generated by NORMAD-REF(http://lorentz.immstr.pasteur.fr/decoys/submission.php) in chimera (version 64-1.9). The format of the pdb file looks like ok while trying to follow the former posts like "http://www.cgl.ucsf.edu/pipermail/chimera-users/2012-June/007704.html". Please help me to find the errors which might have remained unnoticed to me.
Thank you, Mahendra Thapa Doctoral Student,Physics University of Cincinnati,OH <decoy_1.pdb>