[Chimera-users] Can't open the file generated by NORMAD-REF

Elaine Meng meng at cgl.ucsf.edu
Mon Jul 14 08:45:11 PDT 2014


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.html>

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

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On Jul 14, 2014, at 6:54 AM, Mahendra B Thapa <thapamb at 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>


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