[Chimera-users] error parsing ATOM record when coordinate long-ish

[Eric Pettersen]

On Apr 1, 2007, at 12:50 AM, Miguel Ortiz-Lombardia wrote:

> I can't read a particular atom line that looks like:
>
> ATOM      4  CA  GLY A   4    -32.686-186.362  -1.715  1.00 20.00
>     C
>
> I presume that the reason is that the y-coordinate forms a continuous
> string with the x-coordinate. However, this line complies with the PDB
> format; I quote from the RCBS site:
>
> 39 - 46      Real(8.3)        y          Orthogonal coordinates for  
> Y in
>                                          Angstroms

Hi Miguel,
	The problem isn't with the numbers running together, it's that  
they're in the wrong columns.  If you count it out, you'll find that  
your Y coordinate is in columns 38-45 rather than 39-46.  This  
becomes obvious if you put your line next to one from a standard PDB  
file (such as 1GCN, below):

ATOM      4  CA  GLY A   4    -32.686-186.362  -1.715  1.00 20.00
ATOM      1  N   HIS     1      49.668  24.248  10.436  1.00 25.00    
1  1GCN  50

If I insert a space before the start of your coordinates, Chimera  
reads the line okay.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu
                         http://www.cgl.ucsf.edu




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