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@cgl.ucsf.edu

http://www.cgl.ucsf.edu