[Chimera-users] coordinates in PDB format

[Elaine Meng]

Hi Annamaria,
PDB format uses a specific number of columns for the coordinates.  If there were tabs between the coordinates, it would not be in PDB format any more.  The format for ATOM or HETATM lines has X coord in column 31-38, Y in 39-46, Z in 47-54, in other words 8 columns for each coordinate.  Each of those is supposed to have 3 digits after the decimal, but in your case I see that the Z coordinate is so large that pdbrun is forced to use only 2 (so of its 8 columns, there are 5 before the decimal, the decimal itself, and 2 after).

Our documentation includes a brief explanation of PDB format, see "atomic coordinates" section:
<http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html>

The coordinates should be interpreted correctly if you opened the file back into Chimera.

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 Aug 23, 2011, at 9:55 PM, a kauz wrote:

> I am currently trying to extract data (x,y,z coordinates) from a PDB file generated by Chimera (pdbrun command)
> The file looks like this:
> 
> MODEL        1
> HETATM    1      ****    1    7881.2318439.71911918.53  1.00  0.00           H
> HETATM    2      ****    2    7878.3608863.83911538.22  1.00  0.00           H
> HETATM    3      ****    3    7362.1978948.58411340.85  1.00  0.00           H
> HETATM    4      ****    4    8109.6319067.12510778.80  1.00  0.00           H
> HETATM    5      ****    5    8512.9689160.81011582.47  1.00  0.00           H
> HETATM    6      ****    6    8368.0819128.66911020.52  1.00  0.00           H
> HETATM    7      ****    7    7260.6139750.88411592.71  1.00  0.00           H
> HETATM    8      ****    8    5841.5699031.23313127.43  1.00  0.00           H
> HETATM    9      ****    9    6579.8098604.13912097.33  1.00  0.00           H
> HETATM   10      ****   10    7584.5978302.09511466.04  1.00  0.00           H
> HETATM   11      ****   11    8520.92710251.0411690.68  1.00  0.00           H
> HETATM   12      ****   12    9185.69810212.1111417.11  1.00  0.00           H
> 
> 
> 
> (this is just an extract)
> How can I know how many decimal numbers each coordinate has?
> is there a way to set how many decimal numbers will be reported? or to put some kind of tab separation between the coordinates?
> thanks,
> Annamaria
> 
> 
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