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
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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So clearly, the original data is not atomic data. The ****s are because the residue names are more than 4 characters long, i.e. the field has overflowed -- the PDB allows for 3 characters and chimera accepts/writes 4. -- Greg On 8/24/2011 9:15 AM, Elaine Meng wrote:
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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
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a kauz -
Elaine Meng -
Greg Couch