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posted Feb 02 '10 at 08:36

Evgeny%20Fadeev's gravatar image

Evgeny Fadeev
5771

Ok, answering myself. Turns out MOLMOL opens XYZ files. So I wrote a little **[program][1]** in Python that converts PDB files saved by XPLOR to XYZ format. Briefly XYZ format has number of atoms in first line, comment on the second line and remaining lines are [1]: http://nmrwiki.org/wiki/index.php?title=Script_xplo2xyz.py_-_convert_PDB_files_created_by_NIH-XPLOR_to_XYZ_file_format
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No.1 Revision

posted Feb 02 '10 at 08:38

Evgeny%20Fadeev's gravatar image

Evgeny Fadeev
5771

Ok, answering myself. Turns out MOLMOL opens XYZ files. So I wrote a little program in Python that converts PDB files saved by XPLOR to XYZ format.

Briefly XYZ format has number of atoms in first line, comment on the second line and remaining lines are

<atom name=""> <x coor=""> <y coor=""> <z coor="">

No residue numbers go into XYZ file, so it will be impossible to make selections by residues. Maybe I'll fix up the script above to create selection statements too... If that happens I'll post an update here.

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No.2 Revision

posted Feb 02 '10 at 08:54

Evgeny%20Fadeev's gravatar image

Evgeny Fadeev
5771

Ok, answering myself. Turns out MOLMOL opens XYZ files. So I wrote a little program in Python that converts PDB files saved by XPLOR to XYZ format.

Briefly XYZ format has number of atoms in first line, comment on the second line and remaining lines are

<atom name=""> <x coor=""> <y coor=""> <z coor="">

No residue numbers go into XYZ file, so it will be impossible to make selections by residues. residues - only by atom numbers. Maybe I'll fix up the script above to create selection statements too... If that happens I'll post an update here.

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No.3 Revision

posted Feb 02 '10 at 08:54

Evgeny%20Fadeev's gravatar image

Evgeny Fadeev
5771

Ok, answering myself. Turns out MOLMOL opens XYZ files. So I wrote a little program in Python that converts PDB files saved by XPLOR to XYZ format.

Briefly XYZ format has number of atoms in first line, comment on the second line and remaining lines are

<atom name=""> name> <x coor=""> coor> <y coor=""> coor> <z coor="">coor>

No residue numbers go into XYZ file, so it will be impossible to make selections by residues - only by atom numbers. Maybe I'll fix up the script above to create selection statements too... If that happens I'll post an update here.

click to hide/show revision 5
No.4 Revision

posted Feb 02 '10 at 08:58

Evgeny%20Fadeev's gravatar image

Evgeny Fadeev
5771

Ok, answering myself. Turns out MOLMOL opens XYZ files. So I wrote a little program in Python that converts PDB files saved by XPLOR to XYZ format.

Briefly XYZ format has number of atoms in first line, comment on the second line and remaining lines arelooks like this:

<atom name> <x coor> <y coor> <z coor><number_of_atoms>
<comment> 
<atom_name> <x_coor> <y_coor> <z_coor>
...

No residue numbers go into XYZ file, so it will be impossible to make selections by residues - only by atom numbers. Maybe I'll fix up the script above to create selection statements too... If that happens I'll post an update here.

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No.5 Revision

posted Feb 02 '10 at 08:58

Evgeny%20Fadeev's gravatar image

Evgeny Fadeev
5771

Ok, answering myself. Turns out MOLMOL opens XYZ files. So I wrote a little program in Python that converts PDB files saved by XPLOR to XYZ format.

XYZ format looks like this:

<number_of_atoms>
{number_of_atoms}
<comment> 
<atom_name> <x_coor> <y_coor> <z_coor>
...

No residue numbers go into XYZ file, so it will be impossible to make selections by residues - only by atom numbers. Maybe I'll fix up the script above to create selection statements too... If that happens I'll post an update here.

click to hide/show revision 7
No.6 Revision

posted Feb 02 '10 at 08:59

Evgeny%20Fadeev's gravatar image

Evgeny Fadeev
5771

Ok, answering myself. Turns out MOLMOL opens XYZ files. So I wrote a little program in Python that converts PDB files saved by XPLOR to XYZ format.

XYZ format looks like this:

{number_of_atoms}
<comment> 
<atom_name> <x_coor> <y_coor> <z_coor>
number_of_atoms
comment
atom_name   x_coor   y_coor   z_coor
...

No residue numbers go into XYZ file, so it will be impossible to make selections by residues - only by atom numbers. Maybe I'll fix up the script above to create selection statements too... If that happens I'll post an update here.

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