write xyz format file for PDB-CCD
PDBeChem currently provides xyz format files
https://en.wikipedia.org/wiki/XYZ_file_format
not sure how useful they are is but easy to write so just implement.
current files:
- ideal coordinates
cat /nfs/ftp/pub/databases/msd/pdbechem/files/xyz/EOH.xyz
9
EOH
C 0.0070 -0.5690 0.0000
C -1.2850 0.2500 -0.0000
O 1.1300 0.3150 -0.0000
H 0.0390 -1.1970 0.8900
H 0.0390 -1.1970 -0.8900
H -1.3170 0.8780 0.8900
H -1.3170 0.8780 -0.8900
H -2.1420 -0.4240 0.0000
H 1.9860 -0.1370 0.0000- model coordinates:
cat /nfs/ftp/pub/databases/msd/pdbechem/files/xyz_r/EOH.xyz
9
EOH
C 15.2120 49.1980 7.4910
C 16.0690 50.3860 7.1040
O 15.8610 48.1850 8.2560
H 14.3750 49.5790 8.0940
H 14.8580 48.7310 6.5600
H 15.4670 51.0980 6.5200
H 16.4420 50.8800 8.0130
H 16.9200 50.0420 6.4980
H 15.2440 47.4880 8.4470- Currently elements are upper case:
cat /nfs/ftp/pub/databases/msd/pdbechem/files/xyz/FES.xyz
4
FES
FE 0.0000 -0.2130 -1.5310
FE 0.0000 -0.2130 1.5310
S 1.4610 0.3720 0.0000
S -1.4610 0.3720 0.0000but better if the iron atoms are written as Fe.