Mario Valle Web

STM4 – supported formats

Name Extension RW Volume Description Notes
Powdercell CEL *.cel RW Powdercell's structure file ref
CHGCAR *CHG* R Yes VASP format containing also volume data ref 1
CIF *.cif RW Crystallographic Information File ref
Gaussian cube *.cube R Yes Gaussian format containing also volume data ref note
DCD *.dcd + *.pdb R FMD, add to PDB trajectory data ref 2
DL_POLY *HIST* R DL_POLY HISTORY file ref
FpStudio *.fst R FullProf Suite site
Gamess input *.inp R GAMESS input file (generated by the Avogadro modeller) ref 3
Gulp *.gin R GULP input file site
MOL *.mol (and also *.sdf) R From MDL ref
MOL2 Tripos *.m*l2 R From Tripos ref
PDB *.pdb RW Protein Data Bank ref
PDB-Q *.pdbq R An old version of PDB 4
PLT *.plt R Only Electron density map from gOpenMol ref 1
VASP Poscar *POSCAR* RW VASP, also as concatenated file site 7
VASP Poscar + elements *POSCAR* + * RW VASP, also as concatenated file plus a file containing the element types of the various atoms site 7
VASP EIGENVAL *EIGENVAL* R Fermi surfaces site
Shel-X *.res R Shel-X crystallography program site
Siesta * R Siesta site 5
XDATCAR *POSCAR* + *XDATCAR* R Another VASP animated format site
XYZ (Kino) *.xyz RW The simple xyz format, animated also ref
XYZ plus unit cell *.xyz + * R Idem plus a supporting file containing the unit cell 6

Notes

  1. The real format derives from the source code of the VMD plugin
  2. I remember a difference between what has been described and the real file format
  3. The plugin read only coordinates from a $DATA section with symmetry C1
  4. An old version of PDB, prior to 1992. The 'Temperature factor' field starts at colum 71 instead of 61. Should be documented somewhere…
  5. Seems no more active
  6. In the unit cell file each block of three lines contains three floats and refers to one frame. The nine numbers define the three base vectors (one by line).
  7. Read the old and new versions (the one with element names). Write only the new version.