spc_4x4.gif (45 byte)
3. File Conversion
spc_2x2.gif (43 byte)
grd_2.gif (669 byte)
spc_2x2.gif (43 byte)
grd_3.gif (736 byte)


The main features of VEGA file conversion are:

An intelligent algorithm implemented in VEGA recognizes automatically the input file format.


It’s possible to load more than one file at once with the same or different file formats to create a molecular assembly. The calculation of connectivity is performed separately for each file loaded to prevent the connectivity errors of bumping molecules.


The Data De/compressor Engine allows the use of the compressed files without previous unpacking operations: packed files can be managed in the same way of the unpacked files without any external data decompressor. VEGA supports the following packing formats: BZip (.bz2), GZip (.gz), PowerPacker (.pp) and Unix compress (.Z).


The image produced with VEGA program can be exported using the most popular graphic formats (Bmp, Gif, Jpeg, OpenIL, PCX, PNG, PNM, Raw, SGI, Targa and Tiff).


The supported file formats are reported in the following table:





New Biosym .car file (archive 3).


MSI CHARMm text file format.


Cambridge Data File.


Fasta is not a real molecular file, because it can store only the primary structure of proteins and DNA/RNA sequences.


This is the special file format of the molecular mechanics package Gromos.


GROMOS with the coordinates in nano meters.


HyperChem file format.


Interchange File Format. This is a binary file with an AmigaOS chunk structure (like IFF-ILBM, AIFF, etc). All chunks are optional and the structure is totally expandable.


Tripos Sybyl Mol 2 file format.


The Mopac internal coordinates file (.dat) is useful to link Mopac with other software packages. The Mopac keyword CHARGE is automatically calculated by atomic charges. Other keywords can be specified with option.


MSI Quanta binary file. Its complexity and the poor documentation available have not allowed a full implementation of this format. You can only overwrite an existing MSF file (that must be compatible with the input), but not create a new file.


Old Biosym .car file (archive 1).


PDB full standard (default).


PDB full standard with special records to include atomic charges, force field parameters and ATDL description for each atom.   It’s totally compatible with the PDB standard, because the extra information are placed in REMARK records.


PDB full standard with special REMARK records to include atomic charges and force field parameters. It’s also totally compatible with the PDB standard.


Simplified PDB format, more compatible with software packages that have a partial implementation of Brookhaven specifications. Special records (HETATM, TER, CONECT and MASTER) are not used.


PDB full standard with atomic charges placed in the last right column


Cartesian coordinates file. The first record is the total number of atoms and  the next records are for each atom. The atom record contains the element name and X, Y, Z cartesian coordinates.


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