File Conversion

3. File Conversion

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:

Name	Description
BIOSYM	New Biosym .car file (archive 3).
CRD	MSI CHARMm text file format.
CSSR	Cambridge Data File.
FASTA	Fasta is not a real molecular file, because it can store only the primary structure of proteins and DNA/RNA sequences.
GROMOS	This is the special file format of the molecular mechanics package Gromos.
GROMOSNM	GROMOS with the coordinates in nano meters.
HIN	HyperChem file format.
IFF	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.
MOL2	Tripos Sybyl Mol 2 file format.
MOPINT	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.
MSF	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.
OLDBIOSYM	Old Biosym .car file (archive 1).
PDB	PDB full standard (default).
PDBA	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.
PDBF	PDB full standard with special REMARK records to include atomic charges and force field parameters. It’s also totally compatible with the PDB standard.
PDBNOTSTD	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.
PDBQ	PDB full standard with atomic charges placed in the last right column
XYZ	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.

2. Visualization

3.1 Data Interchange