The Sam commands

This menu was named Sam for old times sake. It is associated with commands that control the retrieval and storage of structural data in and out of the O database. The commands generate the datablocks from the entire molecular data structure. They therefore differ from the Read_formatted and Write_formatted commands, that are general commands which can be used with any O datablocks. The Sam commands are the link between the O database and external program systems such as the CCP4 package or PROTEIN.    

When reading or writing coordinate files, the program attempts to identify the kind of coordinates by checking the file type. Recognized file types are :

.rd

files are Dr. Robert Diamond style files. These are usually in Å's along the unit cell axes. This style is used by PROTEIN for FC calculations, where the atom type field is used to describe formfactors.  

.wah

files are Dr. Wayne Arthur Hendrickson style files as used in PROLSQ.  

.pdb

files are the format used at the Protein Data Bank at Brookhaven.  

.xpl

are X-plor style PDB files where column 73 is used as a chain ID.  

.bud

Bill Fureys PHASES coordinate format.  

.xyz

are FRODO binary files, DSN2 format to some. Only works on Vax/VMS.

.o

are binary O database files.

When reading PDB files, the program keeps the unit cell values and the space group. When creating PDB files, the program also writes out the extra records SCALEn, CRYST1 and ORIGx needed by some programs. The program generates a time of creation record [mol]_date when it reads a coordinate file. See section 3.16.10 on how the file-type to file extension mapping is defined.

• Sam_atom_in
• Sam_atom_out
• Sam_list_sequ
• Sam_init_db
• Water_init
• Water_add
• Water_pekpik
• Merge_atoms
• Sam_rename
• Datablocks