The utilities macros are a sample of generally useful routines with no common denominator. They all are placed in the MAIN_UTILS: directory.
The menu is loaded with MAIN_CMDS:load_utils.com.
You are prompted for a PDB file that is read, covalent bonds are calculated and displayed with the MAIN_CMDS:re_image_set.cmds macro. The center of the image is placed into the middle of the molecule.
The macro is MAIN_UTILS:load_pdb.com.
You are prompted for root of a PDB file that is then read. Connectivity table file with extension ".ctab" is read as well. "READ_ATO" reads what is saved with "SAVE_AS".
The macro is MAIN_UTILS:read_atom.com.
Loads a background image of a pdb file. You are prompted for a PDB file, which is processed as in the LOAD_PDB, displayed with a re_image_col.cmds macro (in one color) and stored into the background.
The macro is MAIN_CMDS:utils_background_pdb.cmds.
Calculate covalent bonds. It affects segments names with their names included into the WORK_SEGM.
The macro is MAIN_UTILS:calculate.bonds.
Fills the missing atoms into the residues according to their description in the topology library. Useful also for hydrogen insertion. It affects segments names with their names included into the WORK_SEGM.
Be careful - the N and C- terminal atoms HTn may disappear. OXT however stay.
The macro is MAIN_UTILS:fill_atoms.com.
xpl2MAIN does a simple renaming of atom and residues from an X-PLOR pdb standard to MAIN. The most common mismatches between X-PLOR and MINA are in, but it will not fix all the things It affects segments names with their names included into the WORK_SEGM.
The macro is MAIN_UTILS:xplor_2_main.com.
MAIN2xpl is the reverse conversion from the xpl2MAIN. It will not fix everything, but generally may work. It affects segments names with their names included into the WORK_SEGM.
The macro is MAIN_UTILS:main_2_xplor.com.
Reads the topology library and parameter file from the CSD (Engh \& Huber) force field.
The macro is MAIN_UTILS:get_top_par_19_csd.com.
Reads the topology library and parameter file from the CSD (Engh \& Huber) force field and DNS library.
The macro is MAIN_UTILS:get_top_par_prot_dna.com
Reads the topology library and parameter file for carbohydrate (sugar)rings.
The macro is MAIN_UTILS:get_top_par_sugar.com
Converts amino residue names into the single letter code.
The macro is MAIN_UTILS:ren_to_1_let_code.com.
Converts amino residue names from the single letter code to the 3 letter code.
The macro is MAIN_UTILS:ren_from_1_let_code.com.
Saves the current WORK_SEGM into atom coordinates and connectivity table files.
The macro is MAIN_UTILS:save_as.com.
Reorders residues in all segments part of WORK_SEGM so that amino residues follow the peptide bond connections. Chain and sequence IDs are automatically reassigned. Sequence IDs of each residue startswith the chain ID and followes by the consecutive number of the position in the chain.
The MAIN_UTILS:re_order_chains.com does it.
Displays the framework and graph of a Ramachandran plot and attaches dials to it manipulation.
The macro is MAIN_UTILS:rama.com.
Displays Ramachandran diagram of a protein. Segments names with their names included into the WORK_SEGM are used.
The macro is MAIN_UTILS:rama_prot.com.
SHOW_CEL displays a crystal lattice of 4x4x4 unit cells.
The macro is MAIN_UTILS:show.cell.
Loads 8 X-window server fonts of different size.
Command
> image font use 3
specifies the use of font number 3.
The macro is MAIN_UTILS:load_fonts.com.