2 UTILS File: utils.txt Last modified: 16-jan-2003 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". 3 LOAD_PDB Keyword: LOAD_PDB, load pdb 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". 3 READ_ATO Keyword: READ_ATO, read atoms 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". 3 BACK_PDB Keyword: BACK_PDB, load background pdb 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". 3 CALC_BON Keyword: CALC_BON, covalent bonds Calculate covalent bonds. It affects segments names with their names included into the WORK_SEGM. The macro is "MAIN_UTILS:calculate.bonds". 3 FILL_ATO Keyword: FILL_ATO, fill atoms, missing atoms 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". 3 xpl2MAIN Keyword: xpl2MAIN, atom conversion, conversion, compatibility 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". 3 MAIN2xpl Keyword: MAIN2xpl, atom conversion, conversion, compatibility 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". 3 LIB_PROT Keyword: LIB_PROT, amino acids, Engh&Huber, library, topology, parameter 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". 3 LIB_NU-P Keyword: LIB_NU-P, nucleic acid, Engh&Huber, library, topology, parameter 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" 3 LIB_CHO Keyword: LIB_CHO, carbohydrates, sugar, library, topology, parameter Reads the topology library and parameter file for carbohydrate (sugar)rings. The macro is "MAIN_UTILS:get_top_par_sugar.com" 3 TRP_2_W Keyword: TRP_2_W, one letter code, three letter code Converts amino residue names into the single letter code. The macro is "MAIN_UTILS:ren_to_1_let_code.com". 3 W_2_TRP Keyword: W_2_TRP, one letter code, three letter code 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". 3 SAVE_AS Keyword: SAVE_AS, save Saves the current WORK_SEGM into atom coordinates and connectivity table files. The macro is "MAIN_UTILS:save_as.com". 3 RE_ORDER Keyword: RE_ORDER, organize, renumber, rename, chain 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. 3 RAMACHAN Keyword: RAMACHAN, ramachandran plot Displays the framework and graph of a Ramachandran plot and attaches dials to it manipulation. The macro is "MAIN_UTILS:rama.com". 3 RAMA_PRO Keyword: RAMA_PRO, ramachandran plot 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". 3 SHOW_CEL Keyword: SHOW_CEL, crystal lattice SHOW_CEL displays a crystal lattice of 4x4x4 unit cells. The macro is "MAIN_UTILS:show.cell". 3 LOAD_FON Keyword: LOAD_FON, fonts, character set, size 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".