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MWCLOSE, MCLOSC & MCLOSE write the header records to the output map fileand close the file. They differ in their handling of the density limits,mean and rms deviation. You are strongly recommended to use MWCLOSE(ccp4_map_write_close_user_sum).

when a map file is just being copied, since the RHMEAN & RHRMSarguments can be taken directly from the call toMRDHDR/ccp4_map_read_open_header. This call is also useful when themean & rms need to be weighted (as in rotation functions), so theyneed to be calculated in the main program.

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MTTCPY (ccp4_map_copy_tile) copies all titles from a previously openedinput to the previously opened output file, adding the new TITLE to theend or overwriting the last one if there are already 10 (the maximumwhich can be stored).

MTTREP (ccp4_map_write_replace_title) replaces the NT-th title in theoutput file (after calls to MWRHDR /ccp4_map_read_open_header and MTTCPY /ccp4_map_copy_title), adding a new TITLE to the end or overwriting thelast one if there are already 10.

Note that this differs fromccp4_map_read_open_header_check [MRDHDS] (which it calls)in that the file is not left open but is closed (by a call toccp4_map_read_close [MRCLOS]) before the subroutineterminates. Note also that the map limits are returned in x,y,z orderrather than in fast, medium, slow order.

When used to generate a full descriptioon of a monomer/ligand, Acedrg can take several input file formats used in the computational chemistry: SMILES, mmCIF, SDF/MOL, and SYBYL MOL2 files. It outputs ACEDRG-derived ideal bond lengths, angles, plane groups, aromatic rings and chirality information, and writes them to an file of mmCif format that can be used by the refinement programs and model building programs. AceDRG also outputs a set of coordinates in the PDB file format. An input instruction file is required for running Acedrg in covalent link generation mode.

Input SMILES a typographical line notation for specifying chemical structure "C1=CC=CC(CCC2)=C12", which can be feed into command-lines a_smiles.smi, which contains the above SMILES string and can be feed into command-lines MDL MOL File A MDL Molfile is a file format created by MDL and now owned by Symyx. It contains information about the atoms, bonds, connectivity and coordinates of a molecule. It also includes some header information, the Connection Table (CT) containing atom info, then bond connections and types, followed by sections for more complex information a_molecule.mol, which contains the following information

201 Mrv0541 02231214312D 14 15 0 0 0 0 999 V2000 3.0791 1.6500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6500 -0.8250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0791 -0.8250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.5741 0.6639 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.3645 0.4125 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.5741 -0.6639 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.7935 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7935 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0791 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3645 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0556 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0791 -1.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8305 1.4482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6500 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 9 2 0 0 0 0 2 10 2 0 0 0 0 3 8 1 0 0 0 0 3 10 1 0 0 0 0 3 12 1 0 0 0 0 4 7 1 0 0 0 0 4 11 1 0 0 0 0 4 13 1 0 0 0 0 5 9 1 0 0 0 0 5 10 1 0 0 0 0 5 14 1 0 0 0 0 6 8 1 0 0 0 0 6 11 2 0 0 0 0 7 8 2 0 0 0 0 7 9 1 0 0 0 0M END mmCif File The macromolecular Crystallographic Information File (mmCIF) is an extension of Crystallographic Information File (CIF). Detailed information about mmCif files can be found in PDBx/mmCIF Dictionary Resources

Mol2 file A MOL2 (.mol2) is a flexible representation of molecules, containing atom coordinates, bonds, substructure information. Detailed information about mol2 files can be found in Tripos Mol2 File Format OutputExecution of ACEDRG in different modes will result in different output files. The most frequently used mode is for generation ligand descriptions. ACEDRG writes two output file when job finishes successfully.

(a) Ligand description generation mode:

AceDRG writes two output files: a PDB file (.pdb) containing a set of coordinates; ACEDRG generats a low energy conformer. a mmCIF file(.cif) containing bond lengths, angles, and other stereo-chemical information. An example: #data_comp_listloop__chem_comp.id_chem_comp.three_letter_code_chem_comp.name_chem_comp.group_chem_comp.number_atoms_all_chem_comp.number_atoms_nh_chem_comp.desc_levelUNL UNL . NON-POLYMER 70 39 . #data_comp_UNL#loop__chem_comp_atom.comp_id_chem_comp_atom.atom_id_chem_comp_atom.type_symbol_chem_comp_atom.type_energy_chem_comp_atom.charge_chem_comp_atom.x_chem_comp_atom.y_chem_comp_atom.zUNL N N NT2 0 -3.654 2.378 1.008 UNL C27 C CH1 0.000 -4.053 1.059 0.498 UNL C28 C CH1 0.000 -5.015 0.357 1.466 UNL O4 O OH1 0.000 -6.187 1.144 1.627 UNL C29 C CH1 0.000 -5.373 -1.044 0.973 UNL C21 C CR66 0.000 4.504 -0.782 0.373 ................ loop__chem_comp_bond.comp_id_chem_comp_bond.atom_id_1_chem_comp_bond.atom_id_2_chem_comp_bond.type_chem_comp_bond.aromatic_chem_comp_bond.value_dist_chem_comp_bond.value_dist_esdUNL N C27 single n 1.470 0.013UNL C27 C28 single n 1.532 0.010UNL C27 C26 single n 1.512 0.020UNL C28 O4 single n 1.421 0.011UNL C28 C29 single n 1.523 0.010................ loop__chem_comp_angle.comp_id_chem_comp_angle.atom_id_1_chem_comp_angle.atom_id_2_chem_comp_angle.atom_id_3_chem_comp_angle.value_angle_chem_comp_angle.value_angle_esdUNL C27 N HN1 109.984 3.00UNL C27 N HN2 109.984 3.00UNL HN1 N HN2 108.673 3.00UNL N C27 C28 111.315 2.25UNL N C27 C26 111.865 2.42UNL N C27 H27 108.113 1.50................ _chem_comp_tor.comp_id_chem_comp_tor.id_chem_comp_tor.atom_id_1_chem_comp_tor.atom_id_2_chem_comp_tor.atom_id_3_chem_comp_tor.atom_id_4_chem_comp_tor.value_angle_chem_comp_tor.value_angle_esd_chem_comp_tor.periodUNL sp3_sp3_80 C28 C27 N HN1 -60.000 10.00 3UNL sp3_sp3_112 C27 C26 O3 C25 180.000 10.00 3UNL sp3_sp3_115 C24 C25 O3 C26 180.000 10.00 3UNL sp3_sp3_20 C12 C24 C25 O3 180.000 10.00 3UNL sp3_sp3_121 O3 C25 C9 C11 60.000 10.00 3................ loop__chem_comp_chir.comp_id_chem_comp_chir.id_chem_comp_chir.atom_id_centre_chem_comp_chir.atom_id_1_chem_comp_chir.atom_id_2_chem_comp_chir.atom_id_3_chem_comp_chir.volume_signUNL chir_1 N C27 HN1 HN2 bothUNL chir_2 C27 N C26 C28 negativeUNL chir_3 C28 O4 C29 C27 negative................ loop__chem_comp_plane_atom.comp_id_chem_comp_plane_atom.plane_id_chem_comp_plane_atom.atom_id_chem_comp_plane_atom.dist_esdUNL plan-1 C11 0.020UNL plan-1 C13 0.020UNL plan-1 C14 0.020UNL plan-1 C15 0.020UNL plan-1 C16 0.020UNL plan-1 C17 0.020UNL plan-1 C20 0.020................ loop__pdbx_chem_comp_descriptor.comp_id_pdbx_chem_comp_descriptor.type_pdbx_chem_comp_descriptor.program_pdbx_chem_comp_descriptor.program_version_pdbx_chem_comp_descriptor.descriptorUNL SMILES ACDLabs 10.04 "O=C6c2cc1ccccc1cc2C7C4(c3ccccc3CCC4=O)C(OC5OC(C(O)C(O)C5N)CO)CC67" UNL SMILES_CANONICAL CACTVS 3.341 "N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@H]1O[C@H]2C[C@H]3[C@H](c4cc5ccccc5cc4C3=O)[C@@]26C(=O)CCc7ccccc67" UNL SMILES CACTVS 3.341 "N[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1O[CH]2C[CH]3[CH](c4cc5ccccc5cc4C3=O)[C]26C(=O)CCc7ccccc67"

Usuage Generate descriptions of a ligand using different input file formats SMILES Generate descriptions of a ligand from a SMILES string acedrg -i "C1=CC=CC(CCC2)=C12" -o my_ligand When the job finishes, you will see two output files, my_ligand.cif and my_ligand.pdb. acedrg -i my_ligand.smi -o my_ligand The file - my_ligand.smi, contains a SMILES string, such as C1=CC=CC(CCC2)=C12. Again, the output files are my_ligand.cif and my_ligand.pdb. mmCIF Generate descriptions of a ligand using mmcif ligand file acedrg -c my_ligand.cif -o my_ligand_fromAcedrg Output files: my_ligand_fromAcedrg.cif - description file in a ccp4 mmcif ligand format my_ligand.pdb - coordinate file in the PDB format MDL MOL Generate descriptions of a ligand from mdl/mol file acedrg -m my_ligand.mol -o my_ligand Output files: my_ligand_fromAcedrg.cif - description file in a ccp4 mmcif ligand format my_ligand.pdb - coordinate file in the PDB format SYBL MOL2 Generate descriptions of a ligand using SYBL mol2 (.mol2) file acedrg -g my_ligand.mol2 -o my_ligand Outut files: my_ligand_fromAcedrg.cif - description file in a ccp4 mmcif ligand format my_ligand.pdb - coordinate file in the PDB format Other options: acedrg -h -h signals that AceDRG print out a help manual that contains all options. It will print some info about all input options. acedrg -v -v signals that AceDRG will print out its version number. acedrg -c my_ligand.cif -o my_ligand_fromAcedrg -r a_3_letter_ligand_name -r signals that AceDRG will use the input a_3_letter_ligand_name as the short name for the ligand in the output mmcif file, i.e. my_ligand_fromAcedrg.cif. acedrg -c my_ligand.cif -o my_ligand_fromAcedrg -p -p signals that AceDRG must use the coordinates from the input file. acedrg -m my_ligand.mol -o my_ligand -K (upper case) -K signals that AceDRG will keep protonation state defined in the input file acedrg -i my_ligand.smi -o my_ligand -j n (an integer) -j signals that AceDRG will try to generate n initial conformers and optimize them. Then output one conformer that corresponds to the lowest engergy. acedrg -i my_ligand.smi -o my_ligand -k n (an integer) -k signals that AceDRG will try to generate n initial conformers and optimize them. Then output all those n different files. acedrg -i my_ligand.smi -o my_ligand -l (low case) n (an integer) -l signals that AceDRG will make RDKit to run number of n steps in its geometrical optimizations for the molecule conformers. It is usually used together with option -k or -j to get better conformers. But it may take much longer time. acedrg -o my_atom_types_in_ligand -n -n signals that AceDRG will generate two kinds of atom types (CCP4 type, aceDRG type) for all atoms of the ligand. Then output all atom types in an output file, i.e. my_atom_types_in_ligand.txt Generate a description of a link between two monomers To generte a link one must create a file containing instruction about the covalent bonds to be created. Create an instruction file, e.g. my_instructions.txt Run aceDRG in a command line, using the instruction file in a commamd line, e.g. acedrg -L(upper case) my_instructions.txt -o my_link The output file, e.g. my_link.cif, contains the detailed information about the link. How to create an instruction file. Keywords: The required keywords : RES-NAME-1 ATOM-NAME-1 FILE-1 RES-NAME-2 ATOM-NAME-2 FILE-2 The optional keywords : DELETE CHANGE BOND-TYPE Keywords are case insensitive, the values of the keywords are case sensitive. Details and examples: The instruction file should have a single line, e.g. LINK: RES-NAME-1 2OP FILE-1 2OP_acedrg.cif ATOM-NAME-1 C RES-NAME-2 VAL ATOM-NAME-2 N It means that AceDRG will generate a link between atoms C of 2OP and N of VAL. The description of 2OP is in the file 2OP_acedrg.cif and the description of VAL is from the monomer library. keywords RES-NAME-1 and RES-NAME-2 should be followed by the residue names, e.g. 2OP and VAL keywords ATOM-NAME-1 and ATOM-NAME-2 should be followed by atom names, e.g. C and N. These are atoms from the first residue (defined by RES-NAME-1) and atom in the second ressidue (defined by RES-NAME-2). AceDRG will generate a bond between these atoms. Default bond order is "SINGLE". keyword FILE-1 and FILE-2 should be followed by a mmcif file name which provides detailed information on the ligand. If file name is not given then AceDRG assumes that this monomer should be taken from the standard monomer library. You can generate the mmcif file of the ligand/monomer, e.g. 2OP, by running aceDRG, as described below. If the monomer is present in the PDB then it is a good idea the get mmcif file for thiss monomer, for example for 2OP.cif, from PDB. If the monomer is not in the PDB file then it can be generated using SMILES string, mmcif file, sdf mol file or mol2 file as described above. Run acedrg using 2OP.cif as an input file. acedrg -c 2OP.cif -o 2OP_acedrg -p Put the generated mmcif file, 2OP_acedrg.cif, into the instruction file as in the example instruction file. Additional keywords can be used to control AceDRG acgions in link generation mode: The keyword DELETE can be used to delete one or more atoms from one of the ligands/monomers. e.g. LINK: RES-NAME-1 2OP FILE-1 2OP_acedrg.cif ATOM-NAME-1 C RES-NAME-2 VAL ATOM-NAME-2 N DELETE ATOM OXT 1 which means that atom, OXT, in ligand 1, i.e. 2OP will be deleted when the link is generated. DELETE instructions should be at the end of the instruction line. The keyword, CHANGE, can be used to change one of the bonds a in one of the ligands/monomers. e.g. LINK: RES-NAME-1 CYS ATOM-NAME-1 SG RES-NAME-2 TMP FILE-2 TMP.cif ATOM-NAME-2 C1 CHANGE BOND C1 C2 SINGLE 2 which means that the bond between C1 and C2 in ligand 2, i.e. TMP will be changed into a bond order of single. The keyword, BOND-TYPE, can be used to define the bond order between linked atoms. Default value for bond order is SINGLE. LINK: RES-NAME-1 LYS ATOM-NAME-1 NZ RES-NAME-2 PLP FILE-2 PLP_acedrg.cif ATOM-NAME-2 C4A BOND-TYPE DOUBLE DELETE ATOM O4A 2 which means that the bond order between NZ in LYS and C4A in PLP_acedrg.cif is double. REFERENCES Fei Long, Robert A Nicholls, Paul Emsley, Saulius GraZulis, Andrius Merkys, Antanas Vaitkus and Garib N Murshudov "ACEDRG: A stereo-chemical description generator for ligands" Acta Cryst. (2017), D73, 112-122.

Fei Long, Robert A Nicholls, Paul Emsley, Saulius GraZulis, Andrius Merkys, Antanas Vaitkus and Garib N Murshudov "Validation and extraction of stereochemical information fromsmall molecular databases" Acta Cryst. (2017), D73, 103-111.

HOW TO CITE ACEDRG The main reference for ACEDRG is:

Fei Long, Robert A Nicholls, Paul Emsley, Saulius GraZulis, Andrius Merkys, Antanas Vaitkus and Garib N Murshudov

"ACEDRG: A stereo-chemical description generator for ligands"

Acta Cryst. (2017), D73, 112-122. 17dc91bb1f

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