WriteDict

Overview

WriteDict is a comprehensive refinement dictionary generator that properly handles covalent bond restraints between the ligand and the protein.

Example Commands

The basic usage of writedict is to take an input structure and generate the corresponding .pdb and .cif files for input into COOT or REFMAC5.

> writedict -in 1nhu.ism -out 1nhu_out

This creates the files 1nhu_out.cif and 1nhu_out.pdb. The pdb is always created since the atom names may be remapped from the input. Since the input contains no residue information, the ligand is placed in residue “UNL”.

To add your own residue names for unmapped residues:

> writedict -in 1nhu.ism -out 1nhu_out -residues 153

Note that if the given residue name (153) does not map to the known residue 153 the next residue name in the unmapped residue list will be used. Since none are specified it will go to the standard defaults: “UNL,UN1,UN2…”

Note

When doing whole complexes, renaming residues gets quite complicated since you may not know which residues will map before you run WRITEDICT.

> writedict -in 1nhu.ism -out 1nhu_out -residues LIG -nolookup

Force the residue to be named LIG. (It will also indicate an invalid dictionary)

Warning: LIG   1: Known Residue, but does not map to previous residue: LIG from: RCSB
Warning: LIG   1: previous smiles c1ccc2c(c1)CC3=C(NN=C23)c4ccncc4
Warning: LIG   1: current  smiles c1ccc(cc1)CC(C(=O)[O-])N(Cc2cccc(c2)C(F)(F)F)C(=O)c3ccc(cc3Cl)Cl
Warning: LIG: Keeping residue name (dictionary may be invalid)
Warning: LIG: Adding new residue dictionary
Warning: LIG: already in dictionary from: RCSB but with different structure.
Warning: LIG: c1ccc2c(c1)CC3=C(NN=C23)c4ccncc4
Warning: LIG: c1ccc(cc1)CC(C(=O)[O-])N(Cc2cccc(c2)C(F)(F)F)C(=O)c3ccc(cc3Cl)Cl
Warning: LIG: Overwriting existing residue (dictionary may be invalid)

To ensure planarAniline constraints consistent with the MMFF94s forcefield, use the -planarAniline flag.

> writedict -in 1nhu.ism -out 1nhu_out -planarAniline

Command Line Help

A description of the command line interface can be obtained by executing WRITEDICT with the –help option.

> writedict --help

will generate the following output:

Help functions:
  writedict --help simple      : Get a list of simple parameters
  writedict --help all         : Get a complete list of parameters
  writedict --help <parameter> : Get detailed help on a parameter
  writedict --help html        : Create an html help file for this program

Required Parameters

-in <filename>

File containing a molecule to be fit to density.

[Aliases=**-prot**]

File type	Extension
SMILES	.smi .ism .smi.gz .ism.gz
OEBinary	.oeb .oeb.gz
SDF	.sdf .mol .sdf.gz .mol.gz
MOL2	.mol2 .mol2.gz
PDB	.pdb .ent .pdb.gz .ent.gz
MacroModel	.mmod .mmod.gz

-out <filename prefix>

This specifies a prefix for outputting the refinement dictionary .cif or .xplor and the pdb file. The pdb file ( and pdb.oeb) is always output and should be used for purposes of refinement since WRITEDICT sometimes corrects faulty hydrogen atom names and will include LINK records in the pdb if covalent bonds are detected.

The log file will also be written using this prefix as <filename prefix>.log.

-prefix <filename prefix>: Alias for -out

Optional Parameters

-assignCCP4

If true then CCP4 atom types will be assigned to the output pdb file.

[Default=true]

-includeRotors

Set to true if the output should include rotor torsion terms. If this is set to false, refinement programs will not be able to modify any rotors.

[Default=true]

-suppressH

If true, no hydrogens are output.

[Default=false]

-dictionary_type

Selects the output refinement dictionary format:

Value	Meaning
0 / refmac	REFMAC5 dictionary (default)
1 / xplor	CNS/CNX (XPLOR) dictionary
2 / phenix	PHENIX dictionary
3 / buster	BUSTER dictionary

[Default=refmac]

[Aliases=**-type**]

-planarAniline

Use the MMFF94s variant of the MMFF94 forcefield. This forcefield emulates time-averages structures observed in crystallographic and other structure determination methods.

The MMFF94s forcefield is a variant of MMFF94 that emulates time-averages structures typically observed during crystallographic structure determination, mainly planar geometries at unstrained delocalized trigonal nitrogen centers. However, there are many theoretical studies that show puckering at nitrogen centers. (see MMFF VI. in JCICS)

That being said, due to the prevalence of crystallographic studies, many chemist erroneously consider the time-averaged structure to be correct, hence this variant is available for use.

[Default=true]

[Aliases=**-mmff94s**]

-strict

Change the known residue matching mode.

Options available for residue matching is as follows:

Option

Meaning

exact

Known residue and input residue graphs must match exactly.

substructure

Input residue may be a substructure of the known residue.

Cannot be used with the exact flag.

fuzzybonds

Bond orders do not need to match

atomname

Atom names must match

Options are separated by colons. The default settings are set to limit the number of REFMAC5 issues. -strict exact:substructure will find more matches, but increases the risk of REFMAC5 rejecting the dictionary.

[Default=substructure:fuzzybonds]

-lookup

Attempts to lookup residues from the internal dictionary store using the current -strict status. This is useful to find out if a residue has already been deposited in the RCSB.

If -lookup is not set, mismatching residues will be given new names. [Default=false]

-forceExistingResidueNames

Force WRITEDICT to use the given residues, even if they do not match the deposited residues from the RCSB.

[Default=false]

[Aliases=**-nolookup**,**-force**]

-writeFullDict

If true then all refinement dictionaries are created for all residues. If false only residues that are unknown or are in the set of replaceable residues or covalently bound to a ligand are output. Setting this to true can confuse REFMAC5.

{default=false]

-residues

Comma-separated list of default residue names to assign to unknown components.

[Aliases=**-resnames**,**-res**]

-split: Split separate molecules (and bonded covalent structures) into different dictionaries. [Default=false]

-fix_serial_numbers: Fix serial numbers if there are duplicates in the input files. [Default=false]

-fixResidueHydrogens: If a residue has more hydrogens than the known dictionary entry, remove them. [Default=false]

-fixups: Set fixups for known bugs in refinement packages. Accepts a comma-separated list. Supported value: REFMAC560117_MODRES (fixes LINK issues in CCP4 6.2.0 REFMAC5.6.0117; should be used with MAKE CONNECTIVITY YES).

-verbose: Output copious information of how writedict operates. [Default=false]