MAKEDICT (CCP4: Supported Program)

NAME

makedict - converts PDB file to TNT or PROTIN dictionaries and PROTIN to PDB.

SYNOPSIS

makedict XYZIN [ foo.pdb | foo.dict ] [ DICT foo.dict | XYZOUT foo.pdb ]
[Keyworded input]

DESCRIPTION

Note: PROTIN is now obsolete - use the new REFMAC.

Reads a set of coordinates for the group, in PDB or PROTIN format, and writes out dictionary entry in format for either TNT or PROTIN. The program can also convert a PROTIN coordinate entry to PDB format. Multiple copies of the group may be present (with different residue numbers), in which case bond lengths & angles will be averaged (only useful for TNT output).

KEYWORDED INPUT

The available keywords are:

CENTRE, CHIRAL, INPUT, NONBOND, OUTPUT, PLANE, RADII, RESIDUE, SD

INPUT [PROTIN | PDB]

Input format, Protin or PDB

OUTPUT [TNT | PROTIN <numres> <rscode> | PDB]

TNT
Write output dictionary for TNT

PROTIN
Write output dictionary for Protin
<numres>
Residue number for PROTIN, as it appears in Card 1a of the protin dictionary. The default value is 1, but this should normally be changed.
<rscode>
1-character residue name for PROTIN, as it appears in Card 1a of the protin dictionary. The 3-character residue name is taken from the RESIDUE keyword.

PDB
Output file in PDB format
(e.g. for converting from Protin dictionary form)

RADII <element_name> <radius>

Set bonding radius for elements (C,N,O,S & P are present by default).

RESIDUE <residue_name>

New residue type name, to override input.

PLANE <atom list>

Define list of atoms in plane.

CHIRAL <central atom> <atom2> <atom3> <atom4>

List of atoms in chiral group.

Note the TNT convention for chiral groups: 1st atom is central atom Look from central atom towards the lowest-priority atom (nearly always H), then list the other atoms (which are towards you) in a clockwise order.

CENTRE <atom name>

Atom to consider as centre [default 1st atom]

SD <sd_bond> <sd_angle> <sd_plane> <sd_bfactor>

For TNT output only. Read sd parameters for TNT dictionary.

NONBOND [<type>] <atom pair 1> <atom pair 2> ...

For Protin output only.

List of atomname pairs to be put in the non-bonded contact list. Type is either 1 for single-torsion contacts or 2 [default] for multiple-torsion contacts.

INPUT AND OUTPUT

XYZIN
Input PDB file; with INPUT PDB.
XYZOUT
Output PDB file; with INPUT PROTIN and OUTPUT PDB.
DICT
Output dictionary file; with OUTPUT PROTIN or OUTPUT TNT.

HINTS FOR MAKING PROTIN DICTIONARY ENTRIES

MAKEDICT should be used for making dictionary entries for PROTIN.

You need a set of coordinates for an "ideal" substrate in PDB format (XYZIN) (the coordinates can be anywhere in space as long as they are correctly bonded, i.e. their relative positions must be correct). You also need knowledge of planar and chiral groups (if any), and must supply this information via the PLANE and CHIRAL keywords respectively. Nonbonding contacts can be defined using the NONBOND keyword; covalent bonds should be defined as SPECIAL distances within PROTIN.

Then: take the DICT file output of MAKEDICT and insert each section (separated by comment lines; don't copy these) into the appropriate places of your local copy of the PROTIN dictionary (e.g. mydict.dic). See appendix A of the PROTIN documentation for a description of the different parts of the dictionary.

Finally, assign the logically variable DICTPROTN to mydict.dat when you run PROTIN to prepare restraints with your new substrate.

EXAMPLES

Unix example script found in $CEXAM/unix/runnable/

Example of using MAKEDICT to generate PROTIN dictionary entry:

General examples of input and output scripts

Here is an example where an input PDB is converted into a PROTIN dictionary.

Input PDB: 


REMARK   This file contains the 1dtx pdb coordinates with
REMARK   residue 1 renamed
CRYST1   73.53    39.06    23.15   90.00  90.00  90.00
SCALE1      0.013600  0.000000  0.000000        0.00000
SCALE2      0.000000  0.025601  0.000000        0.00000
SCALE3      0.000000  0.000000  0.043197        0.00000
ATOM    473  N   GLY    59       9.911  -4.709  16.657  1.00 24.03
ATOM    474  CA  GLY    59       9.228  -5.696  17.463  1.00 27.54
ATOM    475  C   GLY    59       9.299  -5.294  18.943  1.00 31.44
ATOM    476  O   GLY    59       9.804  -6.144  19.719  1.00 33.91
ATOM    477  OE  GLY    59       9.027  -4.131  19.297  1.00 34.32
Script: 

#!/bin/sh

makedict XYZIN toxd.pdb DICT junk.dict <<eof
INPUT PDB
OUTPUT  PROTIN
RESIDUE JNK
CENTRE CA
END
eof
Output dictionary: 

## Dictionary entry in Protin format: edit out sections separated by ##
##  Coordinates
                                                 1    1          JNK
   0.68300   0.98700  -0.80600              2         1   -1               N
   0.00000   0.00000   0.00000              1         2   -1               CA
   0.07100   0.40200   1.48000              1         3   -1               C
   0.57600  -0.44800   2.25600              3         4   -1               O
  -0.20100   1.56500   1.83400              3         5   -1               OE
## Distances (bonds & angles)
JNK          1    8
  2  1 1 1  3  2 1 1  4  3 1 1  5  3 1 1  1  3 2 2  2  4 2 2  2  5 2 2  4  5 2 2
The reverse transformation can be done with the following script (you must of course remove the lines beginning with an "#" from the protin entry given above): 

#!/bin/sh

makedict XYZIN junk.dict XYZOUT junk.pdb <<eof
INPUT PROTIN
OUTPUT PDB
END
eof

AUTHORS

Originator: Phil Evans