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MakeLINK

MakeLINK

Copyright © 2004-2010 Global Phasing Limited

All rights reserved.

This software is proprietary to and embodies the
confidential technology of Global Phasing Limited (GPhL).
Possession, use, duplication or dissemination of the software is
authorised only pursuant to a valid written licence from GPhL.

Author: (2004-2007) M. Brandl, (2008-2010) T. Womack


Contents


General Information

MakeLINK constructs a TNT sequence file for a PDB file, by examining the atom positions and the LINK and SSBOND cards. It is particularly useful in cases where the structure has covalent linkages other than peptide and inter-nucleotide phosphate bonds, since it has curated dictionaries for some of the common such linkages and can be made to use user-supplied dictionaries for others.


Command Line Switches and Arguments

Mechanism

Pre-LINK step

All inter-residue contacts

are identified. The contacts are searched for in the following three files:
  1. main connectivity library $BDG_home/tnt/data/connect.dat
  2. user defined connectivity files (e.g. $BDG_home/samples/maketnt/MAKELINK/1EAU/SBDK.connect)
  3. library of atom-specific connectivity data (loaded by default from $BDG_home/database/files/MakeTNT/connectAt.dat)

Contacts corresponding to known link types will be added to the sequence file; close contacts not corresponding to link types will be ignored - if you have introduced one deliberately, add a LINK card. This avoids problems where, for example, a sugar is added to a protein in such a way that some of its atoms other than the one at which it binds covalently clash with ones in the protein.

This is the step that sets up the geometry for the nucleic-acid and peptide parts of the protein.

LINK step

If there are some atoms for which a LINK card exists in the input file, and for which this LINK is expected to represent a covalent bond, but which are not in close contact in the structure, a link will nonetheless be added. This means that you can add (for example) glycosylation to a molecule, and, provided you have added a LINK card, you do not need to worry about getting the geometry of the link correct, or even sensible - it will be pulled in by refinement. Disulphide bonds are handled in the same way.

If the atoms are ones between which a specific linkage type exists, that will be the type used. If not, a bond with a length depending on the atomic numbers on either side of the link will be used; these lengths are defined in $BDG_home/database/files/MakeTNT/connectAt.dat using cards of the form

CONNECT_DEFAULT_BOND 6 6 1.53

If the atoms are not both ones that we expect to form covalent bonds (list here) then no link will be generated; use NOTE BUSTER_DISTANCE restraints in a .Gelly file for restraining metal geometry.

The 'BUSTER LINK' REMARK

To inform MakeLINK that a contact between two particular atoms in a file should be handled using some particular TNT linkage, you can add a card of the form

REMARK 3 BUSTER LINK NZ A 80 C4A B 1 TYPE KPLP

which arranges that the linkage between atoms A|80:NZ and B|1:C4A should be given as type KPLP. The purpose of this mechanism is to allow the information for the refinement of a PDB file to be kept within the PDB file, so that it's not necessary to maintain a separate connectAt.dat file - though of course it is necessary to pass autoBUSTER a file containing a definition of the TNT linkage, eg -l KPLP.dic.

What linkages do we know about?


Output:

Various temporary files are written into the working directory during the run, but should be deleted automatically.

Using the -o option, you can choose your own name for the TNT-sequence file produced by MakeLINK.

If you do not enter a name for the output sequence file, the name of the output sequence file is composed of:

Examples:

Example input files (pdb1uvq.ent, pdb1eau.ent) can be found in $BDG_home/samples/maketnt/MAKELINK/1EAU and $BDG_home/samples/maketnt/MAKELINK/1UVQ.


Advanced configuration

The locations of the element-properties file, main connectivity library and atom-specific connectivity library can be specified using the environment variables

MakeTNT_connectThe main connectivity library
MakeTNT_elementsThe element-properties file
MakeTNT_connectatThe atom-specific connectivity library

or on the command line using entries of the form MakeTNT_connect=/home/user/my_connect.dat.


Tom Womack & Maria Brandl,<buster-develop@GlobalPhasing.com>
Last modification: 16.02.11