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MakeLINK

MakeLINK

Copyright © 2004-2017 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.

Under most circumstances it will now not be necessary to use MakeLINK by hand; if you supply a 'TNT-style link dictionary' (see the Grade-for-Covalent-Linkages Tutorial) on the refine command line then the appropriate bits will be pulled out and passed to MakeLINK automatically.


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.

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.

What goes in a connectivity library?

Atom-type constraints

CATEGORY_AT <category name> <res1> [res2 ...]

defines a category-of-residues comprising the list of residues given on the card - if you want to extend over multiple lines then you can use a hyphen at the end of a line as a continuation character.

For example, in $BDG_home/database/files/MakeTNT/connectAt.dat you will find

CATEGORY_AT BPYR BGC BMA FUC GAL NAG NGA

which defines the category of beta-D- and alpha-L-pyranoses - the significance of this category is that such pyranoses require the same chiral restraint around the C1 atom.

CONNECT_AT <category1> <atom1> <category2> <atom2> <type>

tells MakeLINK that a LINK card between an atom with name atom1 in a residue R of category category1, and an atom of name atom2 in a residue S of category category2, should lead to the production of a linkage of type type.

For example, in $BDG_home/database/files/MakeTNT/connectAt.dat you will find
CONNECT_AT APYR C1 XPYR O2 SA12 !! ALPHA_D_1_2 or BETA_L_1_2
which tells MakeLINK that a link from the C1 of an APYR to the O2 of an XPYR should be handled as of type SA12. Looking in $BDG_home/tnt/data/sugar.dat you find

GEOMETRY SA12 BOND 1.412 0.024 C1 +O2
GEOMETRY SA12 ANGLE 108.1 1.8 C2 C1 +O2
GEOMETRY SA12 ANGLE 111 1.9 O5 C1 +O2
GEOMETRY SA12 ANGLE 115.1 1.6 C1 +O2 +C2
GEOMETRY SA12 CHIRAL 1 1 C1 C2 +O2 O5

to restrain the length of the bond, the three angles around it, and the chirality of the C1 atom of the APYR.

When writing TNT-style link dictionaries, you can keep the category information and the geometry restraints in the same file, and we would strongly recommend this for an easier life: the covalent_grade_create_linkdic.pl tool used in the grade-for-covalent-linkages tutorial generates this sort of combined file.

There is also an alternative format for connectivity libraries, used in $BDG_home/tnt/data/connect.dat, but the format documented above ought to be used for new work.


Tom Womack & Maria Brandl,<buster-develop@GlobalPhasing.com>
Last modified: Thu Jan 5 09:16:12 GMT 2017