| MakeTNT-toolkit User Documentation | previous next |
| MakeLINK |
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All rights reserved.
This software is proprietary to and embodies the
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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.
| % MakeLINK -p <pdb-file> [-s <input-sequence-file>] [-o <output-sequence-file>] [-d <link-parameter-file>] [-a] [-f] |
| Argument | Description | Possible Values | Compulsory | Note |
|---|---|---|---|---|
| -p <pdb-file> | name of PDB-file submitted | no format restrictions, any extension | yes | |
| -s <TNT-sequence file> | name of initial TNT-sequence file to use | no format restrictions, any extension | no; -a is assumed if neither -s nor -o option is given | generated by pdb2seq or manually |
| -o <TNT-sequence file> | name to give to output sequence file | no format restrictions, any extension | no; is filled in as pdb-file.seq or seq-file.1 if not given | no |
| -d <link-parameter file> | Name of library of user defined residue-residue links | no format restrictions, any extension | No; but you can use more than one -d option | user generated, example |
| Switch | Description |
|---|---|
| -a | Generate the sequence file automatically from the PDB input |
| -f | Overwrite the output file if it already exists |
All inter-residue contacts
d = r-atom1 + r-atom2 + 0.30Å;
with r-atom1 and r-atom2 representing the element specific covalent radii (loaded by default from $BDG_home/database/lists/atom.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.
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.
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:
Example input files (pdb1uvq.ent, pdb1eau.ent) can be found in $BDG_home/samples/maketnt/MAKELINK/1EAU and $BDG_home/samples/maketnt/MAKELINK/1UVQ.
which will make a sequence file pdb1uvq.ent.seq;
if you look at this file, you will see lines like
RESIDUE
B|19 ASN 20 XGPEPTIDE 1193 S001
which indicates that the ND1->C1 linkage between ASN residue 20 and (NAG) residue 1193 has been recognised.
As another example, consider
MakeLINK -p pdb1eau.chk.pdb
-a
This will complain
A link of type U01 has been found between OG of A|195 and C2 of B|1 There is no linkage between those atoms described in the LINK cards Please add a LINK record or re-run with -l |
That sequence file will call the link 'U01'. If you happen to have
a description of this kind of linkage handy - say in
$BDG_home/samples/maketnt/MAKELINK/1EAU/SBDK.connect - you can use
MakeLINK -d
SBDK.connect -p pdb1eau.chk.pdb -a -l
and get a sequence file in which the link has a more sensible name. Note that you have to use the -l SBDK.dic option to BUSTER so that it knows the geometry for the residue.
The locations of the element-properties file, main connectivity library and atom-specific connectivity library can be specified using the environment variables
MakeTNT_connect The main connectivity library MakeTNT_elements The element-properties file MakeTNT_connectat The atom-specific connectivity library
or on the command line using entries of the form MakeTNT_connect=/home/user/my_connect.dat.
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.
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.