New Features in TNT
Here you will find a description of the additions to TNT in each release.
The current release is 5F. To see what you will
get by upgrading to the latest release of TNT find the next release after
what you currently have and read to the end of this page.
Table of Contents
This is the first release of this refinement package. I have never before
collected together all of the required and related programs and have almost
certainly forgot something important. There are a number of undocumented
programs in the UTIL area. They are used to analyze a model in various
manners. The plotting programs all use CALCOMP plotting routines, so if
you can't plot such things you don't need to worry about the functions
of the programs. Here is a short summary of the functions of several of
DIFFPLOT -- Plots the differences between two coordinate sets.
BPLOT -- Plots the main chain B values.
MCONT -- Using data PUNCHed by NEWGEO this program contours a TenEyck density
map and can superimpose atomic labels and bonds.
DIRDOT -- Calculates the angle between two direction file shifts in refinement
MODEL -- Calculates a model electron density map from a set of coordinates
for use in a FFT program.
CONVERT -- Converts ATOMx formats to Diamond or AMSON or back again.
Work has already began to attempt to fix the bug related to low B factors
of heavy atoms in ADERIV but a suitable solution has not been found yet.
Work is also progressing toward a more rational description of multichain
proteins. In the present package and most other packages if one has a structure
with two polypeptides of identical sequence each corresponding residue
must have different names and the amino acid sequence must be given twice.
A method to avoid this has been devised and is being written into the next
release of this package.
I am considering how I can handle curvatures within the package. I have
some ideas but I have not worked out the details of a implementation.
Dec 14, 1984 (DET)
I have prepared release 2a and am sending it off. This release has several
improvements over release 2 and all the errors reported Release 2 have
been corrected. The FFT subdirectory programs have been completely reworked
with several new space groups added. They all now conform to a uniform
standard of file units and input parameters. I had hoped to have more Fourier
synthesis programs ready but they have proved more difficult than I had
expected at first. The program EXPANDER is very useful for expanding Fourier
coefficients to lower symmetry space groups, especially to P1 but it will
also expand to monoclinic and orthorhombic space groups. This additional
functionality is not useful until some FS programs exist for those space
I have at long last fixed the problem I was having with temperature
factor gradient calculation. This correction is covered in the write-up
in the sections concerning the new BLUR card for ADERIV. BDERIV is now
no longer useful but has been maintained in the release "just in case".
Mar 5, 1985 (DET)
Here is release 2b. The major difference between 2a and 2b is that I
have fixed a great number of the errors in Release 2A. I have added two
new FFT programs: P2YSF and P2ZSF, and worked a little on MCONT (though
a write-up for that program still does not exist.).
Aug 26, 1986 (DET)
This is release 3. There have been many changes between release 2b and
3. A new structure factor calculation program, which is space group general,
has been added. A great many modifications, corrections, and additions
have been made, the number being too great to allow a complete list. All
known errors have been corrected.
Nov 11, 1986 (DET)
This is release 3A. This release incorporates corrections for all known
errors. A new version of GENERALSF has been included. This version reads
the coordinate file directly, and eliminates the need to write the map
file to disk. This programs expects a different set of input than the old
version and command files will have to be modified.
This version also has a modification to NEWGEO which allows that program
to process EXCLUDE cards with wild cards much faster. Using wild cards
to specify an entire chain could take an enormous amount of time before
but the new code is very fast.
Apr 5, 1987 (DET)
There are few differences between 3A and 3B. Other than a few minor
bugs which have been eliminated the main difference is the inclusion of
a number of new Fourier synthesis programs.
The default behavior of EXPANDER has been changed. Before it always
chose an asymmetric volume with L positive. This was proper for Y sectioning
FFT's, but those programs are no longer used. Now the K direction is always
restricted to positive values and the user can choose to restrict H or
Jun 26, 1987 (DET)
New to this release is the incorporation of the real space refinement
module, and the documentation of the BCORREL and phase refinement modules.
These new modules have not been extensively tested and may incorporate
Also several types of VAX specific code have been changed to FORTRAN-77.
There are still quite a few things which a compiler insistent on FORTRAN-77
will choke on, such as many variables and subroutines with names longer
than six letters.
RFACTOR can now compensate for the lack of a solvent continuum in the
protein structure model. This is effected with the SOLVENT card. The method
used has some quirks and will behave badly in some circumstances.
Oct 5, 1987 (DET)
OVERLAY can now read an arbitrary transformation via the MATRIX and
SHIFT now prints a short summary of all the contributing modules in
the long loop.
ADERIV requires that a BLUR card be given whenever gradients are to
CONVERT now produces CHAIN cards when a PUNCH SEQUENCE command is given.
It does not put linkage information on these cards.
Jan 15, 1988 (DET)
All usage of BYTE arrays for data input have been eliminated. This change
improves the adherence of the source code to FORTRAN- 77 standards. Most
of the remaining non-standard elements of the source code are inconvenient
but not difficult to change.
All of the space-group specific Fourier synthesis programs have been
replaced by GENERALFS. The manual has been modified to describe this new
Feb 22, 1991 (DET)
TNT in general:
Rotation function refinement
Rotation function maps
Use of MAKE for recompiling
Read input from terminal instead of FOR001
Major programs operate on VMS and E&S UNIX
No longer requires Weights
No longer requires scale factors from RFACTOR
Removed CURVATURE command
Difference Paterson coefficients with IO-IC
Added the PUNCH COEFFICIENT command
Rewrote the FUNCTION command
Added GRADIENT and CURVATURE cards
Both write out proper coefficients for FFTDERIV
CURVATURE cards writes out curvatures
New curvature code more accurate
New curvature code can sigma weight
Cleaned up REPORT ANISO code: Now produces standard Bij's
Added checking of incoming parameters against RANGE cards
(Only if those parameters will be shifted)
Added the JIGGLE command
Removed the ADDB card and created ADD
Jul 30, 1991 (DET)
Conjugate direction method added.
Rotation Function Module:
HKL_FILES utility created
ADDHKL, PAKTOHKL removed from package
Symmetry handling corrected.
Curvature still does not work.
COMBINE cards cannot be used with gradient over curvature or conjugate
Jul 23, 1992 (DET)
Removed all INTEGER*2 declarations. This allows the maximum number of atoms
to be raised above the 32K boundary. The current maximum is 80,000 atoms.
The NOTE card has been created. This card contains an unechoed remark.
In effect it causes no action to be performed. Your can use it to include
quite remarks about the contents of a data file.
Added a PUNCH <> BLOCKDATA command. This command writes the FORMFACTOR
card information in a BLOCK DATA format suitable for compiling with the
FFT programs. Also added PUNCH <> ATOMx command for compatibility.
Program has been removed from package. All functions subsumed into RFACTOR.
Real space refinement works once again. The procedure is much simpler than
before. All specific functions are performed by RFACTOR in a fashion directly
analogous to reciprocal space refinement.
Program now can calculate and PUNCH maps. The functions of ADERIV and FFTDERIV
have been incorporated and those programs have been removed from the package.
New program created which replaces GENERALSF, GENERALFS, MAPREADSF, MODEL,
HKL_FILES, ADD_HKL, and includes additional functionality. Eliminates the
need for EXPANDER. The replaced programs have been removed from the package.
NEWGEO has been renamed GEOMETRY
The REPORT GEOMETRY command now produces meaningful statistics for torsion
and pseudorotation angles. They are split into a separate class for each
legal value and the mean and sigma are produced for each.
Moved to the utility area (TNT_UTIL:)
Jan 4, 1993 (DET)
Numerous problems were discovered with the Unix version upon porting to
the Convex. The corrections have been incorporated into the current version.
Makefile macros are now listed for Sun-4 and DECstation workstations in
the MAKEFILE.MIPS file. TNT still will not function on a Stardent.
CHAIN card linkages have been redefined to mean that the linkage is to
the nearest symmetry image of the target.
The LINK card has been created to allow linkages to symmetry related molecules
in single chain structures.
The data request code has been modified to allow the processing of command
verbs. This allows the calling program to perform almost any transformation
of the data using this mechanism.
Aug 5, 1993 (DET)
Added CORRECT source to PUNCH command. This modifier causes the data to
be moved to the correct asymmetric unit and sorted in the proper order
before being dumped to disk.
Added program to package. This program will calculate Wang type envelopes
and produce solvent flattened maps.
RFACTOR, FOURIER, SOLVENT
Added the ability to read and write DSN2 format files.
Can write maps in DSN6 format.
Added SWAP_PHASE coefficient type to replace the functionality of SWAP_HKL.
The coefficients produced contain the amplitude from the FO file (scaled
to the FC's) and the phase from FC.
Added more intelligent B correlation restraints to this program. Also devised
a library of standard values. BCORREL is now obsolete.
Jan 24, 1994 (DET)
Expanded the power of the code which reads the input. One can now continue
a card over several line by having either a "-" or "\" on the end of the
line. One may also declare the remaining portion of the line a comment
with a "!" or "%".
RFACTOR, FOURIER, SOLVENT
When reading PDB files Convert will now convert the C-terminus from a PDB
style one to TNT's CTERM linked residue. In addition Convert will read
the SSBRIDGE cards in a PDB file.
These programs will now write correct DSN6 files on big endian machines.
A program for constraining and restraining a model to noncrystallographic
symmetry has been included in the package. It will refine most such cases.
Mar 13, 1995 (DET)
The continuation character "-" must now be preceded by a blank. This change
was made to reduce the confusion resulting from names which end in this
character, like "CL-".
The TRANSFORMATION statement allows general linear transformations to be
defined and later used with the APPLY command. A transformation can be
expressed as a matrix, the rotation about an axis, Euler angles, or an
equivalent position. Translations can be applied as well. The transformation
can be expressed in the coordinate systems - TNT orthogonal, PDB orthogonal,
Operation in General
Fourier will now find peaks in a map. This is done by PUNCHing coordinates
with a map as a SOURCE. An attempt to estimate the B value a water molecule
would have to have to produce a peak of that height is made. For this calculation
to be accurate the map's density values should be in e/A^3, which means
that a difference map must be multiplied by 2.
Most operations involved in refinement can be performed using canned scripts.
A .tnt file is required. The new commands are:
tnt -- Runs several cycles of refinement
geometry -- Screens for the worst geometry
rfactor -- Prints the R-factor and scaling
correct -- Moves the Fobs to the proper asymmetric unit
diffcor -- Compares two coordinate files
pekpik -- Finds the highest peaks, makes DSN2 file
make_maps -- Makes Fo-Fc and 2Fo-Fc DSN6 maps
to_pdb -- Converts the coordinate file to PDB
from_pdb -- Converts a PDB file to TNT format
to_dsn2 -- Converts the coordinate file to DSN2
Release date: July 6, 2000 (DET)
Convert can reformat TNT style geometry restraints, expressed on GEOMETRY
cards, to Frodo and O's REFI format. While much of the work is done
automatically you will likely need to fine tune the result. A document
has been written to describe the process.
Convert will now read PDB files with multiple models. This usually
only occurs for NMR models. Convert will construct a chain name which
is a combination of the PDB chain name and the model number. For
example chain C of the third model becomes C_3.
An option has been added to the PDB reading subroutine which allows all
hydrogen atoms to be ignored. This option is NO_HYD.
When PUNCHing PDB files Convert will convert a TNT style C-terminus to
a PDB style. This involves moving the extra oxygen into the final
amino acid and naming it OXT. This conversion does not work with
statically disordered C-termini.
When PUNCHing PDB files residues will be written in sequence order.
All peptides and nucleic acids will be written from the beginning to the
end. This does not mean that the polypeptide fragments will come
out in the order you expect, only their amino acids are ordered.
In the past TNT would often write amino acids out of sequence since TNT
does not care about the order of atom records.
Convert now interprets and writes TER cards when working with PDB format
files. This improves the reliability of the sequence file generated
from a PDB file, if the PDB file itself contains TER cards, and most do
The ADD and JIGGLE commands now will use the RANGE statement to generate
upper and lower bounds to B and OCC parameters. These defaults can
be overridden by adding a RANGE modifier to either command.
This script now sets an option which causes Convert to omit all
hydrogen atoms from the new coordinate file.
Added the PUNCH SCALE command. This will write a SET card to a file
which can be read back into the program in another context. This
is useful for calculating R-free.
You may now PUNCH maps with Fourier coefficient types (FO-FC)**2, and IO-IC
directly. In the past you were required to write these coefficients
to disk and transform them with Fourier by explicitly specifying the Patterson
space group. Rfactor now knows how the space group is changed during
the recombination of crystallographic data.
Anisotropic scaling between Fo and Fc is now be performed during refinement
and map calculation. If you have refined a model without anisotropic
scaling the initial scale factors calculated by Rfactor will be underestimated
in magnitude. As you refine they will become larger.
The ACCEPT statement will now allow defaults to be used. If you only
put one number on a line that expects two that number will be presumed
to be the new upper limit and the default value used for the lower limit.
The default is not to impose a limit at all.
The determination of scale factors relating Fobs and Fcalc has been made
much more robust. This step used to fail often and ask for the user
to create SET statements. Even though the program can always calculate
values for the scale factors the actual values may be physically unreasonable.
If they are bad enough the program will terminate, demanding more SET statements.
Even if the program runs you must still be vidgulent and add
SETs if the scale factors are poor.
All Programs (Control File)
You may now read a set of Fourier coefficients and PUNCH out a Patterson
map. This is done with the PATTERSON modifier to the PUNCH command.
Just use PATTERSON in place of SOURCE.
Added the CLEAR card which allows previous information to be ignored.
This is useful for overriding TNT's default geometry library, or scattering
factors. You can also clear the space group or the atoms, if the
need presents itself.
The ASSUME RESIDUE_TYPE statement has been created. This statement
allows you to define the default residue type for a residue which contains
all the atoms in a list of atom names, but no extras. Since this
is the equivalent of a RESIDUE statement without any links, it is only
useful for solvent residues. However, it does allow you to freely create
and delete solvent without being forced to edit the sequence file. Built
into all programs is the ASSUME statement which defines any residue which
contains only an OH atom to be of type HOH. No more sequence file
entries for water molecules!
The TRANSFORMATION card has been extended to include a SHIFT B and SHIFT
OCC term. This allows refinement of structures where the ncs copies
vary in average B factor or occupancy.
This command has been changed to produce PDB format files instead of DSN2.
To regain the old results use the new Pdb2dsn2 command. (The Unix
version of TNT has always behaved in this fashion.)
The minimization method used by default has been upgraded to "atomic block
diagonal preconditioned conjugate gradient". Each module will produce
a 5x5 block for each atom and pass it to Shift. Shift will perform
a "singular value decomposition" of each atom's block, isolate the nonsingular
subspace, construct the pseudoinverse, and calculate the primary shift
by multiplying the pseudoinverse and the gradient. The primary shift
is then modified via the preconditioned conjugate gradient procedure to
generate the actual shift direction. The biggest improvements arising
from this method are the proper handling of atoms on special positions,
without user intervention, and better optimization in the presence of ncs
restraints. The Geometry module does not produce blocks, only diagonals,
because block diagonal degrades convergence for that module.
The CORRECT source in the PUNCH command of Fourier, and therefore the Correct
shell command itself, will now filter out the "notches" in the reciprocal
space asymmetric unit. While Correct previously allowed a small number
of redundant reflections into the HKL file only unique reflections are
now allowed to pass.
A new restraint type, IMPROPER dihedral, has been added. This restraint
can be used in place of a ANGLE restraint in the case of nonplanar atoms
with three ligands. IMPROPER is better at maintaining the pyramidal
shape of these groups than ANGLE. Since the improper dihedrals can
be calculated from the angles one should never attempt to restrain both
at the same time.
One can now PUNCH transformation matrices in several different coordinate
systems. Available options are TNT, PDB, GRID, and FRACTIONAL.
To do so add "SYSTEM PDB", for example, to the end of the PUNCH command
Overlay will now limit B and OCC parameters of transformed models by the
given on the RANGE statement.
This program was created to perform averaging over the ncs related portions
of the asymmetric unit of a map. One map is produced for each CLUSTER.
It does not loop over CLUSTER statements internally; you must give the
program one PUNCH command for each map. A prototype command file
for running this program is given in tnt/doc/gather_map.
When a map is calculated from Fourier coefficients the FOM is now used
to calculate the "best" coefficient instead of blindly taking the F.
Since most maps are calculated using model phases which all have a FOM
of one this change will not affect most operations. It will allow
the proper calculation of MIR maps.