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

Release 1

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 the programs:


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. 

Release 2A

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 groups.

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". 

Release 2B

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.). 

Release 3

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. 

Release 3A

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. 

Release 3B

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 L. 

Release 3C

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 bugs.

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.

Release 3D

Oct 5, 1987 (DET)

OVERLAY can now read an arbitrary transformation via the MATRIX and TRANSLATION cards.

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 be calculated.

CONVERT now produces CHAIN cards when a PUNCH SEQUENCE command is given. It does not put linkage information on these cards.

Release 3E

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 program.

Release 4B

Feb 22, 1991 (DET)

TNT in general:


Release 4C

Jul 30, 1991 (DET)


Utilities: Rotation Function Module: VIRTFFT, EXPANDER: SHIFT:

Release 5A

Jul 23, 1992 (DET)



Release 5B

Jan 4, 1993 (DET)



Release 5C

Aug 5, 1993 (DET)



Release 5D

Jan 24, 1994 (DET)

All Programs


Release 5E

Mar 13, 1995 (DET)

All Programs

FOURIER Operation in General

Release 5F

  Release date: July 6, 2000 (DET)


 From_pdb  RFACTOR  FOURIER  All Programs (Control File)  NCS  Pekpik  SHIFT  FOURIER, Correct  GEOMETRY  OVERLAY, NCS  OVERLAY  Gather_Map  RFACTOR, FOURIER