Appendix A.

New Features for Version 2.6 --- July, 1996}
.} Use isomorphous or anomalous difference map peak as a criterion in the combined MR search. New options DIFFerence and ANOMalous to the command FUNCtion.

New Features for Version 2.5 --- April, 1996
.} Calculate correlation coefficient and R factor values for each solution from POPC option. And check packing as well.
f .} New option ECEC, for doing phased translation function (EOEC) using phases from molecules with T flags.
.} New option HAND for command FUNCtion, for changing the hand of the phases for the EOEC option.
.} New SWap option for command COORdinate.
.} Specify the coordinate type on the same line for the CEnter and TRanslate options of COORdinate.
.} The R factor on I is divided by 2 to place it on the same scale as that on F.

New Features for Version 2.4 --- February, 1996}
.} The region of unit cell to search for TF solutions can now be assigned automatically by the program. This affects F1F1, F2F2, FOFC, IOIC, RFMAp, RFPEak, and RFPC searches. For POPC and EOEC searches, the entire unit cell will still be searched.
.} An R factor is now also calculated for each of the solutions from the RFMAp, RFPEak, RFPC searches. The solutions can be sorted either on the correlation coefficient or the R factor.
.} The program has been successfully compiled and run on a Cray J-90. Small modifications in routine NUPAGE are needed to get the current time.

New Features for Version 2.3 --- December, 1995}
.} For TF based on the RF results (RFMAp, RFPEak, RFPC), the program will save the top few peaks (rather than the highest peak only) in the POPC map and then check packing for each of the peaks. The ones that have good packing will be considered as possible solutions. A new option RFSAve is implemented. The input to RFMAp is slightly different.
.} The atom C1' from each nucleotide is also included for packing check purpose.
.} Various bug fixes.
.} Updated the documentation.

New Features for Version 2.2 --- July, 1995
.} The rotation function results can be directly input to the TF program. Four new options (RFFIle, RFMAp, RFPEak, RFPC) have been implemented for the FUNCtion command.
.} The program will automatically do a packing check for the peaks in the translation function.
.} Modified the packing check to make it run faster.
.} The program will select both Ca and P atoms for packing check.
.} Modified the coordinate I/O routines to fully support the PDB format.
.} Various bug fixes.
.} Updated the documentation.

New Features for Version 2.1 --- May, 1995
.} Structure factor calculation by FFT is now supported.
.} FFT calculations for the POPC and EOEC translation functions are now available in the program. The program will peak search, dump, and contour the functions. The map input/output routines are updated to reflect this change. \
.} Scratch file is now opened with status SCRATCH. All other output files are opened with status UNKNOWN. This will overwrite old files.
.} Provided labeling of the axes in the contour plots. Allow the plotting of a small region of the map (new command CNTRegion).
.} Scattering factors for most common atom types are provided as default. Unknown atoms are ignored.
.} A new scheme is devised for the storage of the structure factors for the R molecule. This eliminated the need to keep two separate versions (high and low symmetry) of the program.
.} The chain and insertion code columns of the PDB file are now supported (new COORdinate CHain command). Only PDB records starting with ATOM and HETA are kept. Hydrogen atoms are removed.
.} Various bug fixes.
.} Updated the documentation and designed several example input files.

Appendix B.

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