This input block defines the information for translation function calculations, including resolution range, large-term cutoff, and others.

        Remember that the following general input commands can also be used in this input block - comment, echo, and title.

        This defines the cut-off values for the selection of large-terms. CUT1 is used for selecting large-terms for the POPC calculation. CUT2 is used for selecting large-terms for the calculation of the correlation coefficient.

        This defines the criteria for the packing check by this program. The number of Ca atom pairs from different molecules in the crystal that are located within DCUT Angstroms of each other will be counted. If this number is greater than NCUT, the program will assume there is a packing problem, and the MR solution will be discarded. For large structures, NMOD can be set to higher values to select every second, third, or fourth Ca atom only, mostly to speed up the calculation.

        To turn off packing check during the TF calculation, use the command 'DCUToff 0.5 50 4'. Packing check can then be done in the SOlution block.

        For (really) large structures, the NMOD parameter can be set to a number between 5 and 10. The program will automatically select those Ca atoms that are located within the outer most shell of the structure for packing. The thickness of this shell is given by the NMOD parameter in this case. Obviously, this will work only if the molecule is roughly spherical in shape. This will not work if the model is a collection of several distinct molecules (for T flagged molecules). So use this option with caution.

        For nucleic acids, the program will automatically select representative atoms as well.

        This terminates the input to this block. The program will start the actual TF calculation based on the input. This input block can then be repeated.

        This defines the name of the file that holds the RF information. This file is used only if RFINput is set to true.

        During the Combined MR calculation, the program generally can take quite a bit of CPU time. If the correct solution has already been found, the user can tell the program to stop the search for the current molecule and take that solution. To do this, temporarily open a file with the name given by FINFIL in the directory where the program is running. Once the program finds the file, it will stop the calculation. There is a simple way of doing this in Unix, with the touch command. For example, touch como.fin will create the file como.fin in the current directory, with no records in it.

        This file can contain additional information in it. Essentially, the dcutoff, rigid, save, selection, solution, sort, and the target commands are supported, and the inputs are interpreted the same way (except NCAMOD of the dcutoff command is not supported here).

        The solution command defines which of the top solution will be kept as the solution for the current molecule. The other commands will apply to the search of the next molecule. For example

solution 2
select 0.3 0.5
save 100

        This specifies which type of molecules will be searched for in the current TF calculation. If TFFLAG is `R', only molecules with the R flag will be searched, similarly for TFFLAG of `U' and `C'. The default is that all three types of molecules will be searched, in the order R, C, and U flags.

        This defines the search grid size. For POPC calculations, the search grid size is determined automatically by the program.

        This specifies that the RF file contains rotation angles. This file can have several header lines, which is terminated by a line with STOP as the first command. (This STOP record MUST be present in the file). After this line, the rotation angles are read in free-format.

        This defines the name of the TF map file, for the input of a TF map.

        This specifies whether a TF map will be read in. TF map files produced from other programs (for example TF) can be read in this way.

        This specifies whether the TF values will be output to a map. The name of this file will be automatically assigned by the program, based on the the name of the model PDB file. For example, if your model is in the file coords.pdb, the output TF map file will be called coords_tf.map. Map output has not been implemented yet.

        This specifies whether the structure factors will be normalized for the calculation of the TF. The maximum allowed value for the normalized structure factors is given by EMAX.

        For this normalization, the reflections are first divided into shells. An average intensity is then calculated for each shell, and the normalized intensity is given by the ratio of the reflection intensity over the average intensity.

        If QPACK is set to true, the program will do a crystal packing analysis (over all the atoms) for the first molecule with the T flag. The distance cutoff between crystallographically-related atoms is given by the DCutoff command (4 or 5A generally works well for packing analysis). The listing of crystal packing contacts is given in the print file.

        This defines the resolution range for the TF calculation.

        This specifies whether rigid-body optimization of the selected solution will be carried out. This is not truely a least-squares refinement, and is somewhat time-consuming. However, the improvement in the quality of the MR solution by this procedure is well-worth the CPU time needed. Efforts are underway to speed up this calculation.

        This defines the center of rotation for the molecule, in fractional coordinates. Default is that the rotation will be carried out around the center-of-gravity of the molecule.

        This defines how many peaks in the TF will be saved. In combined MR calculation, QSVALL specifies whether all the TF peaks for a given rotation angle will be saved (the default). If not, only the peak with the highest TF value will be saved.

        This defines the selection criterion for RF grid points. Those grid points with RF values between RFCUT1 and RFCUT2 of the maximum RF value will be selected. If NRFPK is non-zero, only the top NRFPK of RF peaks in this range will be selected. RFCUT1 can be based on the absolute value, in terms of the maximum value of the RF. For example, RFCUT1 of 0.5 would mean 50% of the height of the highest RF peak.

        This defines the number of shells for dividing the reflection data. This is used for the selection of large terms and for the normalization of reflection intensities.

        This defines which peak in the listing of MR solutions will be selected as the solution to the MR problem.

        This defines how the TF peaks will sorted on output. The default is to sort according to the correlation coefficeint. If NSRTRF is set to 2, the sorting will be based on the crystallographic R factor.

        This defines the TF search region, in fractional coordinates along the unit cell axes. For POPC calculations, the search region is defined automatically by the program.

        This defines the target function for the TF calculation. Currently supported functions are -

• POPC - Patterson-correlation translation function. This is the fastest TF, and is used by the combined MR protocol.


• F1F1 - correlation coefficient and R factor searches. Correlation coefficients based on F and I, and R factors based on F and I will be calculated. Not supported yet.


• EOEC - Phased translation function based on input phase information.


• ECEC - Phased translation function based on model phase information. The phase information will be obtained from the models with the T flag. This function could prove useful in later stages of the MR calculation on a large complex of molecules, to locate the last few molecules in the complex.

        This specifies how often the program will update/report the solutions during the combined MR calculation. A number between 1 and 10 will specify updates after completing each NRPTTF percent (or 100, which ever is smaller) of the rotation angles. A number between 11 and 100 specifies updates after completing every NRPTTF rotation angles.

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