Using qconvert to convert restraint files

The qconvert script converts a restraints file to AQUA format, and simultaneously splits the file into NOE, hydrogen bond, disulphide, generic distance and torsion angle components. The script attempts to determine file type and data types from the file contents. Several options can be set to guide the data interpretation. See Restraint conversion on how to handle when the conversion or splitting fails.

The command syntax is as follows:

    qconvert  [options]  RESTRAINT_FILE  [RESTRAINT_TYPE]

The options (can be given in any order) are:

   [-r RESTRAINT_PREFIX]   [-od OUTPUT_DIR]  [-l]  [-fatal]  [-simple]
   [-t FILE_TYPE]  [-mr|-nomr]  [-i]  [-nosplit]  [-h VALUE]  [-f]  [-c VALUE]

where

RESTRAINT_FILE is the name of the restraints file to be converted into Aqua format, and should include the full path unless the file is in the default directory. (If the restraints are in several files, see below).
[RESTRAINT_TYPE] can be one of: noe, hb, ss, dis, tor. If not given all available types will be handled.
[-r RESTRAINT_PREFIX] optionally sets the value of RESTRAINT_PREFIX which is the root name of all the files output by qconvert, namely:
If the -r option is not used, the RESTRAINT_PREFIX is taken from RESTRAINT_FILE by stripping away the extension and path.
[-od OUTPUT_DIR] is the optional name of the directory into which the output files are to be written. By default they will be written to the current directory.
[-l] if set, show messages from conversion phase (will be shown anyway in case of errors).
[-fatal] if set, exit with error if information on data types is found to be inconsistent; otherwise, just print a warning.
[-simple] if set, skip interpretation of data types and treat all as NOE type. See Restraint conversion.
[-t FILE_TYPE] optionally sets a number (currently 1, 2, 3, 4 or 99) which tells qconvert the file format of the input restraints file, namely:
If the -t option is not used, the file type is determined automatically from the contents of the file. If the type can not be determined it is set to 99.
[-mr|-nomr] defines whether input file is (not) an MR file. (See 'qhelp mr'). If not given, the MR type will be determined automatically.
[-i] if set, the file should contain special identifiers indicating the data type(s), and data types will not be assigned by the script. Default is automatic data type assignment. See Restraint conversion.
[-nosplit] if set, guess file type, but skip splitting, and start conversion directly, assuming that split files already exist. See Restraint conversion.
[-h VALUE] set the 'how' option for the data type interpretation. See Restraint conversion.
[-f] if set, turn on 'fixorig' option. Only relevant for MR files. See 'qhelp mr'.
[-c VALUE] set the value of the 'chain' variable. Only relevant for MR files. See 'qhelp mr'.

The last 5 options are normally not set. The -t option can be used if the script can not determine the file type correctly. See Restraint conversion for more details on problem handling.

Typing 'qconvert' without arguments will give a usage summary.

Important

If restraints reside in different files, the user should take care to give all converted files the same "restraint prefix" if the analysis is to take into account all data.

Example 1

If we have two restraint files called 'mynoes.tbl' and 'mytor.tbl', conversion can be accomplished by:

    qconvert  mynoes.tbl
    qconvert  -r  mynoes  mytor.tbl

giving converted files 'mynoes.noe' and 'mynoes.tor'. Since this particular "restraint prefix" is rather confusing, a better alternative is something like:

    qconvert  -r  mydata  mynoes.tbl
    qconvert  -r  mydata  mytor.tbl

giving converted files 'mydata.noe' and 'mydata.tor'. Note: the extension '.tbl' does not have any special meaning for Aqua. Any extension, or no extension at all, may be used for the original restraint file.

Example 2

To enforce qconvert to recognize a DIANA file, and to show all output, give the command in this form:

    qconvert  -t  4  -l  mynoes.tbl