Commands and their use

The input consists of a sequence of comments, commands and directives.

The commands are headed by ‘%’ character and directives must follow the related command.

Sir2019 recognizes the following commands:

%WINDOW

A window is opened to monitor the process of solution and refinement of the structure (default).

%NOWINDOW

The program is forced to run without graphics.

%DATA

Data input routine.

%INVARIANTS

Invariants routine.

%PHASE

Phasing routine + Direct Space Refinement routine.

%IMPORT file

Used to import a structural model (for Simulated Annealing).

%SANNEL

Simulated Annealing routine.

%REMO

Molecular Replacement routine.

%MAD

Protein structure determination routine using SAD/MAD data.

%END

End of the input file

%JOB string

A caption is printed in the output.

%CONTINUE

The program runs in default conditions from the last given command up to the end.

%STRUCTURE string

This command is used to specify the name of the structure to investigate.

%AMB string

This command is used to specify the name of the Automated Model Building program  (Buccaneer, Nautilus, ARP/wARP, Phenix) to be used (proteins only).

%CAB string

This command is used to specify the name of the Automated Model Building program (Buccaneer, Nautilus, ARP/wARP, Phenix) to be used in the CAB (cyclic automated model-building); proteins only.

%REFINE

This command is used to refine phases produced in a previous run of the program or by a different program. Phantom Derivative procedure is used; proteins only.

%CUDA

If a powerful graphic card is available, it is possible to use some CUDA code to speed up the calculations. CUDA specific drivers have to be installed.

Warning: a patch for nautilus_pipeline and buccaneer_pipeline  is needed in CCP4. Add the blue line at the beginning of these two files:


import sys

sys.path.append(“/home/john/ccp4-7.0/lib/py2/”)

from CCP4pipeline import Control

The program creates the name of some needed files, adding the appropriate extension to the structure name. The file names are:

string.bin  →  direct access file
string.plt   →  coordinate file for graphics
string.pdb  →  coordinate file in PDB format (proteins only)
string.mtz  →  reflections file in MTZ format (proteins only)

If %STRUCTURE command is not used the default string “struct” (instead of the name of the structure) is used to create file names.

Directives are described here, in the sections dedicated to the various routines.

All commands and directives are in free format (between columns 1-80) and are case independent. Only the first four characters are significant. The keywords can start in any position. If the first non-blank character is “>” or “!” then the record is interpreted as a comment; characters following “>” or “!” will be ignored.

Sir2019 preserves intermediate results. The first routine used must be DATA, if it has not been used in a previous run.

The minimal information needed by Sir2019 is constituted by:

    • cell parameters;
    • cell content;
  • reflections.
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