Prime User Manual - ISP

Table 11.5. Keywords for the multirefine input file (Continued)
Keyword syntax Description
Chapter 11: Command Syntax
LOOP_i_RES_j Specify beginning and end of loops. Same as for refinestruct. Required if
SEG_LIST is not given. Depending on the protocol, 1, 2, or an arbitrary number
of loops may be specified. For example, to specify the beginning and end
of loop 0, from residue 10 to residue 20 in chain A, use the following:
LOOP_0_RES_0 A:10
LOOP_0_RES_1 A:20
MAX_JOBS n Maximum number of subjobs that can run at one time. This can be set to a
value less than the value of THREADS if sufficient resources are not available.
Not available with refinestruct.
PRIME_TYPE n Type of refinement to be carried out. Can be specified as either a number or
text string. Different from refinestruct. Available choices are:
0 or default: Equivalent to running a single loop refinement using
refinestruct. Not particularly useful except for completeness and testing
purposes. Does not recognize THREADS keyword.
1 or extended: Used for Extended Sampling from the GUI. Does not recognize
MIN_OVERLAP and MAX_CA_MOVEMENT keywords, as these are used
internally by the protocol. Accepts multiple loops as input which will be
run sequentially.
2 or long_loop: No longer used.
3 or loop_pair: Used for Cooperative Loop Sampling from the GUI.
Exactly two loops must be specified.
2 or long_loop_2: Used for Ultra-extended Sampling from the GUI. Does
not recognize MIN_OVERLAP and MAX_CA_MOVEMENT keywords, as these
are used internally by the protocol. Also does not recognize THREADS keyword,
as the sampling is determined by the loop length. Only one loop can
be specified.
STRUCT_FILE Required. The input structure file in Maestro format. Same as for
refinestruct.
SEG_LIST filename Name of a file containing the list of loops to be refined. For the example given
for the keyword LOOP_i_RES_j, the file would consist of the single line:
loop A:10 A:20
Not available with refinestruct.
THREADS n Number of simultaneous jobs to be run during selected refinement stages.
Determines the sampling level for some protocols. Note: the jobs specified by
THREADS do not have to actually run in parallel—see MAX_JOBS. Not available
with refinestruct.
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