Molecular replacement - MOLREP¶
Input¶
MOLREP is a quick and simple-to-use molecular replacement Task using a homologous search structure, (and optionally) the sequence of the target model. The best solution is subsequently submitted to REFMAC for 5 cycles of refinement.
Full documentation can be found at: http://www.ccp4.ac.uk/html/molrep.html
The Task only searches for a single or multiple copies of one component in each run. The expected number of copies can be input by the user, or estimated by the program, assuming a solvent content of about 50%
For multi-component structures, MOLREP will attempt to place the full complement of the first component(s), and then a second MOLREP task to search for the next component should be carried out with the first solution model defined as a ‘fixed’ structure.
If a sequence is provided, MOLREP will perform a sequence alignment of target sequence to that of a SINGLE CHAIN of the search model, and the input chain is then modified by renaming and pruning non-conserved residues. Therefore, if you wish to use a search model that is a multimer with several copies of a single sequence, it is essential to use CHAINSAW or SCULPTOR to edit all chains of the model.
Essential input items¶
Reflection data (1), Free R set (2), Input model (3). Atom Selection (4): it is possible to select only part of the search model coordinates; e.g. only peptide, or a single chain, or a span of residues.
Prior to running MOLREP, sophisticated model preparation can use the Bioinformatics tools provided. The Interactive Model preparation using MrBump & CCP4mg is comprehensive and produces an ensemble of aligned pruned models. Alignment of the template and target sequence can be obtained from tools such as HHPred, PROMALS3D or FFAS; and these alignments used in the SCULPTOR or CHAINSAW Tasks to edit the search model.
Optional input items¶
If no sequence is input, the search model is used as is.
Sequence of Target Model (5). The sequence of one component only can be provided either from the “Define AU contents” task, selecting the single sequence to be used, or from a Sequence file giving the sequence of a single chain. MOLREP will then perform a sequence alignment of the first chain of the search model and target sequence, and modify the input model by renaming and pruning non-conserved residues. The names of the retained atoms will be changed to match the target, while conserved residues are left unchanged. The residues in the modified model are numbered to be consistent with the target sequence, i.e. if a residue in the target corresponds to a gap in the model, the residue numbers in the output model will contain a gap, but if a residue in the model corresponds to a gap in the target, the residue numbers in the output will be consecutive.
If the AU contents contains multiple sequences, then a single sequence must be selected for each MOLREP pass.
Number of monomers to search for (6). The number of copies of the given model expected can be specified by the user, or automatically estimated by MOLREP. MOLREP will take the best results for a first search, fix this result, and search for second, third, and so on, copies.
Fixed Model: (7) If some of the structure is already known from a previous MR run those coordinates should be entered as the ‘fixed’ structure.
Basic Options¶
Space group Selection. (1). Where there is ambiguity, MOLREP will attempt the first component search in more than one space group. After identifying the most likely space group for the first copy, subsequent searches for multiple copies will be carried out in that space group..
Resolution range (2). MOLREP uses data to the specified resolution limit. The refinement step uses all input data.