Action: SECONDARY_STRUCTURE_RMSD
| Module | secondarystructure |
|---|---|
| Description | Usage |
| Calclulate the distance between segments of a protein and a reference structure of interest |   |
| output value | type |
| a vector containing the rmsd distance between each of the residue segments and the reference structure | vector |
Output components
This action calculates the values in the following table. These values can be referenced elsewhere in the input by using this Action’s label followed by a dot and the name of the value required from the list below.
| Name | Type | Description |
|---|---|---|
| struct | vector | the vectors containing the rmsd distances between the residues and each of the reference structures |
| lessthan | scalar | the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold |
Input
The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.
| Keyword | Type | Description |
|---|---|---|
| RESIDUES | atoms | this command is used to specify the set of residues that could conceivably form part of the secondary structure |
| ATOMS | atoms | this is the full list of atoms that we are investigating |
Further details and examples
Text from manual goes here
References
More information about how this action can be used is available in the following articles:
Syntax
The following table describes the keywords and options that can be used with this action
| Keyword | Type | Default | Description |
|---|---|---|---|
| RESIDUES | input | none | this command is used to specify the set of residues that could conceivably form part of the secondary structure |
| ATOMS | input | none | this is the full list of atoms that we are investigating |
| BONDLENGTH | compulsory | none | the length to use for bonds |
| TYPE | compulsory | DRMSD | the manner in which RMSD alignment is performed |
| D_0 | compulsory | 0.0 | The d_0 parameter of the switching function |
| NN | compulsory | 8 | The n parameter of the switching function |
| MM | compulsory | 12 | The m parameter of the switching function |
| SERIAL | optional | false | do the calculation in serial |
| NOPBC | optional | false | ignore the periodic boundary conditions |
| SEGMENT | optional | not used | this is the lists of atoms in the segment that are being considered |
| STRUCTURE | optional | not used | the reference structure |
| STRANDS_CUTOFF | optional | not used | If in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like |
| CUTOFF_ATOMS | optional | not used | the pair of atoms that are used to calculate the strand cutoff |
| VERBOSE | optional | false | write a more detailed output |
| LESS_THAN | optional | not used | calculate the number of a residue segments that are within a certain target distance of this secondary structure type. Options for this keyword are explained in the documentation for LESS_THAN. |
| R_0 | optional | not used | The r_0 parameter of the switching function |