| This is part of the secondarystructure module |
Calclulate the distance between segments of a protein and a reference structure of interest
- Examples
- Glossary of keywords and components
- Description of components
By default the value of the calculated quantity can be referenced elsewhere in the input file by using the label of the action. Alternatively this Action can be used to calculate the following quantities by employing the keywords listed below. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.
| Quantity | Description |
| struct | the vectors containing the rmsd distances between the residues and each of the reference structures |
| lessthan | the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold |
- The atoms involved can be specified using
| RESIDUES | this command is used to specify the set of residues that could conceivably form part of the secondary structure. It is possible to use residues numbers as the various chains and residues should have been identified else using an instance of the MOLINFO action. If you wish to use all the residues from all the chains in your system you can do so by specifying all. Alternatively, if you wish to use a subset of the residues you can specify the particular residues you are interested in as a list of numbers. Please be aware that to form secondary structure elements your chain must contain at least N residues, where N is dependent on the particular secondary structure you are interested in. As such if you define portions of the chain with fewer than N residues the code will crash. |
- Or alternatively by using
| ATOMS | this is the full list of atoms that we are investigating. For more information on how to specify lists of atoms see Groups and Virtual Atoms |
- Compulsory keywords
| BONDLENGTH | the length to use for bonds |
| TYPE | ( default=DRMSD ) the manner in which RMSD alignment is performed. Should be OPTIMAL, SIMPLE or DRMSD. For more details on the OPTIMAL and SIMPLE methods see RMSD. For more details on the DRMSD method see DRMSD. |
| D_0 | ( default=0.0 ) The d_0 parameter of the switching function |
| NN | ( default=8 ) The n parameter of the switching function |
| MM | ( default=12 ) The m parameter of the switching function |
- Options
| SERIAL | ( default=off ) do the calculation in serial. Do not parallelize |
| NOPBC | ( default=off ) ignore the periodic boundary conditions |
| VERBOSE | ( default=off ) write a more detailed output
|
| SEGMENT | this is the lists of atoms in the segment that are being considered. You can use multiple instances of this keyword i.e. SEGMENT1, SEGMENT2, SEGMENT3... |
| STRUCTURE | the reference structure. You can use multiple instances of this keyword i.e. STRUCTURE1, STRUCTURE2, STRUCTURE3... |
| STRANDS_CUTOFF | 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. This keyword speeds up the calculation enormously when you are using the LESS_THAN option. However, if you are using some other option, then this cannot be used |
| CUTOFF_ATOMS | the pair of atoms that are used to calculate the strand cutoff |
| LESS_THAN | calculate the number of a residue segments that are within a certain target distance of this secondary structure type. This quantity is calculated using \(\sum_i \sigma(s_i)\), where \(\sigma(s)\) is a switchingfunction. |
| R_0 | The r_0 parameter of the switching function. |
1.8.17