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Description of available options
Description: Cutoff distance in angstroms. Default: 3.5
This option allows the user to specify the distance that will be used as the cutoff for defining interacting residues. The default distance is 3.5 angstroms. I.e. all atoms within 3.5 angstroms of the ligand will be considered as interacting with it.
Description: Number by which to change protein residue numbers Default: 0
In order to create a plot with residue numbers that correspond to literature, it is possible to offset the residue numbers to adhere to literature. For example, if your coordinate files start with ALA1, but in the literature this is referred to as ALA31, a residue offset of 30 would be used to produce plots with numbering that is consistent with the literature. The offset can be a negative number if a negative shift is required.
Works with proteins that have several chains - all residues will be shifted.
Warning: This option will not work if you need to offset only a part of the protein or a single chain - residue numbers of all residues associated with the protein will be shifted according to residue offset option.
Description: Minimum fraction of the simulation time that means an interaction is plotted Default: 0.3
Since plotting all interactions that occur during a simulation would often be meaningless and create noisy and ugly plots, a cutoff for interaction frequency has been implemented. Frequency is calculated for all interactions that are analysed by LINTools (e.g. residence time and hydrogen bonding). So if a hydrogen bond has been observed in half of the frames of a simulation, it will be given a frequency of 0.5.
Since LINTools is capable of analysing more than one trajectory, frequencies are summed and the analysis cutoff is multiplied. So for 2 trajectories with 100 frames with analysis cutoff of 0.2, a feature has to appear for 60 frames of total simulation time - does not matter whether all frequency comes from one simulation or it is present in both.
It is possible to choose how many frames will be analysed by setting up start, end and skip options. These are frame numbers not time so take care when submitting. For multiple trajectories, just submit numbers as you would with trajectories. e.g.
lintools -t coordinate_file -x traj1 traj2 traj3 -b 0 100 1000 -e 10000 1000 10000
The order of the frame numbers have to correspond to the order that the trajectories are submitted, so in our example traj2 will be analysed from 100th frame to 1000th frame.
If for some reason you do not want to analyse hydrogen bonds (or it is known that they are very unlikely to occur e.g. with a hydrophobic ligand in hydrophobic pocket) it is possible to exclude this analysis. It will decrease the time required for analysis.
New options will be added with time and the developers would welcome suggestions for new features and feasibility. These can be submitted to the issues.