Lab journal task 4
From Bioinformatikpedia
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The following four alignment methods were used:
- superimpose to target structure (second structure, in our case 1A6Z )
- default parameters
- no target structure to specify
- no parameters to set
- score from 0 to 100
- target 1A6Z
- default parameters
- target in blue, query in green
- structurally equivalent residue pairs: orange (query) and red (target)
- S = Measure of structural similarity based on Gaussian functions (see Sippl & Wiederstein (2012)). If the structurally equivalent parts in query and target match perfectly, S is equal to L. With increasing spatial deviation of the aligned residues, S approaches 0.
- S_r = Typical distance error. For details on the construction of this per-residue measure of structural similarity, see Sippl & Wiederstein (2012).
The pymol alignment uses only the C_alpha atoms per default. Following command can be used to align all atoms: align structure1 and resi 1-n, structure2 and resi 1-m, object=ali12 ,where n equals the number of atoms in structure 1 and m the number of atoms in structure 2.
