Lab journal task 4
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. (align 1de4_a and resi 1-275, 1a6z_a and resi 1-275, object=align)
The actual view can be saved and then used to set the orientation to these values.
my_view = cmd.get_view() cmd.set_view(my_view)
<css>
table.colBasic2 {
margin-left: auto;
margin-right: auto;
border: 2px solid black;
border-collapse:collapse;
width: 70%;
}
.colBasic2 th,td { padding: 3px; border: 2px solid black; }
.colBasic2 td { text-align:left; }
.colBasic2 tr th { background-color:#efefef; color: black;} .colBasic2 tr:first-child th { background-color:#adceff; color:black;}
</css>
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).
