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:

LGA:

• superimpose to target structure (second structure, in our case 1A6Z )
• default parameters

SSAP:

• no target structure to specify
• no parameters to set
• score from 0 to 100

TopMatch:

• 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).

number of alignet residues per pair 1DE4_A 1QVO_A 1S7X_A 1JFM_A 2IA1_A 3NCI_A 1VZY_A 1MUS_A

method name	location
LGA	http://proteinmodel.org/AS2TS/LGA/lga.html
SSAP	http://protein.hbu.cn/cath/cathwww.biochem.ucl.ac.uk/cgi-bin/cath/GetSsapRasmol.html
TopMatch	https://topmatch.services.came.sbg.ac.at/
CE	http://source.rcsb.org/jfatcatserver/index.jsp