Difference between revisions of "Lab journal task 4"
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| + | First, we used Pymol to view the different structures and to construct structural alignments to the template 1A6Z_A. Therfore we used the command " align to structure" from the action menu. |
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| − | | CATH || 1jfm || A || 00 || 3.30.500.10 || 10.3 |
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| − | |- |
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| − | |||
| − | |||
| − | | (1JFM_A) || 10.3 || || || 3.50 || 27.81 || 4.12 || 70.12 || 3.28 || 117 || 3.14 || 3.52 || 240 |
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| − | |- |
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| − | |||
| − | |||
| − | The pymol alignment uses only the C_alpha atoms per default. |
+ | The pymol alignment uses only the C_alpha atoms per default. The following command can be used to align all atoms and create the object ali12<br> |
align structure1 and resi 1-n, structure2 and resi 1-m, object=ali12 <br> |
align structure1 and resi 1-n, structure2 and resi 1-m, object=ali12 <br> |
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,where n equals the number of atoms in structure 1 and m the number of atoms in structure 2. |
,where n equals the number of atoms in structure 1 and m the number of atoms in structure 2. |
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| − | (align 1de4_a and resi 1-275, 1a6z_a and resi 1-275, object=align) |
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| + | We saved the current view of the first alignment |
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| − | The actual view can be saved and then used to set the orientation to these values. |
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my_view = cmd.get_view() |
my_view = cmd.get_view() |
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| + | and then used this variable later to set the orientation to these values, in order to be able to make images from the different alignments always using the same view. |
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cmd.set_view(my_view) |
cmd.set_view(my_view) |
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| Line 72: | Line 65: | ||
* structurally equivalent residue pairs: orange (query) and red (target) |
* structurally equivalent residue pairs: orange (query) and red (target) |
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* 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 = 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. |
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| − | * S_r = Typical distance error. For details on the construction of this per-residue measure of structural similarity, see Sippl & Wiederstein (2012). |
+ | * 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 |
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| − | |||
| − | 1DE4_A |
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| − | |||
| − | |||
| − | 1QVO_A |
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| − | 1S7X_A |
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| − | 1JFM_A |
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| − | 2IA1_A |
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| − | 3NCI_A |
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| − | 1VZY_A |
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| − | 1MUS_A |
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Revision as of 12:26, 12 August 2013
First, we used Pymol to view the different structures and to construct structural alignments to the template 1A6Z_A. Therfore we used the command " align to structure" from the action menu.
The pymol alignment uses only the C_alpha atoms per default. The following command can be used to align all atoms and create the object ali12
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.
We saved the current view of the first alignment
my_view = cmd.get_view()
and then used this variable later to set the orientation to these values, in order to be able to make images from the different alignments always using the same 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).
