Structure superposition tools: Difference between revisions
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==Visualizing Structural Alignments== | ==Visualizing Structural Alignments== | ||
<applet size=' | <applet size='400' frame='true' align='right' caption='Structural alignment of [[1fsz]] with [[1tub]].' | ||
scene='Structural_alignment_tools/Dali_chains_ab_water/1' /> | scene='Structural_alignment_tools/Dali_chains_ab_water/1' /> | ||
Structural alignments are usually visualized as the superimposed backbone traces of the aligned models. The example at right shows the bacterial cell division protein <font color="#d80000"><b>FtsZ</b></font> ([[1fsz]]:A) aligned by [[#Dali|Dali]] with <!--e0b000--><font color="#d0a000"><b>mammalian tubulin</b></font> ([[1tub]]:A). Sequence identity in the structurally aligned regions is about 13%. | Structural alignments are usually visualized as the superimposed backbone traces of the aligned models. The example at right shows the bacterial cell division protein <font color="#d80000"><b>FtsZ</b></font> ([[1fsz]]:A) aligned by [[#Dali|Dali]] with <!--e0b000--><font color="#d0a000"><b>mammalian tubulin</b></font> ([[1tub]]:A). Sequence identity in the structurally aligned regions is about 13%. | ||
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</jmolButton> | </jmolButton> | ||
</jmol> | </jmol> | ||
* This morph of the alignment is generated by [[#FATCAT|FATCAT]], which reports 3.02 Å RMSD for 298 structurally aligned residues, 10.2% sequence identity for the structurally aligned residues. The morph shows the 334-residue sequence of the query (FtsZ) changing from the query conformation to the conformation of the aligned target (tubulin). It does not show the non-aligned loops of tubulin that can be seen as thin backbone traces in the initial scene above. | * This <scene name='Structural_alignment_tools/Morph_1fsz_1tub_a_fatcat/1'>morph of the alignment</scene> is generated by [[#FATCAT|FATCAT]], which reports 3.02 Å RMSD for 298 structurally aligned residues, 10.2% sequence identity for the structurally aligned residues. The morph shows the 334-residue sequence of the query (FtsZ) changing from the query conformation to the conformation of the aligned target (tubulin). It does not show the non-aligned loops of tubulin that can be seen as thin backbone traces in the initial scene above. | ||
It is very helpful to color the target alpha carbons by deviation from the query model: red indicates large deviations (poor alignment) while blue indicates small deviations (good alignment), with white indicating average alignment. The stand-alone programs [[#DeepView = Swiss-PDBViewer]] and [[#PyMOL]] color alignments by RMSD but the results cannot be easily exported to Jmol. Surprisingly, none of the servers listed below color their alignments by deviation. Unfortunately, I found NO way to color the alignment by RMSD in Jmol. | It is very helpful to color the target alpha carbons by deviation from the query model: red indicates large deviations (poor alignment) while blue indicates small deviations (good alignment), with white indicating average alignment. The stand-alone programs [[#DeepView = Swiss-PDBViewer]] and [[#PyMOL]] color alignments by RMSD but the results cannot be easily exported to Jmol. Surprisingly, none of the servers listed below color their alignments by deviation. Unfortunately, I found NO way to color the alignment by RMSD in Jmol. | ||
