Structure superposition tools: Difference between revisions
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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%. | ||
*The non-aligned segments are white in the query (<font color="#d80000"><b>FtsZ</b></font>) and thin in the target (<font color="#d0a000"><b>tubulin</b></font>). This scene is available in [[#Dali|Dali]] except that the target color has been changed to make it more distinct from the red query. (<scene name='Structural_alignment_tools/Dali_chains_ab_water/1'>Restore initial scene</scene>.) | *The non-aligned segments are white in the query (<font color="#d80000"><b>FtsZ</b></font>) and thin in the target (<font color="#d0a000"><b>tubulin</b></font>). This scene is available in [[#Dali|Dali]] except that the target color has been changed to make it more distinct from the red query. (<scene name='Structural_alignment_tools/Dali_chains_ab_water/1'>Restore initial scene</scene>.) | ||
*<font color=" | *Because the alignment is about 300 residues long (and the protein chains are longer), it is hard to see details of the alignment in the complexity. Buttons below show 50-residue segments of the query (<font color="#d80000"><b>FtsZ</b></font>) and backbone for target (<font color="#d0a000"><b>tubulin</b></font>) where the α carbons are within 3.5 Å. (The RMSD for this alignment is 3.2 Å.) | ||
<jmol> | <jmol> | ||
<jmolButton> | <jmolButton> | ||
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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. | ||
[[#FATCAT]] offers a [[morphs|morph]] in Jmol that helps to visualize the structural relationship between the two aligned models. | [[#FATCAT]] offers a [[morphs|morph]] in Jmol that helps to visualize the structural relationship between the two aligned models. | ||
