Structure superposition tools: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Markus Wiederstein, Wayne Decatur, Ronald Ayoub, Joel L. Sussman, Angel Herraez

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 When the models being compared have substantial differences, and especially if they have multiple domains, more tolerant estimates of the closenss of fit have been employed, notably in [[CASP]]. One of these is the ''global distance test total score'', or [[Calculating_GDT_TS|GDT_TS]]. See also [[Theoretical models]].
-==Visualizing Structural Alignments==
+==Visualizing Structural Superpositions==
 <applet size='400' frame='true' align='right' caption='Structural alignment of [[1fsz]] with [[1tub]].'
 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 superpositions 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) superposed by [[#Dali|Dali]] with <!--e0b000--><font color="#d0a000"><b>mammalian tubulin</b></font> ([[1tub]]:A). Sequence identity in the structurally superposed 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>.)
-*Because the alignment is about 300 residues long (and the protein chains are longer), it is hard to see details of this 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 target &alpha; carbons are within 3.5 &Aring;. (The RMSD for this [[#Dali|Dali]] alignment is 3.2 &Aring;.)
+*Because the superposition is about 300 residues long (and the protein chains are longer), it is hard to see details of this 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 target &alpha; carbons are within 3.5 &Aring;. (The RMSD for this [[#Dali|Dali]] alignment is 3.2 &Aring;.)
 <jmol>
 <jmolButton>
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 </jmolButton>
 </jmol>
-* This <scene name='Structural_alignment_tools/Morph_1fsz_1tub_a_fatcat/1'>morph of the alignment</scene> was generated by [[#FATCAT|FATCAT]], which reported 3.02 &Aring; RMSD for 298 structurally aligned residues, and 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. The morph makes it easy to see that the core fold is stable, while the larger changes occur in surface loops.
+* This <scene name='Structural_alignment_tools/Morph_1fsz_1tub_a_fatcat/1'>morph of the alignment</scene> was generated by [[#FATCAT|FATCAT]], which reported 3.02 &Aring; RMSD for 298 structurally superposed residues, and 10.2% sequence identity for the structurally superposed 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. The morph makes it easy to see that the core fold is stable, while the larger changes occur in surface loops.
-It is very helpful to color the target alpha carbons by deviation ("RMSD") 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|DeepView = Swiss-PDBViewer]] and [[#PyMOL|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 ("RMSD") from the query model: red indicates large deviations (poor superposition) while blue indicates small deviations (close superposition), with white indicating average superposition. The stand-alone programs [[#DeepView = Swiss-PDBViewer|DeepView = Swiss-PDBViewer]] and [[#PyMOL|PyMOL]] color superpositions by RMSD but the results cannot be easily exported to Jmol. Surprisingly, none of the servers listed below color their superpositions by deviation, except [[#Dali|Dali]]. Unfortunately, there is NO built-in way to color the superposition by RMSD in Jmol.
 ==Conclusions==