Structure superposition tools: Difference between revisions
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Eric Martz (talk | contribs) |
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* 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 Å 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 Å 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. | ||
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|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. | ||
==Conclusions== | ==Conclusions== | ||
