Structure superposition tools: Difference between revisions
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) |
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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]] | [[#Dali]] offers to color its alignments in Jmol by ''structure conservation''. For the target, aligned regions have thick backbone traces while unaligned regions have thin backbones; for the query, aligned regions are red while unaligned regions are white. | ||
[[#FATCAT]] offers a [[morphs|morph]] in Jmol that helps to visualize the structural relationship between the two aligned models. | |||
==Recommendation== | ==Recommendation== | ||