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#76 Does a poor alignment in cealign negate a good alignment in super?

v1.6.2.0
open
nobody
None
5
2018-03-09
2018-03-09
Grace Ferri
No

I was hoping you might be able to provide me with more information as to how to interpret my output from these commands, as I don't seem to find any formal documentation on the usage of the super command. Can I use my output to validate a hypothesis of structural similarity between two proteins?

If it's useful, I obtained the following results from a "super" alignment:
super p1, p2
MatchAlign: aligning residues (91 vs 160)...

MatchAlign: score 73.999

Executive: RMS = 0.331 (69 to 69 atoms)

I assume this output indicates a "good" alignment based on both structure and sequence according to the 3-D coordination of CA atoms, since the super command was used.

I gathered the following output from a "cealign" command:
cealign p3, p4

RMSD 4.393816 over 64 residues

Since the sequence similarity is low, I assume this is a "decent" alignment based on structure only.

Does a poor alignment in cealign negate a good alignment in super?

Discussion

  • Thomas Holder

    Thomas Holder - 2018-03-09

    Ticket moved from /p/pymol/bugs/198/

     
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