#76 Does a poor alignment in cealign negate a good alignment in super?
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?
Please post questions like that to the pymol-users mailing list:
https://sourceforge.net/projects/pymol/lists/pymol-users
Also, if you provide a specific example (e.g. PDB codes) it will be much more likely that someone understands the problem and can help you.
"super" aligns on structure only (sequence independent) as well. See:
https://pymolwiki.org/index.php/Align
https://pymolwiki.org/index.php/Super
https://pymolwiki.org/index.php/Cealign
Ticket moved from /p/pymol/bugs/198/