Dear all,
I am now trying to compare two structures by alignment in pymol. The two
proteins are similar structures from the same family with about 500 residues. I
find that the "cealign" command gives much better result that the "align"
command. With the "cealign" command, the two structures aligned well, but with
"align" command two structure don't aligned well. The rmsd value given with the
"cealign" is much smaller than that given with the "align".
However, when I try the align a small region of the two structures, I get the
reverse result. I create new objects corresponding to the small region I am
interested in from the two whole proteins, respectively and align the two new
objects with "align" and "cealign". I find the rmsd value given with "align" is
much smaller that than given with "cealign".
I wish know the work principle behind "align" and "celign", the calculation
formula of them and what cause the difference between aligning the whole
proteins and small regions. Could you help me with these?
Best regards.
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