Dear pymol users, I am trying to align two very similar trimeric molecules. I tried different alignment commands including "align", "cealign" and "super", but none of them gives satisfying effect. Athough the backbone conformations and orientations of two two molecules look very similar, there are obvious displacements between them after alignment with these three commands. The rmsd of the two molecules for these three methods are 2.250, 4.682, 2.206 and 2.206, respectively. I wonder whether there is any better alignment command or there are any parameters that can be passed to these three alignment commands to improve the effects. Could you help me check this? The pdb files of these two molecules, the image for the two molecules after using "super" command, and the alignment effect in the publication I mentioned can be found at the following link.
https://drive.google.com/file/d/1ff3XgTexgdul-SezUz75dVoCx2cL5YPL/view?usp=sharing With many thanks.
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