I attempted to superimpose two protein structures using UCSF Chimera, and the calculated RMSD was 1.33. However, the structures were not properly aligned. I also calculated RMSD using PyMOL, which resulted in a much higher value of 56.889. Additionally, there are sequence differences, including amino acid deletions and insertions.
Could these structural and sequence variations be affecting the alignment? What would be the best approach to improve the superimposition in such cases? Are there specific settings in Chimera or PyMOL, or alternative methods, that could help achieve better alignment despite these differences?
I would appreciate any insights or suggestions from those experienced in structural bioinformatics.
The align code in PyMol is "align AAAA, BBBB". You can try align two protein in PyMol. In my case, align two different receptor protein in the same subtype is OK. But be aware that two protein in your image seem disordered, which may affect your alignment.
Dear Ruikang Sun Thank you for your response. I performed the same superimposition of the two structures (Human and Hominids) in Chimera, and the alignment appears identical to what is observed in PyMOL. However, despite an RMSD value of 1.33, the structures do not seem to be properly superimposed.
If you have any insights or suggestions on this issue, I would appreciate your guidance.
You may try to align structures using specific residues which you are confident about overlapping. In such way, you might be better able to identify discrepancies.
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