Allowing structure alignments to be read in without re-fitting

[Kyle Stiers]

Hello, I would like to suggest/ask about using alignments of multiple PDB files performed outside of bio3d and then using subsequent tools in Bio3D for analysis. I suggest this because it is often routine or more convenient to align things in other programs such as PyMOL or Coot.

I have been attempting to do this with a set of structures that are topologically very similar but have distinctly different regions. I’ve aligned them how I want them to be aligned in PyMOL but even when I use the argument ‘'fit=False’' in pdbfit() and pdbaln() the RMSDs that come out skyrocket to >40 Å, despite them being very low in PyMOL.

I’m confident this could be done in Bio3D with fit.xyz() if I was more comfortable with selecting indices, but that seems like an unnecessary step if I can have them correctly aligned prior to loading for downstream analyses.

Thanks!

Kyle Stiers

P.S. in the short-term, how would one go about fitting based on some residues in a specific chain over a list of pdb objects (say from pdbaln() with fit=F) with pdbfit/fit.xyz?

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[Xinqiu Yao]

Hi Kyle,

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Thanks for the proposal. Can you provide a short example to reproduce the problem you have described? I remember, with fit=FALSE, the function should take input as is.

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For your additional question, both fit.xyz() and pdbfit() should work giving a set of atom indices is provided. These indices can be from, e.g., core.find(), or user defined with atom.select() . Take a look of the PCA tutorial (http://thegrantlab.org/bio3d/tutorials/principal-component-analysis) for examples.