Outputting core.pdb

[Former user]

Hi everyone, I have aligned ~140 pdbs and ran the core.find() function. It gives me around 95 non-gap positions from around 400. I tried outputting a core.pdb, so I can visualize where the invariant regions are. However, the outputted PDB file is only showing ALA, and it also isn't showing the aligned structures with it. It is only showing specific points of alanine residues, but no helix or sheet or anything. Is that suppose to be normal? because in the tutorial, there is a visual where the core outputted PDB shows the invariant region. I have tried using VMD and PyMOL, but they give me the same structures of alanine residues. Any suggestions on how to get a more detailed visual of invariant regions with the sse's incorporated?

Thanks in advance, Daniel

[Xinqiu Yao]

Hi,

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core.find() is mainly to identify core residues for subsequent superimposition or fitting. To get superimposed structures, you still need to call the function pdbfit() or similar.

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For example,

core <- core.find(pdbs)
core.inds <- print(core, vol=0.5)
xyz <- pdbfit(pdbs, core.inds, outpath="corefit_structures")

# In a Linux terminal, type `vmd -m corefit_structures/*.pdb` to show superimposed structures
# To know where cores are located in each structure,
# find the corresponding residue numbers by following line
pdbs$resno[1, core.inds$atom]

# Then, use the 'atom select' feature of VMD to highlight those core residues

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Hope it helps.