How to choose PDB ID for -> Residue number (reference PDB ID)

[Former user]

Hi everyone, I was just wondering if there is a command that allows us to choose our reference PDB ID when plotting? I'm thinking that Bio3D just takes the 1st read-in PDB structure? Please let me know if I can choose my referencing PDB ID.

[Daniel Lim]

I am comparing many homological structures to 1 protein, and I would like that the residue number (reference PDB: to my specific PDB). Please let me know if they’re any commands that will do the job! Thank you all in advance.

[Xinqiu Yao]

Hi,

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Can you tell what specific commands/functions were you asking about?

[Daniel Lim]

Hi,

How do I select which reference PDB the plot takes? Is there any way I can choose, or is it just choosing the 1st PDB that is read in? What can I do to choose my reference PDB? Thank you in advance!

[Xinqiu Yao]

By “reference PDB”, do you mean the PDB used to generate the x-axis labels (residue numbers) and secondary structure annotations? If so, you can specify them by the resno= and sse= arguments. Type ?plot.bio3d for more detail.