NULL values for: XYZ cartesian coordinates,

[Former user]

Hi Bio3D, I am reading about 140 structures. Which is the best way to read them in because I already have them aligned through PyMOL. Is it more accurate if I aligned them again using Bio3D? Also, whenever I read the pdbs in, I am having trouble gathering the xyz coordinate matrix because they all say it is NULL, same with resno and so forth. However, when I do read 1/140 individually, they have no problem showing the xyz coordinates or residue. I think I am reading them in incorrectly, please feel free to reach out!

Daniel

[Xinqiu Yao]

Hi,

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The best way to deal with multiple structures in Bio3D is to create a ‘pdbs’ object. There are multiple ways to do it:

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If you already have an alignment, try following lines

aln <- read.fasta('Your_alignment_file_in_FASTA_format')
pdbs <- read.fasta.pdb(aln)

One thing you need to assure is that the “id” of each sequence must be the path of the corresponding PDB file, and so read.fasta.pdb() can find the structure and read it.

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If you want Bio3D to re-align it, simply use the pdbaln() function:

files <- list.files('folder_where_PDB_structures_are_located', '\\.pdb$', full.names=TRUE)
pdbs <- pdbaln(files)

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Hope it helps.