NMA of local PDB files

[Barry Grant]

My name is Luis Leon. Im working with the bio3d package and i have a question that i can't resolve with the web page. Is possible to make the analysis of ensemble NMA of multiple structures, with my own pdbs? These PDBs are located in my computer and they are not located in any database. On the other hand, there will be soon a new release with the biostructure visualization tool?

Thanks in advance Best regards

-- Luis León Paredes PhD. Research Center for Genetics and Genomics School of Medicine Clínica Alemana-Universidad del Desarrollo Av. Las Condes 12438

[Barry Grant]

Hi Luis, Absolutely, Just give the read.pdb() and/or pdbaln() functions your input file names rather than the PDB database identifiers. E.g.

myflies <- c("myflies1.pdb", "myflies2.pdb", "someOtherDir/myfile3.pdb")
pdbs <- pdbaln(mayflies) 
modes <- nma(pdbs)

I am copying your question to our issues tracker where where can respond also.