Reading multiple pdb files

[Former user]

Hi. I have multiple conformation of my same protein but as multiple of files.I want to do a structure comparison and then a PCA. How can I do so? Making a single file multi model file is an option but I wanted to know if this option is correct. Please helo ASAP

Bhawna

[Barry Grant]

If they are different sequences (or indeed if they are the same sequence) you can follow the regular analysis route explained in detail in the various tutorials and docs.

For example see: http://thegrantlab.org/bio3d/tutorials/structure-analysis

and the sections "Working with multiple PDB files" (there are also sections on reading and working with multi-model files, as well as doing more advanced things like core fitting etc.)

Here is a basic example to get you started:

# A vector of your PDB file names
myflies <- c("file1.pdb", "file2.pdb", "file3.pdb")

# Align and superpose them
pdbs <- pdbaln(myfiles, fit=TRUE)

## Do a quick PCA
pc <- pca(pdbs, rm.gaps=TRUE)
plot(pc)

[Xinqiu Yao]

Not a bug