xyz coordinates

[Former user]

Hello,I'm trying make a PCA with pdb files,by I get following error:

myfile <- list.files( pattern=".pdb",full.names=TRUE)
xyz <- NULL
for(i in myfile) {
     xyz = rbind(xyz, read.pdb(myfile)$xyz)
}
Error in file(con, "r") : argument 'description' incorrect

[Xinqiu Yao]

In the 4th line, use xyz = rbind(xyz, read.pdb(i)$xyz) and you should solve the problem.

Btw, if you are doing PCA on a bunch of X-ray pdb files (belonging to the same protein family but having different sequences), a recommended practice is doing following steps:

• Build a 'pdbs' object containing aligned pdb structures using the function pdbaln().
• Find 'core' positions and fit structures based on cores (alternatively, fit structures based on all C-alpha atoms).
• Call pca() to the fitted coordinates.

See the Bio3D tutorial for more details.

[lylia]

Thank you for your quickly response I did alignement with another program and identified my core and I just want to do a PCA,but your solution works perfectly.

Thank you

[Barry Grant]

resolved