Unexpected behavior of Center of Mass (com.xyz)

[Former user]

I was expecting that com.xyz as applied below would return center of mass of selected set of residues (B.inds) for all 3000 frames stored in xyz. However, I only only obtain a single value and not a vector containing com of all 3000 frames stored in xyz.

Input

B.inds <- atom.select(pdb, "//B/1:99///CA/") com.xyz(xyz[,B.inds$xyz])

output

B.inds <- atom.select(pdb, "//B/1:99///CA/")

Build selection from input string * Selected a total of: 99 intersecting atoms *

com.xyz(xyz[,B.inds$xyz]) [1] 1.478358 1.479368 1.479699

[Lars Skjærven]

Hi, you're right. at the moment the com.xyz() function only takes a vector as input (as also specified in the documentation). I'll update this tomorrow. In the meantime you can do

apply(xyz, 1, com.xyz)

Thanks for noting this.

[Lars Skjærven]

updated with commit