How to print mean position (x,y,z) of each atom

[Atul]

I have pdb file and dcd file (1000 frames). I want to find the mean position (x,y,z) of each atom.

Session info R version 3.2.3 (2015-12-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.4 LTS

locale: [1] LC_CTYPE=en_IN LC_NUMERIC=C LC_TIME=en_IN
[4] LC_COLLATE=en_IN LC_MONETARY=en_IN LC_MESSAGES=en_IN
[7] LC_PAPER=en_IN LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_IN LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] bio3d_2.3-3

loaded via a namespace (and not attached): [1] parallel_3.2.3 Rcpp_0.12.16 grid_3.2.3

[Xinqiu Yao]

Hi,

What you need is to fit each frame to a reference (e.g. the first frame) and calculate the mean of each column.

dcd <- read.dcd('traj.dcd')
xyz <- fit.xyz(dcd[1, ], dcd)
colMeans(xyz)

Please read bio3d tutorials for more detailed explanation.