how to remove non C-alpha atoms from dcd file.

[Former user]

Hi bio3D developers,

in the secontion ( Network generation from molecular dynamics data) of Protein Structure Networks with Bio3D ( http://thegrantlab.org/bio3d/articles/online/cna_vignette/cna_vignette.spin.html). " To reduce file size and speed up example execution, non C-alpha atoms have been previously removed ". this indicates that you kow how to remove non C-alpha atoms from dcd file.

Since my protein have 1050 resiudes ( microseconds trajectory ), I can not do Network analysis from molecular dynamics data. Could you tell how to remove non C-alpha atoms from dcd file, and get the dcd file with C-alpha atoms?

(it is time consuming for me to do Protein Structure Networks with Bio3D. I spent more than two hours on my protein (single strucuture) to genenrate structure networks. Only one CUP was used. If multi-CPU are used, it should be faster. )

[Xinqiu Yao]

Hi,

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You need a PDB that matches the DCD trajectory. Then, you can pick up all C-alpha atoms by creating an ‘atom.select’ object based on the PDB and use that object to choose a subset of the trajectory. For example,

## 'top.pdb' is a PDB file that matches the trajectory exactly
##  (i.e., they have the same number and order of atoms)
pdb <- read.pdb('top.pdb')
trj <- read.dcd('traj.dcd')
ca.inds <- atom.select(pdb, 'calpha')
ca.coord <- trj[, ca.inds$xyz]

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