dcd file

[Former user]

I have tried to convert pdb file to dcd format by using the function in bio3d using command line. But when I search for the file, it is not present in the directory. So, I should I create dcd file format from a pdb file? please let me know.639

[Lars Skjærven]

It would help if you include the code snippet you are working with. Which functions are you using? I'm guessing you would need something like:

pdb <- read.pdb("1d1d", multi=TRUE)
write.ncdf(pdb$xyz.models, trjfile="hey.nc")  

Note that write.dcd() does not currently exist in bio3d (as far as I can see).

[Barry Grant]

I am going to close this issue as it is updated in Issue #96.

I will add that to do this version 2.1.0 or above (as on the new 'feature_pdb_dataframe' and 'feature_visualize_dataframe' branches) entails:

pdb <- read.pdb("2LWI", multi=TRUE)
write.ncdf(pdb$xyz, trjfile="mytrj.nc")

Whilst on previous versions 2.0.1 and below, the syntax is slightly different:

pdb <- read.pdb("2LWI", multi=TRUE)
write.ncdf(pdb$xyz.models, trjfile="mytrj.nc")