Is it possible to save ".dat" before plotting?

[Ash]

I am dealing a number of multi-chain proteins. Bio3D automatically plot the calculated "RMSD/RMSF" and correlated motion etc. Is there a way, to save a ".dat" file, lets say for RMSD, because I am interested to make a single figure where I can plot domain RMSD and full length backbone. Regards,

[Barry Grant]

Do you mean .RData files? If so use the save() function. If you mean something else like CSV or TSV (tab separated) see write.csv(), write.table() etc.

[Ash]

Thank you, sir. Actually, I want to calculate RMSD and RMSF values for individual domains in a system and then plot them all in one plot. For example, the VMD script "rmsd.tcl" generate an output file 'rmsd.dat'. Later, a user can plot those with xmgrace or other programs. Here Bio3D, calculates values for rmsd and rmsf etc, but donot generate that kind of DAT file. So is it possible to save those values from here, and then plot all of them in one figure, like below.

[Xinqiu Yao]

Use write.table() to write a plain text file for vectors/matrices/data.frames. See help(write.table) for more detail.