write PC1 data into csv format prior to export and analysed by external software

[Former user]

Hi,

I have calculated PCA for a system. I even found residues contribution to PC1. i want to export the value/data of PC1 with residue number into CSV. This will be helpful for comparative analysis of multiple PC1 from multiple trajectories of same protein.

[Xinqiu Yao]

The PC loading along with a PDB object might be what you were seeking for. You can create a “data.frame” with one column the residue number and the other column the residue wise loading. For example,

## Haven't tested but just to show the idea.
## May need to adjust a bit. 
dat <- data.frame(res=pdb$atom$resno[pdb$calpha], pc=pca$au[, 1])
write.csv(dat, file="pc1_loading.csv")

‌