Chain T and Chain F get turned into TRUE and FALSE

[Jonathan Gough]

If you: 1. read in a set of similar PDB files 2. split them into their individual chains 3. then align them one to another 4. and then write them out

Chain F gets turned into False Chain T gets turned into True

Here are the commands used:

library(bio3d) files <- Sys.glob("*.pdb") chainsplit <- pdbsplit(files, path = "split_chain") pdbs <- pdbaln(chainsplit) pdbs <- pdbfit(pdbs, outpath="H_aligned/") quit()

Here is the sessioninfo()

sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
[3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
[5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8
[7] LC_PAPER=en_US.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

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

other attached packages: [1] bio3d_2.2-2

loaded via a namespace (and not attached): [1] parallel_3.3.1 grid_3.3.1

Here is a few lines of the output

Files in split_chain are fine: ATOM 6750 N PRO T -2 41.981 46.785 -59.398 1.00 77.59 N ATOM 6751 CA PRO T -2 40.554 46.947 -59.683 1.00 77.49 C ATOM 6752 C PRO T -2 39.669 45.873 -59.013 1.00 77.52 C ATOM 6753 O PRO T -2 39.019 46.140 -57.997 1.00 77.41 O ATOM 6754 CB PRO T -2 40.490 46.831 -61.217 1.00 77.43 C ATOM 6755 CG PRO T -2 41.772 46.139 -61.615 1.00 77.42 C ATOM 6756 CD PRO T -2 42.783 46.608 -60.624 1.00 77.43 C

Files in H_aligned are broken (True!): ATOM 6750 N PRO TRUE -2 9.879 57.636 71.111 1.00 77.59 N ATOM 6751 CA PRO TRUE -2 10.739 57.013 72.119 1.00 77.49 C ATOM 6752 C PRO TRUE -2 11.868 57.941 72.621 1.00 77.52 C ATOM 6753 O PRO TRUE -2 11.779 58.500 73.718 1.00 77.41 O ATOM 6754 CB PRO TRUE -2 11.320 55.796 71.376 1.00 77.43 C ATOM 6755 CG PRO TRUE -2 11.136 56.103 69.909 1.00 77.42 C ATOM 6756 CD PRO TRUE -2 9.871 56.889 69.839 1.00 77.43 C

[Lars Skjærven]

Hi Jonathan, Please make sure you're running the latest version of bio3d (2.3-1). Use install.packages("bio3d") to upgrade from 2.2-2 to the latest version at CRAN.

Then you can try the example below and report back the content of fit/1sx4_F.pdb and fit/1sx4_T.pdb ?

> files <- get.pdb("1sx4", gzip=T)
> split <- pdbsplit(files)
> pdbs <- pdbaln(split) 
> pdbs$xyz <- pdbfit(pdbs, outpath="fit/")

> p <- read.pdb("fit/1sx4_T.pdb_flsq.pdb")
> head(p$atom$chain)
[1] "T" "T" "T" "T" "T" "T"