Problem Still Persists : Reading PDB file from a Local Disk.
Issue #425
resolved
> library(bio3d)
> setwd("/home/prasanth/GNM/AURKA/GNM/Free/")
> pdb <- read.pdb("4j8n.pdb")
Error in .read_pdb(file, multi = multi, hex = hex, maxlines = maxlines, :
basic_string::substr
> pdb <- read.pdb("4j8n.pdb", maxlines = -1, multi = FALSE, rm.insert = FALSE, rm.alt = TRUE, ATOM.only = FALSE, hex = FALSE, verbose = TRUE)
Error in .read_pdb(file, multi = multi, hex = hex, maxlines = maxlines, :
basic_string::substr
> pdb <- read.pdb("4j8n.pdb", maxlines = -1, hex = FALSE)
Error in .read_pdb(file, multi = multi, hex = hex, maxlines = maxlines, :
basic_string::substr
> pdb <- read.pdb("4j8n")
Note: Accessing on-line PDB file
I am using R 3.2.2 and RStudio 1.0.44 (Ubuntu machine)
Comments (4)
-
reporter -
- edited description
-
hmmm...
> library(bio3d) > get.pdb("1rx2") trying URL 'http://www.rcsb.org/pdb/files/1rx2.pdb' Content type 'text/plain;charset=UTF-8' length unknown .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... ......... downloaded 159 KB [1] "./1rx2.pdb" > pdb <- read.pdb("1rx2.pdb") PDB has ALT records, taking A only, rm.alt=TRUE > sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.1 LTS locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=nb_NO.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=nb_NO.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=nb_NO.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=nb_NO.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] bio3d_2.3-1 loaded via a namespace (and not attached): [1] parallel_3.2.3 tools_3.2.3 Rcpp_0.12.8 grid_3.2.3 tcltk_3.2.3
Can you try the same as me outside RStuido, i.e. in the conventional R console through the terminal?
-
- changed status to resolved
User misunderstanding of how file paths work
- Log in to comment
The program accesses the on-line database (RCSB) to download structure even though the directory of the file (pdb) was set. You had commented to add ".pdb" extension, which still makes its search over on-line. Without extension of .pdb, I am not able to access my local file.