how to load a local pdb files

[rene]

I'm trying make a dendrogram with pdb files, but i cant load my local edited pdb files, how can i do this? thanks

[Barry Grant]

Basically, just use their file names as input to the read.pdb() or pdbaln() functions. The first will read individual files (so you could apply it in a loop for example) the second will read all your files and then align them (useful if there sequences are different or they are of different length etc.). Here is an example of a few ways to do this:

library(bio3d)
# make a vector of *.pdb file names from the contents of the current directory
myFileNames = list.files(path=".", pattern=".pdb")

# option 1. read each file individually (not tractable if you have lots of files obviously)
pdb.1 <- read.pdb(myFileNames[1])
pdb.2 <- read.pdb(myFileNames[1]) ## etc... see option 3 for example of putting this in a loop

# option 2. read and align all structures
pdbs = pdbaln(myFileNames)

# option 3. if they are of identical composition and you only want xyz coordinates
xyz <- NULL
for(i in myFileNames) {
   xyz = rbind(xyz, read.pdb(myFileNames)$xyz)
}

# you can also use the apply function if you are familiar with that instead of the 'for loop' above

Also note that if your structure composition is identical in each file it is often easier to concatenate into one multi-model file and read in one go with a single call to read.pdb() whilst using the multi=TURE option.

This tutorial will be helpful in this regard: http://thegrantlab.org/bio3d/tutorials/structure-analysis

[rene]

Hi Barry, Thank you for the answer. I could able to load the pdb files locally.

myfiles <- list.files(path="C:/Users/rsepulveda/Desktop/structuras_para_dendograma/pdbcortados", pattern=".pdb") pdbs = pdbaln(myfiles, exefile="C:/Users/rsepulveda/Downloads/muscle3.8.31_i86win32.exe") Reading PDB files:

Error in if (substr(file, 1, 4) == "http") { : missing value where TRUE/FALSE needed

[rene]

> myfiles <- list.files(path="C:/Users/rsepulveda/Desktop/structuras_para_dendograma/pdbcortados", pattern=".pdb")

> pdbs = pdbaln(myfiles, exefile="C:/Users/rsepulveda/Downloads/muscle3.8.31_i86win32.exe")

Reading PDB files:

Error in if (substr(file, 1, 4) == "http") { : 
missing value where TRUE/FALSE needed

[Lars Skjærven]

Can you output the content of myfiles here? e.g. the first few elements of the vector?

Can you also report the output of

head(readLines(myfiles[1]))

you can also try

read.pdb(myfiles[1])

[Lars Skjærven]

also, make sure you are using bio3d_2.2-3.

[rene]

ok, it was a R problem running in win7, you must run R like administrator, that is all, I hate win in all her versions. thank to all

[rene]

4QJY.pdb
> myfiles <- list.files(path="C:/structurasparadendograma/cortados", pattern=".pdb")
> pdbs = pdbaln(myfiles, exefile="C:/Users/rsepulveda/Downloads/muscle3.8.31_i86win32.exe")
  Note: Accessing online PDB files using 4 letter PDBID
Error in pdbaln(myfiles, exefile = "C:/Users/rsepulveda/Downloads/muscle3.8.31_i86win32.exe") : 
   ** Missing files: check filenames
2GSA.pdb
2VPW.pdb
2YEA.pdb
2YED.pdb
3AYA.pdb
3DTA.pdb
3MKA.p

[Xinqiu Yao]

Hi,

Can you print out the content of 'myfiles'? Just make sure the variable has desired values. Also note that by default list.files() returns just file names without path prefix (see help(list.files)). A proper way could be

myfiles <- list.files(path="C:/structurasparadendograma/cortados", pattern=".pdb", full.names=TRUE)

[rene]

thank you very much, work very welll