Cannot get pdbaln and muscle to work

[Pedram Mehrabi]

Hello,

I recently installed the latest version of R and bio3d. I've been attempting to compile difference distance matrices but cannot get pdbaln to work.

I initially attempted to try the tutorials you have posted.

 pdbs <- pdbaln( get.pdb( c( "4q21", "521p"), path = tempdir() ), outfile = tempfile() )
trying URL 'http://www.rcsb.org/pdb/files/4q21.pdb'
Content type 'text/plain;charset=UTF-8' length unknown
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
......
downloaded 156 KB

trying URL 'http://www.rcsb.org/pdb/files/521p.pdb'
Content type 'text/plain;charset=UTF-8' length unknown
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .
downloaded 121 KB

Reading PDB files:
/tmp/RtmpRgj0HX/4q21.pdb
/tmp/RtmpRgj0HX/521p.pdb
.
Error in .read_pdb(file, multi = multi, hex = hex, maxlines = maxlines,  : 
  Could not convert string to double ("   ")

If I use the weblink for muscle, it seems to work just fine.

> pdbs <- pdbaln(c("4q21.pdb","521p.pdb"), web.arg=list(email="[e-mail]"))
Reading PDB files:
4q21.pdb
521p.pdb
   PDB has ALT records, taking A only, rm.alt=TRUE
.   PDB has ALT records, taking A only, rm.alt=TRUE
.

Extracting sequences

pdb/seq: 1   name: 4q21.pdb 
   PDB has ALT records, taking A only, rm.alt=TRUE
pdb/seq: 2   name: 521p.pdb 
   PDB has ALT records, taking A only, rm.alt=TRUE

I can open muscle up just fine in terminal

/usr/bin/muscle

MUSCLE v3.8.31 by Robert C. Edgar

...

However it still does not work if I specify the filepath to muscle directly in R.

> pdbs <- pdbaln(c("4q21.pdb","521p.pdb"), exefile="usr/bin/muscle")
Reading PDB files:
4q21.pdb
521p.pdb
.
Error in .read_pdb(file, multi = multi, hex = hex, maxlines = maxlines,  : 
  Could not convert string to double ("   ")

I was wondering if anyone can proffer any suggestions as to how I can resolve this problem?

I should also note that I tried this both in Rstudio and R in terminal and got the same results.

Thank you

[Xinqiu Yao]

Can you put '/' in the head of the path to your muscle, i.e. exefile="/usr/bin/muscle", and try it again?

Alternatively, you can put the path to your default search path in e.g. '.bashrc' (Linux) or '.bash_profile' (Mac). Then, you can ignore the 'exefile' argument.

Let me know if it works.

[Pedram Mehrabi]

I tried both suggestions both in R in terminal and Rstudio . I'm getting the same outcome.

It seems odd, because muscle seems to be working fine in terminal.

Thank you

[Xinqiu Yao]

It is indeed odd. Can you try following codes and paste output here for further diagnostic?

pdb1 <- read.pdb("4q21.pdb")
pdb2 <- read.pdb("521p.pdb")
pdb1
pdb2
aln <- seqaln(seqbind(pdbseq(pdb1), pdbseq(pdb2)), id=c("4q21.pdb", "521p.pdb"))
pdbs <- read.fasta.pdb(aln)
sessionInfo()

[Lars Skjærven]

assuming this is resolved. reopen if needed