DSSP: Error in file(con, "r") : cannot open the connection

[Bill CX]

Hi there, I run into problem with this, can someone help me solve this issue?

pdb <- read.pdb("1bg2")
sse <- dssp(pdf)

and the console:

> pdb <- read.pdb("1bg2")
  Note: Accessing on-line PDB file
  HEADER    MOTOR PROTEIN                           04-JUN-98   1BG2               
Warning message:
In read.table(text = sapply(raw.atom, split.fields), stringsAsFactors = FALSE,  :
  not all columns named in 'colClasses' exist
> sse <- dssp(pdb)
Error in dssp.pdb(pdb) : An error occurred while running command
 'dssp /var/folders/6x/8tvx99f93ksd6byg6cmzb7pc0000gn/T//Rtmp2uWMdE/file35fc2426eae8 /var/folders/6x/8tvx99f93ksd6byg6cmzb7pc0000gn/T//Rtmp2uWMdE/file35fc770837e2'

Session Info:

R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] bio3d_2.2-4

loaded via a namespace (and not attached):
[1] parallel_3.3.0 tools_3.3.0    grid_3.3.0    

[Xinqiu Yao]

Hi,

It is likely because the DSSP program is not properly installed or the path to DSSP is not recognized. Could you try sse <- dssp(pdb, verbose=TRUE) and copy&paste the output message here for further diagnosis?

[Bill CX]

I did install the dssp on mac, but it might not correctly installed, can you show me how to install the dssp the way you installed on Mac?

Here is the error

sse <- dssp(pdb, verbose=TRUE)

 .. 00000673 atom(s) from 'string' selection 
 .. 00000673 atom(s) in final combined selection 

Running command:
  dssp /var/folders/6x/8tvx99f93ksd6byg6cmzb7pc0000gn/T//RtmpGhq8Mf/fileb8cd18a2c12 /var/folders/6x/8tvx99f93ksd6byg6cmzb7pc0000gn/T//RtmpGhq8Mf/fileb8cd16535288 
sh: dssp: command not found
Error in dssp.pdb(pdb, verbose = TRUE) : 
  An error occurred while running command
 'dssp /var/folders/6x/8tvx99f93ksd6byg6cmzb7pc0000gn/T//RtmpGhq8Mf/fileb8cd18a2c12 /var/folders/6x/8tvx99f93ksd6byg6cmzb7pc0000gn/T//RtmpGhq8Mf/fileb8cd16535288'
In addition: Warning message:
In dssp.pdb(pdb, verbose = TRUE) :
  Residues with missing backbone atoms detected: 169-A

[Xinqiu Yao]

Do you know where your DSSP is installed? If so, simply providing the full path to the program with dssp(pdb, exefile='path_to_dssp') can solve the problem. Make sure the name of the executable is properly specified (e.g. it is sometimes called 'mkdssp').

The installation from source is pretty straightforward and its instruction can be found at http://swift.cmbi.ru.nl/gv/dssp/.

[Bill CX]

Not working, and I followed the instruction for installing DSSP, and still not working.

[Bill CX]

Also how can you make the structure figures, I did this and no pymol window or structure show up.

> # read two G-protein structures
> a <- read.pdb("4q21")
  Note: Accessing on-line PDB file
  HEADER    ONCOGENE PROTEIN                        25-SEP-91   4Q21               
Warning message:
In read.table(text = sapply(raw.atom, split.fields), stringsAsFactors = FALSE,  :
  not all columns named in 'colClasses' exist
> b <- read.pdb("4lhy")
  Note: Accessing on-line PDB file
  HEADER    PROTEIN TRANSPORT                       01-JUL-13   4LHY               
Warning message:
In read.table(text = sapply(raw.atom, split.fields), stringsAsFactors = FALSE,  :
  not all columns named in 'colClasses' exist
> 
> # perform iterative alignment
> aln <- struct.aln(a, b)

 Initial RMSD (168 atoms): 20.551
 Cycle 1: 17 atoms rejected
  Mean: 13.4 Std: 11 Cut: 35.4
  RMSD (151 of 168 atoms): 15.666
 Cycle 2: 14 atoms rejected
  Mean: 10.3 Std: 8.6 Cut: 27.4
  RMSD (137 of 168 atoms): 11.701
 Cycle 3: 14 atoms rejected
  Mean: 7.5 Std: 6.8 Cut: 21.1
  RMSD (123 of 168 atoms): 8.138
 Cycle 4: 10 atoms rejected
  Mean: 4.4 Std: 5.1 Cut: 14.6
  RMSD (113 of 168 atoms): 5.718
 Cycle 5: 10 atoms rejected
  Mean: 3.1 Std: 3.8 Cut: 10.6
  RMSD (103 of 168 atoms): 3.53
 Cycle 6: 8 atoms rejected
  Mean: 1.7 Std: 2.5 Cut: 6.6
  RMSD (95 of 168 atoms): 2.125
 Cycle 7: 8 atoms rejected
  Mean: 0.9 Std: 1.4 Cut: 3.8
  RMSD (87 of 168 atoms): 1.595
 Cycle 8: 12 atoms rejected
  Mean: 0.8 Std: 1 Cut: 2.9
  RMSD (75 of 168 atoms): 1.021
 Cycle 9: 6 atoms rejected
  Mean: 0.6 Std: 0.6 Cut: 1.9
  RMSD (69 of 168 atoms): 0.693
> 

[Xinqiu Yao]

Hi,

All the commands you used above do not open any pymol/vmd window. You need to write coordinates to HD and open it with external programs. For example, if you want to show the fitted structure generated by 'struct.aln()', try write.pdb(b, xyz=aln$xyz, file='4lhy_fitted.pdb'). Then open the file with VMD/Pymol in your shell.

Also, about the DSSP error. Have you tried to find the location of the dssp installed in your Mac and use it as the 'exefile' argument as I indicated above? What error message did you get by this?

[Lars Skjærven]

Note that struct.aln() will write the fitted structures in PDB format to directory fitlsq/ by default. Thus, after running the struct.aln() command above, you should browse to you working directory and open the PDB files with names fixed.pdb and mobile.9.pdb. You will have to open PyMOL manually as XQ writes here.

Also, since you have R 3.3.0 you should update to the latest version of Bio3D. Use the development version:

install.packages("devtools")
library(devtools)
install_bitbucket("Grantlab/bio3d", subdir = "ver_devel/bio3d/")

That should fixed the problem with you have with read.pdb().

[Barry Grant]

We should update the dssp() documentation to include more explicit install instructions.

This comes up occasionally with muscle() also and having better online install instructions that both sets of docs could point to would help.

https://bitbucket.org/Grantlab/bio3d/issue/206/unable-to-launch-muscle-package-from

https://bitbucket.org/Grantlab/bio3d/issue/145/where-should-be-muscle-or-dssp-placed

https://bitbucket.org/Grantlab/bio3d/issues/254/seqaln-cannot-access-muscle-installed