Hi Amitoj, I think the problem is that you write the PDB file but never tell Chimera about it -- i.e. you need to add it to the command that starts Chimera. So change your cmd<-paste to: cmd <- paste (exepath, "chimera.exe", " ", tovmd, sep="") which will result in the command string: "C:/Senior_Design/Chimera/bin/ chimera.exe random_temp_file_name.pdb". --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On May 28, 2010, at 3:05 PM, Amitoj Chopra wrote:

Eric,

We got it to work with chimera. Here is our code.

chimera <- function(pdb, exepath = "C:/Senior_Design/Chimera/bin/") { tovmd <- tempfile() write.pdb(pdb, file = tovmd)

cmd <- paste(exepath, "chimera.exe", sep="") cat(cmd)

system(cmd)

unlink(tovmd) }

The only problem is that it opens up chimera but doesnt show the PDB we are trying to view, for this case, 1ly2. Do you know somewhere we went wrong. pdb should be 1ly2. Thanks.

On Thu, May 27, 2010 at 3:42 PM, Eric Pettersen wrote: I am in no way an R expert (or even an R newbie), but given what R documentation I've looked at I see two problems with the below. One is that you are on Windows, and the code for Windows is commented out (the "system" call after "if (os1 == "windows")") The other problem is that you left "vmd -pdb" in the paste() call, so the command it will try to execute is "/Program Files(x86)/Chimera/bin/ chimera.exevmd -pdb <pdb-file-name-here>" which obviously won't work. Changing "vmd -pdb " to just " " will fix that I think.

--Eric

On May 27, 2010, at 3:03 PM, Amitoj Chopra wrote:

...

Thank you Eric. Would something like this work.

C:\Program Files\Chimera\bin\chimera.exe

view.chimera<- function(pdb, exepath = "/Program Files(x86)/Chimera/ bin/chimera.exe", ...) { ## Change exepath to the location of your vmd tovmd <- tempfile() write.pdb(pdb, file = tovmd, ...)

cmd <- paste(exepath, "vmd -pdb ", tovmd, sep="") cat(cmd)

os1 <- .Platform$OS.type if (os1 == "windows") { ## Insert cmd for calling vmd on windows ## system(shQuote(cmd)) } else { system(cmd) } unlink(tovmd) }

pdb <- read.pdb("4q21") view.chimera(pdb)

It doesnt seem to be able to run. I am thinking of what to put in the "window" because that is what goes to the cmd line. Thanks.

Amitoj

On Thu, May 27, 2010 at 2:53 PM, Eric Pettersen wrote: On May 27, 2010, at 12:27 AM, Amitoj Chopra wrote:

...

Is there any way to use the R script and bio3d package to open a pdb with Chimera using R? Thank you.

Hi Amitoj, If R can run external system commands then this is possible. Use bio3d to write a PDB file and then use R to start Chimera from the command line with the PDB file name as an argument, as documented here:

http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/startup.html

If you don't know how to run external commands from R, you would probably have to ask about that on the R mailing list.

--Eric

Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu