Unable to load pymol

[George Tzotzos]

I searched the archive for this problem but couldn't find a satisfactory answer.

I'm using OpenSource PyMol v.1.7.x

PyMOL is installed in /usr/local/bin

When I issue view.dccm(cij, pdb, launch = TRUE)

I get the following error message

Unable to find application named 'MacPyMOL' Error in view.dccm(cij, pdb, launch = TRUE) : An error occurred while running command 'pymol'

I'd appreciate any suggestions for a work around for this problem. Below is my sessionInfo() in case it is of any help

sessionInfo() R version 3.2.1 (2015-06-18) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.4 (Yosemite)

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

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

other attached packages: [1] bio3d_2.2-3

loaded via a namespace (and not attached): [1] magrittr_1.5 ncdf_1.6.8 parallel_3.2.1 igraph_1.0.1
[5] grid_3.2.1 lattice_0.20-31

[Xinqiu Yao]

Hi,

You can specify executable explicitly in the command, e.g. view.dccm(cij, pdb, exefile='/usr/local/bin/MacPyMOL', launch=TRUE).

[Lars Skjærven]

Hi George, Thanks for noting this.

Xinqiu: my pymol is installed under "/Applications/MacPyMOL.app/" and in order to start it from the terminal i have to do "open -a /Applications/MacPyMOL.app". Silly stuff. Unfortunately I haven't been able to launch it from within the R terminal on OSX.

George: For now you should run the view.dccm command without the launch argument. The function will generate a python script for you (along with writing the PDB). After running the view.dccm command, start pymol with open -a /Applications/MacPyMOL.app/ corr.py

Hope it helps. Lars

[Barry Grant]

Perhaps not directly helpful here but on a mac I can launch pymol from the terminal with:

/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL

Then you can obviously set whatever alias you like (e.g. in your ~/.bashrc file) to make this easy, e.g.

alias pymol='/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL'

[Barry Grant]

Side-note: Should we have a new OpenGL based view.dccm() and what should the output look like?

I know the pymol functionality has been moved to pymol() and pymol.dccm() but it appears that the launch=TRUE option on mac is still suspect (even though the "open -a MacPyMOL" works from the command line). Should this be made more robust somehow?

[Lars Skjærven]

Jupp. Perhaps set exefile to NULL, and based on the OS we set exefile internally to

• pymol for unix systems
• /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL for OSX

And only when the user specifies exefile (not null) this input is used for the execution ?

[Xinqiu Yao]

Any update for this issue?

I think the view() family of functions will finally solve all these system dependency problems. Currently, we just do the suggested: Set exefile=NULL by default and update it internally depending on the OS type. This strategy should apply to all functions that call pymol or vmd.

[George Tzotzos]

I wonder if there's been a solution to this problem.

I've done a clean install of R and bio3d. Followed the different suggestions given above, e.g. view.dccm(cij, pdb, launch=FALSE) view.dccm(cij, pdb, exefile='/opt/local/bin/pymol', launch=TRUE) view.dccm(cij, pdb, exefile='/opt/local/bin/pymol') view.dccm(cij, pdb) In all of the above cases, I get the same Error: could not find function "view.dccm" Thanks in advance for any advice.

[George Tzotzos]

Apologies. I retract.

Figured out my mistake. Should had used: pymol.dccm(cij, pdb, type="launch")