"ChimeraX --cmd" doesn't recognise multi-word commands

[Tristan Croll]

Enough said, really. As far as I can tell from trying every permutation I can think of, this isn't currently possible. Would be really useful to be able to run, e.g.

ChimeraX --cmd remotecontrol xmlrpc true

[Eric Pettersen]

Hi Tristan,

You have to put quotes around a multi-word command.

--Eric

[tic20@…]

Hi Eric,

I tried that. 

ChimeraX —cmd “remotecontrol xmlrpc true” 

... opened ChimeraX, complained about the remotecontrol command being incomplete, then tried to open “xmlrpc” and “true” as files.

In Linux, fwiw.

T
 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
 

 

[Eric Pettersen]

That makes no sense to me. Your _shell_ *has* to pass the quoted string to ChimeraX as a _single_ argument. How could ChimeraX possibly be getting three arguments instead?

--Eric

[tic20@…]

... Hmm. Weird - I spent a quarter of an hour or so trying different approaches on my workstation yesterday (including quoting the command, I swear). Yet now when I try it on my laptop it works flawlessly. Sorry.

 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
 

 

[Eric Pettersen]

It happens to all of us. :-)

--Eric

[tic20@…]

So I finally worked out what was going on here, and it's kinda dumb. I 
had the ChimeraX executable wrapped in a little bash script - originally 
because I had to provide it with a custom LD_LIBRARY_PATH, then because 
I needed to set OPENBLAS_NUM_THREADS=1 to overcome a weird 
multiprocessing bug in libOpenBLAS, then because I was too lazy to 
change it:

#!/bin/bash

#CHIMERA_HOME=/home/tic20/apps/chimerax

#export 
LD_LIBRARY_PATH=/home/tic20/apps/gcc-4.9.2/lib64:/usr/local/cuda/lib64:$LD_LIBRARY_PATH

#OPENBLAS_NUM_THREADS=1 chimerax-daily $*

chimerax-daily $*


... which helpfully strips out the quotes from my arguments, so what 
ChimeraX sees is a list of single words. D'oh!

On 2018-06-22 19:09, ChimeraX wrote:

[Greg Couch]

Use $@ instead of $*.

[tic20@…]

Ah - awesome! Thanks for the tip.

On 2018-12-07 16:39, ChimeraX wrote: