The problem was that Amith was using a chimerax that was an alias that runs chimerax inside a singularity container.  A singularity container is used so all of the runtime libraries that ChimeraX needs are guaranteed to be there.

So the fix was to modify the alias to bind the scratch directories to the singularity container, ie.,

    alias chimerax='singularity run --bind /wynton/scratch,/scratch PATH-TO-CHIMERAX_SIF.sif'

instead of just:

    alias chimerax='singularity run PATH-TO-CHIMERAX_SIF.sif'

    -- Greg

Hi Amith,

That rather cryptic error message just means that the directory you listed in the cd command either does not exist or you do not have permission to read it.  You could try

cd /wynton/scratch

then if that works try

cd /wynton/scratch/avranga1008

and just keep going until you find the directory that is causing the problem.

Tom

On Apr 6, 2022, at 6:30 PM, Rangarajan, Amith via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

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Hello everyone,

i am new to using chimerax in --no gui mode

$ chimerax --nogui
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California.  All rights reserved.
cmd> pwd
Executing: pwd
Current working directory is: /wynton/home/jacobson/avranga1008
cmd> cd /wynton/scratch/avranga1008/0-binana/0-docked-poses
cd /wynton/scratch/avranga1008/0-binana/0-docked-poses
...^
Expected name of a folder to open/read; a name of 'browse' will bring up a file browser or a keyword

please share your thoughts on how to change dir in the no gui mode.
thanks,
amith

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