[chimerax-users] wynton --nogui : how to use cd command ?

[Greg Couch]

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

On 4/6/2022 6:46 PM, Tom Goddard via ChimeraX-users wrote:
> 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 at cgl.ucsf.edu> wrote:
>>
>> This Message Is From an External Sender
>> This message came from outside your organization.
>> 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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