wynton --nogui : how to use cd command ?
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
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:
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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
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@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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Greg Couch -
Rangarajan, Amith -
Tom Goddard