Dear ChimeraX, I have a ChimeraX session .cxs file that was created a while ago. I wonder if there is a way to open the file to see the actual commands, parameters used in that session. Is there is tool/way to read .cxs file? Thank you for your help. Ibrahim Ibrahim M.Moustafa, Ph.D. Pennsylvania State University Biochemistry & Molecular Biology Dept. Millennium Science Complex University Park State College, PA16802 Phone: (814) 863 5940 Fax: (814) 865 7927
So I'm not sure if this will help you. I don't recall if the log was saved in older versions of ChimeraX. The log is where you would find a record of the commands given in a session. For debugging purposes, there is the "debug sdump session.cxs text-filename" ChimeraX command that will generate a text version of session.cxs. If it fails, then there is probably a bug in the session file. HTH, Greg On 6/6/2023 12:23 PM, Moustafa, Ibrahim M. via ChimeraX-users wrote:
Dear ChimeraX,
I have a ChimeraX session .cxs file that was created a while ago. I wonder if there is a way to open the file to see the actual commands, parameters used in that session. Is there is tool/way to read .cxs file?
Thank you for your help.
Ibrahim
Ibrahim M.Moustafa, Ph.D. Pennsylvania State University Biochemistry & Molecular Biology Dept. Millennium Science Complex University Park State College, PA16802
Phone: (814) 863 5940 Fax: (814) 865 7927
_______________________________________________ ChimeraX-users mailing list --chimerax-users@cgl.ucsf.edu To unsubscribe send an email tochimerax-users-leave@cgl.ucsf.edu Manage subscription:
Hi Ibrahim, Unless it is extremely old (like several years), the session would include the whole Log contents from when you saved it. When you restart the session, there may be a triangle in the Log to show its contents from that time. Also, there are commands you can run after restarting the session that will report current settings, e.g. lighting (just the single word, without additional keywords) will report all the current lighting settings. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html> Along similar lines, see also commands: material volume settings info models color list custom view list clip list ...and there may be some others I'm not thinking of at the moment. There are help pages for all of the above in the User Guide. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 6, 2023, at 12:23 PM, Moustafa, Ibrahim M. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX,
I have a ChimeraX session .cxs file that was created a while ago. I wonder if there is a way to open the file to see the actual commands, parameters used in that session. Is there is tool/way to read .cxs file?
Thank you for your help.
Ibrahim
Ibrahim M.Moustafa, Ph.D. Pennsylvania State University Biochemistry & Molecular Biology Dept. Millennium Science Complex University Park State College, PA16802
Phone: (814) 863 5940 Fax: (814) 865 7927
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription:
Thank you Elaine, appreciate it! Ibrahim ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, June 6, 2023 3:53 PM To: Moustafa, Ibrahim M. <ria2@psu.edu> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] ChimeraX .cxs session file Hi Ibrahim, Unless it is extremely old (like several years), the session would include the whole Log contents from when you saved it. When you restart the session, there may be a triangle in the Log to show its contents from that time. Also, there are commands you can run after restarting the session that will report current settings, e.g. lighting (just the single word, without additional keywords) will report all the current lighting settings. <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Flighting.html&data=05%7C01%7Cria2%40psu.edu%7Cf4c63f8ae20c4287bb5708db66c7c4d0%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C638216780410406285%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=56%2FWwbBW1oTpLagSs5vpT9PafWbi95wvkOZAZr63U3s%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html>> Along similar lines, see also commands: material volume settings info models color list custom view list clip list ...and there may be some others I'm not thinking of at the moment. There are help pages for all of the above in the User Guide. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 6, 2023, at 12:23 PM, Moustafa, Ibrahim M. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX,
I have a ChimeraX session .cxs file that was created a while ago. I wonder if there is a way to open the file to see the actual commands, parameters used in that session. Is there is tool/way to read .cxs file?
Thank you for your help.
Ibrahim
Ibrahim M.Moustafa, Ph.D. Pennsylvania State University Biochemistry & Molecular Biology Dept. Millennium Science Complex University Park State College, PA16802
Phone: (814) 863 5940 Fax: (814) 865 7927
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription:
participants (3)
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Elaine Meng -
Greg Couch -
Moustafa, Ibrahim M.