Re: [chimerax-users] error with open :: 'foreach' has no suffix
Yes, that was quite helpful. The 'foreach' option only became available starting with the 1.3 release. You are running 1.2.5, so you need to upgrade. --Eric
On Feb 14, 2022, at 3:35 PM, Rangarajan, Amith <Amith.Rangarajan@ucsf.edu> wrote:
This Message Is From an External Sender This message came from outside your organization. hi Eric,
i have submitted a bug report
thanks amith From: Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> Sent: Monday, February 14, 2022 3:15 PM To: Rangarajan, Amith <Amith.Rangarajan@ucsf.edu <mailto:Amith.Rangarajan@ucsf.edu>> Cc: ChimeraX Users Help <ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] error with open :: 'foreach' has no suffix
This Message Is From an External Sender This message came from outside your organization. Hi Amith, I don't care so much about the contents of your script per se — I'd like to see the contents of the log when the error occurs. Do this: run the command that generates the "'foreach' has no suffix" error and then use Help→Report A Bug and submit a bug report. That will include the contents of the log, which is what I need to see. Thanks!
--Eric
On Feb 10, 2022, at 4:52 AM, Rangarajan, Amith <Amith.Rangarajan@ucsf.edu <mailto:Amith.Rangarajan@ucsf.edu>> wrote:
This Message Is From an External Sender This message came from outside your organization. Dear Tom and Eric,
I used notepad ++ to make sure that the cxc file was not a .txt ( i am on windows) and i am still getting the error ( foreach has no suffix) . i have attached my .cxc script .
I am trying to read a set of .mae files and write a log file with RMSD and some distance measurements.
I am new to chimera and would benefit a lot from your review of my script and possible fixes for this issue.
thank a lot for your time.
best regards, amith From: Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> Sent: Tuesday, February 8, 2022 10:36 AM To: PETTERSEN, ERIC <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> Cc: Rangarajan, Amith <Amith.Rangarajan@ucsf.edu <mailto:Amith.Rangarajan@ucsf.edu>> Subject: Re: [chimerax-users] error with open :: 'foreach' has no suffix
This Message Is From an External Sender This message came from outside your organization. Hi Eric,
Not quite sure I understand your theory abut Amith's error. In current ChimeraX daily build using non-existent files with open command
open something.cxc foreach somethingelse.py
No such file/path: something.cxc
gives a very sensible error message and does not try to interpret "foreach" as a file name.
Tom
On Feb 8, 2022, at 9:40 AM, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi Amith, That error message indicates to me that the first file name (script.cxc) isn't being recognized as a ChimeraX command script file. So take a hard look at the command you typed and make sure that the suffix for that file is ".cxc" and not something mistyped like ".cxs" or whatnot.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Feb 8, 2022, at 6:25 AM, Rangarajan, Amith via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
This Message Is From an External Sender This message came from outside your organization. Hi,
I am trying to run a script and want to use foreach ( open script.cxc foreach *.pdb) to iterate through several pdb files in the working directory.
I had no issues with running it earlier, but since last few tries, i am getting an error stating that ""'foreach' has no suffix""
I am not able to figure out how to debug this.
I am using the latest build of chimerax.
I will highly appreciate your suggestions on fixing this.
best amith _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users>
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users> <RMSD-distance-final.cxc>
hi Eric, thanks for letting me know. I am sorry if i bothered you too much for this. i have both chimerax versions on my machine bur the chimerax 1.25 is the one still pinned to the task bar and was not aware that i was using it. thanks again for your time, best amith ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Monday, February 14, 2022 3:38 PM To: Rangarajan, Amith <Amith.Rangarajan@ucsf.edu> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] error with open :: 'foreach' has no suffix Yes, that was quite helpful. The 'foreach' option only became available starting with the 1.3 release. You are running 1.2.5, so you need to upgrade. --Eric On Feb 14, 2022, at 3:35 PM, Rangarajan, Amith <Amith.Rangarajan@ucsf.edu ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd Yes, that was quite helpful. The 'foreach' option only became available starting with the 1.3 release. You are running 1.2.5, so you need to upgrade. --Eric On Feb 14, 2022, at 3:35 PM, Rangarajan, Amith <Amith.Rangarajan@ucsf.edu<mailto:Amith.Rangarajan@ucsf.edu>> wrote: This Message Is From an External Sender This message came from outside your organization. hi Eric, i have submitted a bug report thanks amith ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>> Sent: Monday, February 14, 2022 3:15 PM To: Rangarajan, Amith <Amith.Rangarajan@ucsf.edu<mailto:Amith.Rangarajan@ucsf.edu>> Cc: ChimeraX Users Help <ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] error with open :: 'foreach' has no suffix This Message Is From an External Sender This message came from outside your organization. Hi Amith, I don't care so much about the contents of your script per se — I'd like to see the contents of the log when the error occurs. Do this: run the command that generates the "'foreach' has no suffix" error and then use Help→Report A Bug and submit a bug report. That will include the contents of the log, which is what I need to see. Thanks! --Eric On Feb 10, 2022, at 4:52 AM, Rangarajan, Amith <Amith.Rangarajan@ucsf.edu<mailto:Amith.Rangarajan@ucsf.edu>> wrote: This Message Is From an External Sender This message came from outside your organization. Dear Tom and Eric, I used notepad ++ to make sure that the cxc file was not a .txt ( i am on windows) and i am still getting the error ( foreach has no suffix) . i have attached my .cxc script . I am trying to read a set of .mae files and write a log file with RMSD and some distance measurements. I am new to chimera and would benefit a lot from your review of my script and possible fixes for this issue. thank a lot for your time. best regards, amith ________________________________ From: Tom Goddard <goddard@sonic.net<mailto:goddard@sonic.net>> Sent: Tuesday, February 8, 2022 10:36 AM To: PETTERSEN, ERIC <pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>> Cc: Rangarajan, Amith <Amith.Rangarajan@ucsf.edu<mailto:Amith.Rangarajan@ucsf.edu>> Subject: Re: [chimerax-users] error with open :: 'foreach' has no suffix This Message Is From an External Sender This message came from outside your organization. Hi Eric, Not quite sure I understand your theory abut Amith's error. In current ChimeraX daily build using non-existent files with open command open something.cxc foreach somethingelse.py
No such file/path: something.cxc
gives a very sensible error message and does not try to interpret "foreach" as a file name. Tom On Feb 8, 2022, at 9:40 AM, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hi Amith, That error message indicates to me that the first file name (script.cxc) isn't being recognized as a ChimeraX command script file. So take a hard look at the command you typed and make sure that the suffix for that file is ".cxc" and not something mistyped like ".cxs" or whatnot. --Eric Eric Pettersen UCSF Computer Graphics Lab On Feb 8, 2022, at 6:25 AM, Rangarajan, Amith via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: This Message Is From an External Sender This message came from outside your organization. Hi, I am trying to run a script and want to use foreach ( open script.cxc foreach *.pdb) to iterate through several pdb files in the working directory. I had no issues with running it earlier, but since last few tries, i am getting an error stating that ""'foreach' has no suffix"" I am not able to figure out how to debug this. I am using the latest build of chimerax. I will highly appreciate your suggestions on fixing this. best amith _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users <RMSD-distance-final.cxc>
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Eric Pettersen -
Rangarajan, Amith