Re: [chimerax-users] correct format for attribute information file (.defattr)
Hello everyone,
I am trying to add mutation counts as a attribute and use it to generate a map of hotspots on the protein .
I followed the format provided on chimerax documentation and i am getting this error :
SyntaxError: Line 12 in KIT-mutations-count.defattr is either not of the form 'name: value' or is missing initial tab
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\std_commands\defattr.py", line 107, in defattr raise SyntaxError("Line %d in %s is either not of the form 'name: value'"
i am on windows 11 using chimerax 1.3.
thanks amith
Dear All,
I am sorry , i hit send before completely explain the issue. I think it is a formatting issue on the defattr input file, which i am not able to identify.
I have attached the input file as attachment.
Kindly review and suggest what could be done to fix the same.
thanks again for your support.,
best amith ________________________________ From: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Rangarajan, Amith via ChimeraX-users chimerax-users@cgl.ucsf.edu Sent: Thursday, February 24, 2022 9:47 AM To: ChimeraX Users Help ChimeraX-users@cgl.ucsf.edu Subject: Re: [chimerax-users] correct format for attribute information file (.defattr)
Hello everyone, I am trying to add mutation counts as a attribute and use it to generate a map of hotspots on the protein . I followed the format provided on chimerax documentation and i am getting this error : ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd Hello everyone, I am trying to add mutation counts as a attribute and use it to generate a map of hotspots on the protein . I followed the format provided on chimerax documentation and i am getting this error : ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd Hello everyone,
I am trying to add mutation counts as a attribute and use it to generate a map of hotspots on the protein .
I followed the format provided on chimerax documentation and i am getting this error :
SyntaxError: Line 12 in KIT-mutations-count.defattr is either not of the form 'name: value' or is missing initial tab
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\std_commands\defattr.py", line 107, in defattr raise SyntaxError("Line %d in %s is either not of the form 'name: value'"
i am on windows 11 using chimerax 1.3.
thanks amith
Hi Amith, It is exactly what the error message says: the assignment lines (which start at line 12 of the file) are missing the initial tab. I.e. you have to put a tab in front of each column in these lines, as it says in the format description:
https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html
Maybe you are not familiar with tab? It is a key on the left side of the keyboard. It was used to indent paragraphs in the old days of typewriters.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 24, 2022, at 9:51 AM, Rangarajan, Amith via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear All, I am sorry , i hit send before completely explain the issue. I think it is a formatting issue on the defattr input file, which i am not able to identify. I have attached the input file as attachment. Kindly review and suggest what could be done to fix the same. thanks again for your support., best amith From: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Rangarajan, Amith via ChimeraX-users chimerax-users@cgl.ucsf.edu Sent: Thursday, February 24, 2022 9:47 AM To: ChimeraX Users Help ChimeraX-users@cgl.ucsf.edu Subject: Re: [chimerax-users] correct format for attribute information file (.defattr)
Hello everyone, I am trying to add mutation counts as a attribute and use it to generate a map of hotspots on the protein .
I followed the format provided on chimerax documentation and i am getting this error :
SyntaxError: Line 12 in KIT-mutations-count.defattr is either not of the form 'name: value' or is missing initial tab
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\std_commands\defattr.py", line 107, in defattr raise SyntaxError("Line %d in %s is either not of the form 'name: value'"
i am on windows 11 using chimerax 1.3. thanks amith <KIT-mutations-count.defattr>
Dear Meng,
Thanks for the guidance.
I was getting other whitespaces into the file. i was using ms visual code to create the file earlier , then upon switching to notepad ++ i was able to get rid of the error.
best, amith ________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Thursday, February 24, 2022 10:23 AM To: Rangarajan, Amith Amith.Rangarajan@ucsf.edu Cc: ChimeraX Users Help ChimeraX-users@cgl.ucsf.edu Subject: Re: [chimerax-users] correct format for attribute information file (.defattr)
Hi Amith, It is exactly what the error message says: the assignment lines (which start at line 12 of the file) are missing the initial tab. I.e. you have to put a tab in front of each column in these lines, as it says in the format description:
https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html
Maybe you are not familiar with tab? It is a key on the left side of the keyboard. It was used to indent paragraphs in the old days of typewriters.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 24, 2022, at 9:51 AM, Rangarajan, Amith via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear All, I am sorry , i hit send before completely explain the issue. I think it is a formatting issue on the defattr input file, which i am not able to identify. I have attached the input file as attachment. Kindly review and suggest what could be done to fix the same. thanks again for your support., best amith From: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Rangarajan, Amith via ChimeraX-users chimerax-users@cgl.ucsf.edu Sent: Thursday, February 24, 2022 9:47 AM To: ChimeraX Users Help ChimeraX-users@cgl.ucsf.edu Subject: Re: [chimerax-users] correct format for attribute information file (.defattr)
Hello everyone, I am trying to add mutation counts as a attribute and use it to generate a map of hotspots on the protein .
I followed the format provided on chimerax documentation and i am getting this error :
SyntaxError: Line 12 in KIT-mutations-count.defattr is either not of the form 'name: value' or is missing initial tab
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\std_commands\defattr.py", line 107, in defattr raise SyntaxError("Line %d in %s is either not of the form 'name: value'"
i am on windows 11 using chimerax 1.3. thanks amith <KIT-mutations-count.defattr>
participants (2)
-
Elaine Meng -
Rangarajan, Amith