Issue with POKY exported .str file (NMR-STAR 3.1 file format )

[Arun Gupta]

Hello All,

I am interested to run CheSPI Chemical shift Secondary structure Populations Inference (CheSPI) analysis which specifically requires the assigned chemical shifts in NMR-STAR 2.1 file format as input. Hence, I am particularly using the (https://bmrb.pdbj.org/software/conv/) BMRB webpage described Convert NMR-STAR 3.1 table  format conversion tool to convert the POKY exported assignment 271021_NMR_CS.str file (NMR-STAR 3.1 file format ) to NMR-STAR 2.1 file format. However, each time, I am getting the same error “Parser error (crit) in line 1: Invalid token: protein”, Uploaded file does not appear to be in valid input format. Also, I tried to use the POKY exported assignments “shifts” file in sparky format as input for the format conversion tool. But then, it flags different error for sparky format file “Parser error (crit) in line 1: Invalid token: Group”. Does anyone have faced similar issues with POKY exported assignment in .str files (NMR-STAR 3.1 file format) or sparky file format. I am attaching the “271021_NMR_CS.str” and “shifts” files for reference. Any suggestions or comments are welcome.

Thanks

Arun

[Lee, Woonghee]

Dear Arun,

 

I think it is good to ask Mulder group about NMR-STAR 3.1/3.2 support. I am copying Frans in this email. The Github webpage is here: https://github.com/protein-nmr/CheSPI Actually, it is not a lot of work modifying the code to implement in POKY but I need Frans’s approval on that first.

 

Best,

Woonghee

 

 

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Woonghee Lee, I.E.I.P., M.S., Ph.D.

 

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From: <nmr-s...@googlegroups.com> on behalf of Arun Gupta <arung...@gmail.com>
Date: Wednesday, October 27, 2021 at 9:48 AM
To: "nmr-s...@googlegroups.com" <nmr-s...@googlegroups.com>
Subject: [NMR POKY/SPARKY] Issue with POKY exported .str file (NMR-STAR 3.1 file format )

 

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[NMR POKY/SPARKY USER GROUP]

Dear Arun,

This is an old post, but I think is good to notice for ones who wants to use CheSPI.

You can access CheSPI from POKY Notebooks (File -> POKY Notebooks or a little icon in the main window). 

Best,

Woonghee