Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Licensing · Video Overview· RNA Covers

Author Topic: Running 1ehz example: issue .ntParams  (Read 19184 times)

Offline jimamoto

  • non-commercial
  • with-posts
  • *
  • Posts: 3
    • View Profile
Running 1ehz example: issue .ntParams
« on: February 28, 2020, 06:02:57 pm »
Hello,
I am exploring the functions of dssr.  However, when I try the 1ehz example on pg.61 of the manual the following command jq .ntParams 1ehz-dssr.json fails and only produces “null”.  All the other commands seem to work just fine, except the ones that include .ntParams.  I expect that something is going wrong, but I am unsure of where to begin to solve the issue.  Any guidance will be greatly appreciated.

Jason

Offline xiangjun

  • Administrator
  • with-posts
  • *****
  • Posts: 1650
    • View Profile
    • 3DNA homepage
Re: Running 1ehz example: issue .ntParams
« Reply #1 on: February 28, 2020, 06:47:17 pm »
Hi Jason,

Good catch! The key ntParams in the DSSR JSON output was changed to nts a long time ago. However, the manual has not been updated accordingly. That's why you got the "null" output since the JSON file does not contain any objects named ntParams.

Simply replace .ntParams by .nts in the commands listing would resolve the issue. The DSSR Manual has now been corrected.

Best regards,

Xiang-Jun


 

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University