Show Posts

This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.

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

Topics - jimamoto

Pages: [1]
RNA structures (DSSR) / Running 1ehz example: issue .ntParams
« on: February 28, 2020, 06:02:57 pm »
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.


I am trying to use dssr to analyze a pdf file containing multiple frames.  Unfortunately, when I use dssr whether I use --nmr or --json it only gives me information on a single frame.  I have tried adding model to the name of the output file, but it does not produce torsions for each one.  I am new at using dssr and I figure I am making a simple mistake. 
Below are two of the ways I have tried to call dssr.
x3dna-dssr --input=../../Linear2b_Layer8_24.8-31.0Kcal_noWat_Frame_1-100.pdb --nmr -json -o=Lin2_Lay8_NoWat_Frame_1-100-all.json
x3dna-dssr --input=../../Linear2b_Layer8_24.8-31.0Kcal_noWat_Frame_1-100.pdb --nmr  -o=Lin2_Lay8_NoWat_Frame_1-100-model.out

Thank you for your time and help.

Jason Imamoto

Pages: [1]

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.