Messages

1

RNA structures (DSSR) / 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

2

RNA structures (DSSR) / Re: Using dssr to analyze PDB containing multiple frames

« on: March 08, 2019, 10:31:55 pm »

Attached is a few output files that I received when I ran the command.

The exact command entered
x3dna-dssr --input=../../Linear2b_Layer8_24.8-31.0Kcal_noWat_Frame_1-100.pdb --nmr  -o=Lin2_Lay8_NoWat_Frame_1-100-model.out
The output contains only 1 model out of the 100 that were in the pdb.

Also I forgot to mention I am running  v1.7.7-2018apr20 of dssr.

Thank you.
Jason Imamoto

3

RNA structures (DSSR) / Using dssr to analyze PDB containing multiple frames

« on: March 08, 2019, 10:14:38 pm »

Hello,
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