Messages

1

Bug reports / Trouble running 3DNA on a Macintosh

« on: October 14, 2016, 02:00:49 pm »

I'm having trouble running 3DNA on my Mac.  I followed the installation instructions exactly, and all the files are in the appropriate directory, but when I run the "find_pair" command, it doesn't work.  Here's a log of my commands and the system's response:

Steve-Harveys-MacBook-Pro-2:bin steveharvey$ pwd
/Users/steveharvey/bin/x3dna-v2.3/bin

Steve-Harveys-MacBook-Pro-2:bin steveharvey$ ls
alc2img      blocview   ex_str      frame_mol   o1p_o2p      rebuild      stack2img   x3dna_ensemble
analyze      cehs      fiber      get_part   pdb2img      regular_dna   std_base   x3dna_setup
anyhelix   comb_str   find_pair   mutate_bases   r3d_atom   rotate_mol   step_hel   x3dna_utils

Steve-Harveys-MacBook-Pro-2:bin steveharvey$ ./find_pair -h
Illegal instruction: 4

Steve-Harveys-MacBook-Pro-2:bin steveharvey$ find_pair -h
-bash: find_pair: command not found

2

General discussions (Q&As) / Re: A/B Index

« on: October 14, 2016, 01:52:04 pm »

The ABI Index is described in the following paper, which explains why it was developed:  Waters, Lu, et al. (2016) J Phys Chem B 120:8449-8456.

3

RNA structures (DSSR) / Torsion angles

« on: July 16, 2015, 02:40:54 pm »

Please add output of all backbone torsions plus chi for the entire chain.  3DNA prints them out but only for double-stranded regions, and it reports these as "strand 1" and "strand 2".  This is appropriate for dsDNA, but not for ssDNA or ssRNA molecules.  THANKS.