Messages

1

General discussions (Q&As) / Re: Missing files from analyze?

« on: April 24, 2012, 01:33:39 am »

Just curious, what do you mean by "chopping up" your RNA? Did you know that the default settings of find_pair automatically locate all double helical regions in an RNA structure, and store the fragments in file "hel_regions.pdb"? Does this functionality help?

I didn't know that, and it does help! Thanks!

2

General discussions (Q&As) / Re: Missing files from analyze?

« on: April 23, 2012, 05:30:16 pm »

Yes, that was exactly my problem. (I finally figured it out about an hour after I posted) I just "chopped up" my RNA, isolating the helix I was interested it and ran it through as a ds RNA, and it worked beautifully.

Thank you!

3

General discussions (Q&As) / Missing files from analyze?

« on: April 23, 2012, 04:01:32 pm »

I'm new to using 3DNA, and I'm trying to analyze a hairpin RNA. I ran my .pdb file through find_pair in order to generate the .inp file for analyze, however, when I run analyze, I don't get all the output files I'm supposed to. It only generates sample.out, auxiliary.par, bp_helical.par,  bp_step.par, and ref_frames.dat. The file I really want, stacking, is missing.

Right now I'm using a Mac (10.6. with 3DNA v2.1beta (downloaded Apr 20). Does anyone have any ideas why I'm missing these files? Do I need to install other programs before they'll work?

Thanks!