Missing files from analyze?

[Leslie]

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!

[xiangjun]

Welcome to 3DNA!

Are you using the "-s" option [for single-strand (ss)] with your RNA structure? In its current setting, 3DNA generates the "stacking.pdb" file only for a duplex. I will consider adding "stacking.pdb" for ss-DNA/RNA if it's useful to you -- so far, you're the only 3DNA user having this "problem", if I understand your post correctly.

Xiang-Jun

[Leslie]

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!

[xiangjun]

Glad to see "it worked beautifully". So 3DNA is not that hard to pick up.

I just "chopped up" my RNA, isolating the helix I was interested

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?

Prompted by you initial question, I am considering to refine the "analyze" program to output "stacking.pdb" for single-stranded DNA/RNA structures as well. This is yet another example of how a user's question helps improve 3DNA.

Xiang-Jun

[Leslie]

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!