Messages

1

General discussions (Q&As) / Re: Recognition of stacked base pairs

« on: September 09, 2019, 05:31:27 pm »

I downloaded the new version of x3dna (v2.4.4-2019sep09) and I confirm that overlap area is now calculated correctly.

Thank you very much for showing me the root of the problem, comprehensive explanation and release of new version of x3dna.


With kind regards,
Aleš

2

General discussions (Q&As) / Recognition of stacked base pairs

« on: September 08, 2019, 11:52:43 am »

Dear all,

I have a structure of parallel duplex anchored by i-motif (pdb is attached - C3GAGA_full.pdb). The step G4-A5 is particularly interesting for me because of cross-strand stacking of the bases (G4A5.pdb). When I run analyze command on whole structure (C3GAGA_full.pdb) I get total overlap area in the G4-A5 step equal to zero. I found some help in the topic "Base Stacking analysis" here on the forum (http://forum.x3dna.org/howtos/base-stacking-analysis/). I believe that following comment from xiangjun regarding the distance threshhold for recognition of stacked bases is critical to my problem:

 "The distance cutoff is 4.5 Å. If the shortest distance of any two-pair between the two sets of atoms is larger than the cutoff, then the stacking area is set to 0."

I also tried to run analyze on the extracted G4-A5 step (G4A5.pdb) which to my surprise gave me total overlap area of 12.04.

1) Is there any explanation why the overlap area in the G4-A5 step in the full structure is zero but in extracted structure is 12.04?
2) Is it possible that zero overlap is result of low threshold?
3) If so, is it possible to change the threshold and how?

Hopefully I attached all relevant files.

Thank you in advance, any help is much appreciated.