Messages

1

RNA structures (DSSR) / Re: How to look for abasic site using DSSR

« on: November 27, 2023, 11:26:41 am »

Hello, for instance, in PDB 1FZL, there is an abasic site, and the residue is a modified nucleotide with the resname PYP (pyrene deoxyriboside). X3DNA is not recognizing that residue. However, I see that for residue 3DR (on chain B), where only the sugar-phosphate backbone is present, x3dna is recognizing that and computing backbone torsions. Is there any way to compute backbone torsions for non-standard residues like PYP? Thank you!

2

RNA structures (DSSR) / Re: How to look for abasic site using DSSR

« on: November 27, 2023, 09:58:01 am »

Hi Honglue,

I've added an option --abasic to DSSR to take abasic sites as nucleotides, as long as main-chain backbone atoms are preserved: P, O5', C5', C4', C3', and O3'. Quick tests on 1l2c and 1l2d show that this new DSSR feature is working as designed (e.g., C.HPD18 is listed in an internal loop). Understandably, the abasic nucleotides won't be involved in base pairing and stacking interactions.

The DSSR on the download page (still labeled v1.6.8-2017mar28) has been updated. Have a try and report back if it solves your problem.

Xiang-Jun

Hi, I am trying to use --abasic command (./x3dna-dssr --abasic -i=test.pdb) on version 1.9.8(2019Oct16), but it's not recognizing the abasic site even if I have P, O5', C5', C4', and C3' atoms. Wondering if --abasic works properly only on the DSSR v1.7.2-2017nov20 release; if so, how can I download the older version? Thank you!