3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: pqtak on April 22, 2009, 08:41:14 pm

Title: how to minimize DNA built with fiber?
Post by: pqtak on April 22, 2009, 08:41:14 pm: Hi,
I am wondering how to minimize the BDNA built with fiber. Some bonds are broken and I want to improve the DNA by minimization.
Title: Re: how to minimize DNA built with fiber?
Post by: xiangjun on April 22, 2009, 11:49:17 pm: Could you be more specific? Which model did you use, and what's the sequence? The fiber models from 3DNA should have standard geometry and proper linkage. I am wondering how it could have broken bonds.

Xiang-Jun
Title: Re: how to minimize DNA built with fiber?
Post by: pqtak on April 27, 2009, 03:30:07 pm: Hi,
Here what you say in one example:

"Please note that in the rebuilt bdl084_3dna.pdb file, some O3'(i-1) to P(i) linkages can be quite long (broken). This structure can be easily minimized to obtain a better backbone linkage."

I got some long O3'(i-1) to P(i) bonds and would like to minimize the structure to fix it.
Title: Re: how to minimize DNA built with fiber?
Post by: pqtak on April 27, 2009, 03:38:09 pm: Hi Xiangjun,
this DNA came from a protein-DNA complex, but the initial parameters were not good. So, I rebuilt it with your program, but before I put it back in the structure of the complex for the refinement, I want to connect all O3'-P linkages. Some distances are >2.5 A.
Title: Re: how to minimize DNA built with fiber?
Post by: pqtak on April 27, 2009, 04:10:43 pm: By the way, I find that dna residues numbering is not very convenient in the rebuilt dna; chain B continues the numbering from chain A. So, I have to change the numbering manually.