Hello all,
I'm trying to fill the gaps in a protein-DNA complex of a moderate size (~ 15k heavy atoms). There are two protein chains with 13 missing pieces overall, most are 2 to 8 AA, but two are fairly long (~ 15 AA). I'm modeling ONLY the missing parts for I don't want the X-ray structure perturbed, and I included DNA molecule as a ligand (with HETATM identifier and "." in alignment).
>From reading this mailing list, I've realized that it's better to generate a lot of models using a faster routine (e.g. refine.very_fast) and then take the best one, rather than do longer refinement and generate less models.
The question I wanted to ask, is what is the best assess method I can use, considering the nature of my task? I'm using DOPE right now, but in the manual I've also seen mentioning of DOPE-HR. Would it slow down the loop refinement process a lot (or at all)?
Thank you for any suggestions.
-- Alex Predeus Michigan State University
On 3/15/12 9:33 PM, Alexander Predeus wrote: > The question I wanted to ask, is what is the best assess method I can > use, considering the nature of my task? I'm using DOPE right now, but in > the manual I've also seen mentioning of DOPE-HR. Would it slow down the > loop refinement process a lot (or at all)?
DOPE-HR is simply DOPE with a smaller bin size. It shouldn't be any slower to evaluate it than DOPE - and assessment with DOPE takes only a fraction of a second, so you wouldn't notice any difference anyway. DOPE is more widely used and tested than DOPE-HR, so I would recommend that.
Ben Webb, Modeller Caretaker
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Alexander Predeus -
Modeller Caretaker