[phenixbb] give-up-quick Phaser in Rosetta

Morten Grøftehauge mortengroftehauge.work at gmail.com
Wed Jul 10 02:11:23 PDT 2013


Okay, thanks Tom. I'll try the MRage thing. I checked the output from
HHpred and there's 100 pdb models with a Prob of 100, E-value between
10^-42 and 10^-34, identity 13-26%. A bit hard to pick the right model from
those options. Or easy. So far it's looking hard.

Cheers,
Morten



On 9 July 2013 17:50, Terwilliger, Thomas C <terwilliger at lanl.gov> wrote:

>  Hi Morten,
>
>  Yes, this is a disadvantage of the way mr_rosetta runs for now.  It
> tries everything, then picks the best.  I can think of two options:
>
>  1. Try out phenix.MRage which is optimized to try many things in
> parallel in MR.  Then take the best one and run mr_rosetta with it.
>
>  2. Run separate mr_rosetta jobs for each search model, and when you see
> one that is working, trash the others.
>
>  All the best,
> Tom T
>
>   On Jul 9, 2013, at 10:41 AM, Morten Grøftehauge wrote:
>
>  Dear Phenixbb,
>
>  I was wondering if there was any way of getting Rosetta to give up
> easily and move on to another search model?
> Say I have 20 or more equally awful search models. I think there's a
> possibility that one of them will knock it out of the park (i.e. TFZ > 8).
> But even if I have Phaser set to fast search I will end up with an
> exhaustive search because the search models are so bad.
>
>        fast_search_mode= True Run phaser with selection_criteria_rot_value and
>                         then if no obvious solution, repeat with cutoff
>                         lowered by search_down_percent      search_down_percent= 25 Used if fast_search_mode=True. Run phaser with
>                            selection_criteria_rot_value and then if no obvious
>                            solution, repeat with cutoff lowered by search_down_percent
>
>
>  If I set search_down_percent to 75 does this mean that Phaser will give
> up easily and move on to the next model? Is this a terrible strategy
> CPU-time-wise?
> I am of course aware that search_down_percent is much more likely to give
> me the right solution for a given model but in this case there are just so
> many possible search models.
>
>  Cheers,
> Morten
>
>
>  --
> Morten K Grøftehauge, PhD
> Pohl Group
> Durham University
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-- 
Morten K Grøftehauge, PhD
Pohl Group
Durham University
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