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
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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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-- Morten K Grøftehauge, PhD Pohl Group Durham University