[phenixbb] Problems placing second component in Phaser

Morten Groftehauge mortengroftehauge.work at gmail.com
Mon Feb 18 06:30:50 PST 2013

Hi Gabor,

Sounds good but I was hoping for something I could tell phenix.mr_rosetta
that would allow it to find a good second solution. Phenix insists on
rerunning place model even if you tell it that the model is already placed.
So instead of continuing with the placement that worked I end up with one
chain based on my original model another one scattered all over the place...

I'll try with AMPLE and see what happens there.


On 18 February 2013 13:01, Gabor Bunkoczi <gb360 at cam.ac.uk> wrote:

> Hi Morten,
> this is weird. One way around is to manually superpose the mr_rosetta
> model onto the original in the full solution, and just do a refinement with
> Phaser (you can (kind of) do this automatically by running MRage with both
> models). Another idea is to decrease the rotation peak cutoff when finding
> the second molecule (PEAKS ROT CUTOFF keyword).
> BW, Gabor
> On Feb 18 2013, Morten Groftehauge wrote:
>  Hi guys,
>> So I have a solution that covers some of target and I ran it through
>> phenix.mr_rosetta and I am actually kinda happy with the output from
>> there.
>> However, while I can place both (NCS=2) with the original model I only
>> seem
>> to be able to place one of the rosetta models, even with 'packing
>> function'
>> set to 'all' or 'allow'.
>> Original model -
>> Refinement after placing component 1: LLG 175
>> Refinement after placing component 2: LLG 620
>> Rosetta model (packing 'all') -
>> Refinement after placing component 1: LLG 295
>> Refinement after placing component 2: LLG 390
>> Rosetta model (packing standard) -
>> Refinement after placing component 1: LLG 295
>> Refinement after placing component 2: LLG 350
>> More notably there is little to no increase in TFZ with the placement of
>> the second component...
>> There are more residues in the Rosetta model and I would expect more
>> clashes but this looks weird.
>> Cheers,
>> Morten
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Morten K Grøftehauge, PhD
Pohl Group
Durham University
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