[phenixbb] Problems placing second component in Phaser

[Terwilliger, Thomas C]

Hi Morten,
I added last week the option of a fixed model in mr_rosetta.  So (if it works at least) you should be able to feed in one chain as a fixed model and then look for the other one.   I suspect this may have some problems however if the two chains are the same (which I think may be the case here).  Mr_rosetta might get confused about them because it uses their sequences to keep track of what is what...
All the best,
Tom T

On Feb 18, 2013, at 7:30 AM, Morten Groftehauge wrote:

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.

Cheers,
Morten


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