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Hi Morten,
<div>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...</div>
<div>All the best,</div>
<div>Tom T</div>
<div><br>
<div>
<div>On Feb 18, 2013, at 7:30 AM, Morten Groftehauge wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div dir="ltr">Hi Gabor,
<div><br>
</div>
<div style="">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...</div>
<div style=""><br>
</div>
<div style="">I'll try with AMPLE and see what happens there.</div>
<div style=""><br>
</div>
<div style="">Cheers,</div>
<div style="">Morten</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 18 February 2013 13:01, Gabor Bunkoczi <span dir="ltr">
<<a href="mailto:gb360@cam.ac.uk" target="_blank">gb360@cam.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Morten,<br>
<br>
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).<br>
<br>
BW, Gabor
<div>
<div class="h5"><br>
<br>
On Feb 18 2013, Morten Groftehauge wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi guys,<br>
<br>
So I have a solution that covers some of target and I ran it through<br>
phenix.mr_rosetta and I am actually kinda happy with the output from there.<br>
However, while I can place both (NCS=2) with the original model I only seem<br>
to be able to place one of the rosetta models, even with 'packing function'<br>
set to 'all' or 'allow'.<br>
Original model -<br>
Refinement after placing component 1: LLG 175<br>
Refinement after placing component 2: LLG 620<br>
Rosetta model (packing 'all') -<br>
Refinement after placing component 1: LLG 295<br>
Refinement after placing component 2: LLG 390<br>
Rosetta model (packing standard) -<br>
Refinement after placing component 1: LLG 295<br>
Refinement after placing component 2: LLG 350<br>
<br>
More notably there is little to no increase in TFZ with the placement of<br>
the second component...<br>
<br>
There are more residues in the Rosetta model and I would expect more<br>
clashes but this looks weird.<br>
<br>
Cheers,<br>
Morten<br>
<br>
<br>
</blockquote>
<br>
<br>
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<br>
<br clear="all">
<div><br>
</div>
-- <br>
Morten K Gr�ftehauge, PhD
<div>Pohl Group</div>
<div>Durham University</div>
</div>
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