On Tuesday, 5 January 2021 23:38:02 PST Luca Mazzei wrote:
> Hi all,
The generic answer is to make another Phaser run using the three good
placements as a known substructure and searching for a single copy of
the monomer. Since it might be minor collisions that are causing a
bad translation score, you could relax the acceptance criteria for clashes.
The more interesting answer might be to inspect a difference map
made from the three good placements only. My past experience with
such cases is that the missing copy is often apparent by eye and
you can place it manually in Coot by dragging the whole molecule
as a rigid group into the difference density. Not perfectly, but
close enough to get the rest of the way with rigid body refinement.
This step may also reveal an obvious clash with one or more of the
three previous placements that is due to flexible loop you could
cut out and rebuild later.
good luck and best wishes for the New Year,
Ethan
>
> I am struggling with the MR of a homo-dimer using Phaser. Matt_coeff strongly
> suggests the presence of 4 mol per asym unit (space group P6222). The results
> after a search of 4 mol per asymmetric unit of my monomer are the following:
>
> ** SINGLE solution
>
> ** Solution written to SOL file: phaser_3f6v_A1_MOLREP.sol
>
> ** Solution written to PDB file: phaser_3f6v_A1_MOLREP.1.pdb
> ** Solution written to MTZ file: phaser_3f6v_A1_MOLREP.1.mtz
> Solution annotation (history):
> SOLU SET RFZ=3.9 TFZ=8.5 PAK=3 LLG=65 TFZ==10.0 RFZ=2.6 TFZ=17.0 PAK=3
> LLG=326 TFZ==29.8 (& TFZ==22.5 & TFZ==19.7)
> LLG+=(326 & 529 & 593) LLG=795 TFZ==5.4 PAK=5 LLG=795 TFZ==5.4 PAK=5
> LLG=795 TFZ==5.4
> SOLU SPAC P 62 2 2
> SOLU 6DIM ENSE autoMR EULER 125.3 60.8 300.2 FRAC 0.17 -0.13 0.08
> BFAC -9.34 #TFZ==10.0
> SOLU 6DIM ENSE autoMR EULER 305.4 60.8 300.2 FRAC 0.27 -0.16 0.08
> BFAC -5.29 #TFZ==29.8
> SOLU 6DIM ENSE autoMR EULER 294.7 119.1 120.3 FRAC 0.45 0.01 0.26
> BFAC 0.34 #TFZ==22.5
> SOLU 6DIM ENSE autoMR EULER 305.5 61.6 300.1 FRAC 0.11 -0.16 0.08
> BFAC 29.19 #TFZ==5.4
> SOLU ENSEMBLE autoMR VRMS DELTA -0.2463 #RMSD 0.93 #VRMS 0.79
>
> It seems (also looking at the maps) that it correctly places three monomers
> out of four. How can I use this information to improve the search of the
> fourth monomer using the same template model?
>
> Thanks in advance for your help,
>
> Best regards
>
> Luca Mazzei
>
> Luca Mazzei - PhD
> Laboratory of Bioinorganic Chemistry
> Department of Pharmacy and Biotechnology (FaBiT)
> Alma Mater Studiorum - University of Bologna
> Viale Giuseppe Fanin, 40 - 40127, Bologna - Italy
> Tel: +39 0512096235
>
>
>
>
>
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--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
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