[phenixbb] [ccp4bb] Need Solve/Resolve advice [shameless crosspost to phenixbb]

Peter Zwart PHZwart at lbl.gov
Wed Apr 30 12:41:51 PDT 2008


(sorry for the crosspost / jumping between bb's), but I don't like
advertising phenix on the ccp4bb.

If new to Solve (or old as well), try using phenix.autosol.
The gui is relatively intuitive, the command line (at least for SAD)
as simple as possible and the documentation is very thorough.

Before running autosol, try running xtriage and find out if you have
translational pseudo symmetry.

If you have more then a single molecule in the ASU, there will be NCS,
unless all molecules have *extremely* different conformations. The NCS
might not be proper/closed though.



2008/4/30 Megan Guelker <megdg at rice.edu>:
> CCP4bb subcribers,
>  I am a new user to Solve/Resolve and am using it on a Mad dataset. Solve
>  outputs three sites:
>  pdb coordinates             fractional coordinates
>  -15.833 35.392 38.440       0.0486 0.4315 0.1615
>   7.834 76.449 38.475       0.5487 0.9320 0.1617
>   16.310 60.866 37.449       0.5432 0.7420 0.1574
>  I noticed that the fractional coordinates for the first two sites are
>  separated by 0.5 units in x and y, and they appear to be the same site from
>  looking at the density surrounding them. I know that Solve can output some
>  sites with repetition if they are results from different seeds.
>  I have tried running Solve again with ADDSOLVE and these sites as input (all
>  three and combinations of the three) and have not been able to pull out any
>  additional sites. I have also tried using various resolution ranges for
>  Solve. The same three sites are always output.
>  The FOM for the map produced by Solve is 0.45. Resolve improves the FOM to
>  0.66.
>  The protein has 148 aa with 4 Se sites per protein. The crystals are in
>  space group P3221, and there are six copies per asymetric unit. There is no
>  non-crystallographic symmetry.
>  I am a new user to Solve, and haven't been able to find an explanation for
>  why the output sites are so similar and separated by 0.5 units. Does anyone
>  have any experience with this type of result? I would appreciate any input
>  and suggestions on how to locate additional sites.
>  Thank you for your consideration,
>  Megan Guelker
>  --
>  Megan Guelker
>  Graduate Student
>  Rice University
>  Department of Biochemistry & Cell Biology
>  6100 Main St. - MS 140
>  Houston, TX 77005
>  713-348-2492 (lab)
>  megdg at rice.edu

P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX: http://cctbx.sf.net

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