[phenixbb] RESOLVE with RNA/protein structure at low resolution
terwilliger at lanl.gov
Wed Aug 19 10:05:10 PDT 2009
The RESOLVE database doesn't have RNA+protein in it, nor does it have
low-resolution histograms, but you can create a new entry very
easily. Here is how:
1. Find a PDB structure that has the characteristics that you want
2. Calculate a map with this model at the resolution you are
phenix.pdbtools --f-model high_resolution=5 refine_1.pdb
3. Generate histograms with phenix.resolve. Here is a script:
labin FP=FMODEL PHIB=PHIFMODEL
4. Now the file hist_values.dat will have your histograms:
5.002693 32.71021 ! resolution Boverall
1 ! 1=protein 2 = solvent
0.10198E-01 1.8145 0.41525E-01 ! a1 a2 a3
0.14425E-01 0.46920 0.77521 ! a4 a5 a6
0.23653E-06 0.34718E-08 0.0000 ! a7 a8 a9
2 ! 1=protein 2 = solvent
0.27101E-01 6.4460 -0.61802 ! a1 a2 a3
0.12788E-01 0.55421 -0.39797E-02 ! a4 a5 a6
0.0000 0.0000 0.0000 ! a7 a8 a9
5. Paste the contents of hist_values.dat at the end of $PHENIX/
solve_resolve/ext_ref_files/segments/rho.list . NOTE: you need one
blank line between sections, and an extra 2 blank lines at the very
end of the file...otherwise resolve will give a bad error message.
6. Now when you run phenix.resolve...say "database 7" and it will use
your new histograms. It will write a message in the log file like this:
Histogram DB entry # 7 ("5 14.27721 ! resol")
which should match what you pasted in to the rho.list file...so you
know it took your histograms.
All the best,
On Aug 18, 2009, at 3:10 PM, Peter Grey wrote:
> Hello all,
> I try to solve the structure of RNA and RNA/protein complex at low
> resolution (5A). Phases come from partial model MR solution.
> I would really welcome advice about density modification in such
> cases with RESOLVE..
> Does the RESOLVE database of density distributions contain RNA/
> protein examples ?
> Can RESOLVE work at low resolution given that histograms profiles
> are at resolutions from 1.2 A to 4 A ?
> Many thanks for you help,
> phenixbb mailing list
> phenixbb at phenix-online.org
Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545
Tel: 505-667-0072 email: terwilliger at LANL.gov
Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
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