[phenixbb] RESOLVE with RNA/protein structure at low resolution

Tom Terwilliger terwilliger at lanl.gov
Wed Aug 19 10:05:10 PDT 2009

Hi Peter,

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  
interested in:
   phenix.pdbtools --f-model high_resolution=5 refine_1.pdb

3. Generate histograms with phenix.resolve. Here is a script:

#!/bin/csh -f
hklin refine_1.pdb.mtz
solvent_content 0.5
database 5
mask_cycles 1
minor_cycles 1

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,
Tom T

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,
> Peter.
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb

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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