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 "refine_1.pdb"

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
phenix.resolve<<EOD
hklin refine_1.pdb.mtz
labin FP=FMODEL PHIB=PHIFMODEL
get_histograms
no_build
solvent_content 0.5
database 5
mask_cycles 1
minor_cycles 1
EOD


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
[email protected]
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: [email protected]
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