dimer  1.0 Beta version 

Disclaimer
    This program and its related software are provided "as is".  
    The program is the property of the Federal government and 
    is the result of a research that was carried out in the 
    Structural Biophysics Laboratory of the National Cancer 
    Institute, NIH.  The authors make no warranties, either 
    express and implied, as to any issues and matters 
    whatsoever with regard to the software.  In particular, any 
    and all warranties of merchantability and fitness for any 
    particular purpose are explicitly excluded.  In no event will 
    the NIH,  the Structural Biophysics Laboratory,  the 
    National Cancer Institute,  or the authors be liable for any  
    loss  of  profits or productivities, any  incidental,  special,  
    exemplary,  or  consequential damages  of  any  nature 
    whatsoever (including without limitation, loss of  use or 
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    the use or performance of the software.    
    
version = '1.0_beta',  
description = 'use NMR and SAXS data to compute complex structure',
author='Jinbu Wang',
author_email='jinbuw@ncifcrf.gov',


Grid Search to find best structure fiting to SAXS eperimental data

usage: dimer.exe  <saxs_data_file_name >  <monomer pdb file> 

      where 
          saxs_data_file name: the SAXS experimental data file name
          monomer pdb file:    the pdb file includes euler angles and only monomer A 
  
      The results are saved into four directories in current directory.
          top10:  top 10 percent conformers by rmsd in I(q) 
          fspdb:  all pdb files 

Input parameters are embedded in SAXS data file, for example:
Rg, Rg_error, Dmax, Dmax_error, rmsd_cutoff

The following is the SAXS data input fill "tectoRNA18.dat"  in subdirectory example.


#  Rg and Dmax come from SAXS experiment.                                                                       
#  Rg_error and Dmax_error are error tolerance for Rg and Dmax respectively because of rigid-modeling.          
#  Rg is in  the range between Rg - Rg_error and Rg + Rg_error.                                         
#  Dmax is in the range between Dmax - Dmax_error   and Dmax - Dmax_error.                              
#  rmsd_cutoff is the threshold from the score function.                                                
#  All structures with higher rmsd than this threshold will be discarded by this search.                

#  Each non-SAXS data line must begin with "#" character.
#  Parameters must have white space before and after "=".
#  Rg and Dmax come from SAXS experiment.
#  Rg_error and Dmax_error are error tolerance for Rg and Dmax respectively because of rigid-modeling.
#  Rg is in  the range between Rg - Rg_error and Rg + Rg_error.
#  Dmax is in the range between Dmax - Dmax_error   and Dmax - Dmax_error.
#  rmsd_cutoff is the threshold from the score function. 
#  All structures with higher rmsd than this threshold will be discarded by this search.
#
#  Rg = 24.0         
#  Dmax = 95.0       
#  Rg_error = 1.5
#  Dmax_error = 10
#  rmsd_cutoff = 0.15  
# q       I(q)
0.00	0.2539
0.01	0.24886
0.02	0.23485
0.03	0.21519
0.04	0.18988
0.05	0.16175
0.06	0.13329
0.07	0.10723
0.08	0.084616
0.09	0.065924
0.10	0.050982
0.11	0.03953
0.12	0.030843
0.13	0.024222
0.14	0.019314
0.15	0.015627


How to Test the RNA example in windows command console?
 


type in example directory


..\bin\dimer.exe tectoRNA18.dat   initial-rigid-monomer_A.pdb


***************************
It will take several minutes to finish.

tectoRNA18.dat              -- input parameters and SAXS data.
initial-rigid-monomer_A.pdb -- tectoRNA monomer pdb file with one set of Euler angles.