[modeller_usage] To generate P(r) of SAXS from a PDB model

[Zhong Huang <>]

Hi folks,

   I am trying to generate P(r) of SAXS from PDB models using the following code. However, the P(r) does not look like corrected one. The computed 1-D curve decreases monotonically from 0-300 Angstrom, which is against published curve obtained from the experimental data. Is there any thing wrong with my code? Thank you in advance.



env=environ()
env.libs.topology.read(file='$(LIB)/top_heav.lib')
#print env
env.libs.parameters.read(file='$(LIB)/par.lib')
from sys import exit
log.verbose()
### Calculate SAXS spectrum of correct structure
mdl = complete_pdb(env, 'PDB')
atmsel = selection(mdl)
saxs = saxsdata(env)
saxs.ini_saxs(atmsel=atmsel, s_min= 0.0, s_max=0.5, maxs=500, nmesh=400,
   natomtyp=15, represtyp='heav',
   filename='$(LIB)/formfactors-int_tab_solvation.lib',
   wswitch = 'uniform', s_low=0.5, s_hi=0.0, s_hybrid=0.0,nr = 5000,dr=.1,nr_exp=300,dr_exp=1.0,
   spaceflag= 'real', use_lookup=False)
### append SAXS data to energy structure
mdl.env.edat.saxsdata.append(saxs)
mdl.saxs_intens(saxsd=saxs, filename='i_s.txt', fitflag=False)
mdl.saxs_pr(saxsd=saxs,filename="pr.txt")










-- 
Best
Zhong