Problem for allocating space

guoguang at ALFA.MBB.KI.SE guoguang at ALFA.MBB.KI.SE
Thu Nov 13 10:15:45 EST 1997


Hi, X-PLOR users

I am trying to do a bulk solvent correction to a fairly big protein (total 
2200 residues in an assymetric unit) and with 160,000 reflections. However
the program (xplor 3.851) crashed with following message

 XREFINE>   do (fpart=ft(mask)) ( all ) 
 XMAPAL: allocating space for real space object.
 Total of   2880000 map elements were selected.
 %VEHEAP-ERR: could not satisfy storage request for     2916002 bytes
 Subroutine DIE called . Terminating

How should I cope this? 

thanks in advance for any hints

Guoguang

p.s: my input file
 remarks  file xtalrefine/setup_bulksol.inp 
 remarks
 remarks  Generates a "flat" bulk solvent model
 remarks 
 remarks  Computes solvent mask, do an FFT, optimize k and B, stores in FPART
 remarks  and writes new reflection file. 
 remarks
 remarks 
 remarks   - run this job
 remarks   - check that the solvent parameters are reasonable (solvent density 
 remarks     and B-value) and that there is a significant drop in R value 
 remarks     especially at low resolution.   If unsatisfactory, try
 remarks     fixing either the solvent B-factor or solvent density level. 
 remarks   - use setup_bulksol.cv reflection file in all subsequent jobs
 remarks   - use lower resolution bound in all subsequent jobs
 remarks  Authors: Jian-Sheng Jiang, William I. Weis and Axel T. Brunger
 

 ! Cite the following references when using this protocol:
 !
 ! J.-S. Jiang and A.T. Brunger, Protein hydration
 ! observed by x-ray diffraction: solvation properties of
 ! penicillopepsion and neuraminidase crystal structures,
 ! J. Mol. Biol. 243, 100-115 (1994).
 !


!----------------------------------------------------------------------------

 
{===>} parameter 
 @/nfs/disk1/guoguang/xplor/parhcsdx.pro
@/nfs/disk1/guoguang/pdc/par.tdp
@/nfs/disk1/guoguang/pdc/par.mg
@par.cit
@/nfs/disk1/guoguang/xplor/param19.sol   { Read empirical potential       }
end           {*Read parameters.*}

{===>} structure @gen.psf end       {*Read structure file.*}

{===>} coor @gen.pdb                              {*Read coordinates.*}


{===>} evaluate ($scatter_library="/usr/programs/xplor3.84/xtallib/scatter.lib")  
                                                     { Form factor library. }
                                             
{===>}                { Space group. Uses International Table conventions.  } 
                      { with supercripts substituted by parenthesis.        }                                            
 evaluate ($SG="P1" ) 

{===>}                                                         { Unit cell. }
 evaluate ($a=69.87)
 evaluate ($b=92.01)
 evaluate ($c=97.99)
 evaluate ($alpha=103.68)
 evaluate ($beta=94.54)
 evaluate ($gamma=112.32)


{===>}
 evaluate ($ref="/nfs/disk2/doreen/cof/p1cof2c.cv")   { Input reflection file. 
Includes}
                                           { test set for cross-validation. }
 
{===>}
 evaluate ($out_ref="/nfs/scratch/guoguang/bulksol.cv")    { Output reflection 
file.        }

{===>}
 evaluate ($low_res=15.0)                       {* low resolution limit.  *}
 evaluate ($high_res=1.86)                        {* high resolution limit. *}
 
{===>} 
 evaluate ($f_cut=1.0)                        {* F/sigma amplitude cutoff. *}

{===>}    
 evaluate ($f_low=0.00)                    {* Absolute amplitude cutoffs. *}
 evaluate ($f_high=1000000) 



{===>}                       {* Select atoms to be included in refinement. *}
 vector ident (store1) (known) 

{===>}
 evaluate ($ncs_flag=NONE) { RESTRAIN or STRICT or NONE ! ncs information.  }
 
{===>}
 evaluate ($ncs_file="ncs.inp" )  { NCS-restraints/constraints file name.        
  }
                           { Examples are in xtalrefine/ncs_strict.inp      }
                           { and xtalrefine/ncs_restrain.inp.               }
 
{===>}
 evaluate ($k3=0.33) {* Optional: fix set solvent density level by setting}
                       {* this parameter to a positive value.               }
                       
{===>}
 evaluate ($b3=50.) {* Optional: fix set solvent b-factor by setting     }
                       {* this parameter to a positive value.               }
           
!----------------------------------------------------------------------------

 xrefine

   @/usr/programs/xplor3.84/xtallib/spacegroup.lib       { Read symmetry 
library. }

   a=$a b=$b c=$c  alpha=$alpha beta=$beta gamma=$gamma { Define unit cell. }
  
   @$scatter_library                             { Read form factor library }

   nreflections= 160000
   reflection @$ref end

   resolution_limits= $low_res $high_res

   do (fobs=0) (amplitude(fobs) <= $f_cut * sigma) 

   fwindow $f_low  $f_high    

   method=FFT          
   
   fft 
      memory=3000000   
   end                 
   
 
   selection=( store1 ) 

end

 if ($ncs_flag=STRICT) then
    @@$ncs_file
 elseif ($ncs_flag=RESTRAIN) then
    @@$ncs_file
    flags include ncs end
 end if
              
xrefin
   
   update                        {*Update Fcalcs and print current rfactor.*}
   
   print rfactor
   
end                  


 xrefine
  
   {* compute a solvent mask and store it in mask *}
   declare name=mask domain=real end
   mask               
     mode=vdw  		{ use vdw radii                     }
     solrad=0.25        { a probe radius adds to vdw radii  }
     shrink=0.25        { the shrink radius                 }
     nshell=1           { the number of shells              }
     to=mask            { output to the mask map            }
   end
   
   {* Fourier transformation of the solvent mask and store it in fpart*}
   do (fpart=ft(mask)) ( all )

   {* solvent parameters refinement via by the multiscale routine *}
   multiscale
      bfmin=0. bfmax=200.
      set1=fobs   k1=-1       b1=0
      set2=fcalc  k2=1.0      b2=0 
      set3=fpart  k3=$k3      b3=$b3        
      selection=( $high_res <= d <= $low_res 
             and  $f_low <= amplitude(fobs) <= $f_high
             and test=0 )
      resk=5.0             { resolution boundary for two FFKs }
      update=false
      bmin=10.
      bmax=300.
      
      ?
   end

   {* compute refined solvent structure factors in fbulk *}
   do (fpart=$k3*exp(-$b3*s()*s()/4.0)*fpart) ( all )
   
   display  bulk solvent model parameters: density level = $k3 e/A^3,  B-factor= 
$b3 A^2
   remarks  bulk solvent model parameters: density level = $k3 e/A^3,  B-factor= 
$b3 A^2
   
   print rfactor
   
   do (fcalc=complex(0,0)) ( all )

                  {*Write a new reflection file including the solvent FPART.*}
   write reflection 
      output=$out_ref sele=( all ) 
   end   

 end

 stop



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