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refine.inp map error

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  • Alex Smith
    Hello All: I am having a problem with refine.inp. Actually, it is the map building part that is causing the problem. The refinement is carried out and .pdb
    Message 1 of 2 , Feb 2, 2004
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      Hello All:

      I am having a problem with refine.inp. Actually, it
      is the map building part that is causing the problem.
      The refinement is carried out and .pdb files are
      generated but I get no maps due to the following
      error:

      CNSsolve> xray
      XRAY> declare name=dtarg domain=reciprocal
      type=complex end
      XDECLARE: Object DTARG has been declared.
      XRAY> declare name=total domain=reciprocal
      type=complex end
      XDECLARE: Object TOTAL has been declared.
      XRAY> declare name=fmap domain=reciprocal
      type=complex end
      XDECLARE: Object FMAP has been declared.
      XRAY> end
      CNSsolve>
      CNSsolve> xray
      XRAY> predict
      PREDict> mode=dtarget(fcalc)
      PREDict> to=dtarg
      PREDict> selection=(ref_active=1)
      Total of 3797 structure factor elements were
      selected.
      PREDict> atomselection=( &atom_select )
      SELRPN: 1947 atoms have been selected out of 1947
      PREDict> end
      FCALC: #scatt.= 1947 #anomalous= 0 #special pos.= 0
      occupancies=1
      XSFAL: allocating space for complex reciprocal space
      object.
      XFFT: using grid [ 20, 54, 72] and sublattice [
      20( 21), 54( 55), 72]
      XRAY> end
      CNSsolve>
      CNSsolve> xray
      XRAY> predict
      PREDict> mode=reciprocal
      PREDict> to=fcalc
      PREDict> selection=(all)
      Total of 15699 structure factor elements were
      selected.
      PREDict> atomselection=( &atom_select )
      SELRPN: 1947 atoms have been selected out of 1947
      PREDict> end
      FCALC: #scatt.= 1947 #anomalous= 0 #special pos.= 0
      occupancies=1
      %XFGRCHK error encountered: Grid in x-direction too
      coarse (FFT GRID or MAPRes).
      (CNS is in mode: SET ABORT=NORMal END)
      *****************************************************
      ABORT mode will terminate program execution.
      *****************************************************
      Program will stop immediately.

      ============================================================
      Maximum dynamic memory allocation:
      7034000 bytes
      Maximum dynamic memory overhead:
      1000 bytes
      Program started at: 11:03:18 on 02-Feb-2004
      Program stopped at: 11:15:28 on 02-Feb-2004
      CPU time used: 361.6100 seconds

      ============================================================

      Any suggestions would be helpful. I have varied the
      grid size from 0.2 to 0.4 with no successs.

      Alex


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    • Gerard DVD Kleywegt
      ... the combination of your a-axis length, the resolution and the map grid makes that cns feels that the grid along x is too coarse. in the refine.inp file
      Message 2 of 2 , Feb 2, 2004
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        > %XFGRCHK error encountered: Grid in x-direction too coarse (FFT GRID or
        > MAPRes).

        the combination of your a-axis length, the resolution and the map grid makes
        that cns feels that the grid along x is too coarse. in the refine.inp file
        look for the line:

        {===>} grid=0.33;

        and change the number 0.33, e.g. to 0.25 (or even smaller if you still get the
        same error message)

        of course, you don't need to re-run the entire refine.inp job since you
        already have the new pdb file. so just run the model_map.inp (and don't forget
        to change the number 0.33 there as well !) job instead to just do the map
        calculations

        --gerard

        ******************************************************************
        Gerard J. Kleywegt
        [Research Fellow of the Royal Swedish Academy of Sciences]
        Dept. of Cell & Molecular Biology University of Uppsala
        Biomedical Centre Box 596
        SE-751 24 Uppsala SWEDEN

        http://xray.bmc.uu.se/gerard/ mailto:gerard@...
        ******************************************************************
        The opinions in this message are fictional. Any similarity
        to actual opinions, living or dead, is purely coincidental.
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