scattering factor library & heme

Dave Schuller schuller at indigo1.biomol.uci.edu
Mon Nov 18 13:19:15 EST 1996


We have the latest greatest version of X-plor, 3.851 running on SGI
Irix 5.3.

We are trying out some of the new style scripts and have run into a
problem with use of the scattering library, XTALLIB:scatter.lib
(where XTALLIB is defined as $XPLOR/xtallib ).  With the new scripts,
R-factors jumped by about 0.05 and we have now found the source of
this:  X-plor is using the scattering factors for Neptunium for our
heme pyrrhole nitrogens!

from TOPPAR:toph19.hem :
  ATOM NA   TYPE=NP    CHARGE=-0.18   END
  ATOM NB   TYPE=NP    CHARGE=-0.18   END
  ATOM NC   TYPE=NP    CHARGE=-0.18   END
  ATOM ND   TYPE=NP    CHARGE=-0.18   END

from XTALLIB:scatter.lib :
SCATter ( chemical N* and not 
        ( chem "Ne" or chem "NE" or 
          chem "Na" or chem "NA" or chem "Na+1" or chem "NA+1" or 
          chem "Ni" or chem "NI" or chem "Ni+2" or chem "NI+2" or chem "Ni+3" or chem "NI+3" or
          chem "Nb" or chem "NB" or chem "Nb+3" or chem "NB+3" or chem "Nb+5" or chem "NB+5" or
          chem "Nd" or chem "ND" or chem "Nd+3" or chem "ND+3" or
          chem "Np" or chem "NP" or chem "Np+3" or chem "NP+3" or chem "Np+4" or chem "NP+4" or
          chem "Np+6" or chem "NP+6" ))
  12.212600 0.005700 3.132200 9.893300 2.012500 28.997499 1.166300 0.582600 -11.528999
...
SCATter ( chemical "Np" or chemical "NP" )
  36.187401 0.511929 23.596399 3.253960 15.640200 15.362200 4.185500 97.490799 13.357300

----------------------------------------
We can work around this for the present, but clearly something needs
to change, either the heme topology or the scattering library.

Ideally I think a program should be able to assign an element ID to an
atom; selections for scattering factors and atom types, etc. could
then be restricted to those actually possible for that element.  This
would eliminate the need for ugly workarounds, like my habit of naming
calciums "MG" to avoid having them confused with alpha carbons. (BTW,
does anyone have a better way of dealing with this?)

Oh well, I suppose this is asking for a bit too much, especially if
compatibility is to be maintained.  I will restrict myself to asking
for a fix for the specific problem mentioned above.

=======================================================================
"You can learn a lot about a machine by how it fails"  Bruce Schneier
=======================================================================
                        Dave Schuller
                        modern man in a post-modern world
                        University of California-Irvine
                        schuller at uci.edu



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