SA Omit Maps

[Ethan A Merritt]

In article <35CF5021.2F1C at newssun.med.miami.edu>,
Tristan J. Fiedler M.Sc. <tfiedler at NEWSSUN.MED.MIAMI.EDU> wrote:
>Hello Xplorers!
>
>I am currently refining a large protein structure and would like to
>exclude several aa side chains from the refinement and xFo-yFc map
>making procedure.  Is it best to:
>
>1.	Physically remove the atoms from the input pdb file
>2.	Use the 'delete' statement as follows:
>3.	Set the atoms occupancy to '0'
>4. 	None of the above.  Please suggest...


The correct answer is 4, none of the above.
What you should do is simply to omit these atoms from the list
of contributors to the scattering factor summation.
This retains the geometric restraints, thereby preventing
the endpoints of the omited region from unraveling.


!  select omited residues
   vector identify (store1) (residue xxx:yyy)

!  omit nearby waters as well
   vector identify (store2) 
	  (byresidue(segid SOLV and (recall 1 around 4.5)))

xrefine
	select (not (recall 1 or recall 2))
	?
	[... normal refinement or map calculation commands]
end



			Ethan A Merritt
			merritt at u.washington.edu