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Re: [ccp4bb]: refining two conformations related by crystallographic symmetry

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Addition to the summary-

Apparently this was the case of an answer so obvious that everyone assumed I had
received the answer already by ten private emails, so didn't bother to reply
(perhaps also a case of a nubie troubling the newsgroup with a question he could 
have answered for himself by reading the FAQs) - anyway my summary showed 
at least one person that I still hadn't got it. Lest anyone save my summary
as the final word, let me point out that the procedure Weiru showed me was
for a pre-release version of CNS, and the correct procedure with CNS-SOLVE 1.0
is described in the CNS FAQ as reported by Manisha Goel:

 from the CNS online site, http://cns.csb.yale.edu/v1.0/
 the last question under the heading refinement in FAQ gives the script and
 explains where to make these changes.
It says:
A. You can use the igroup statement to turn the pvdw (Packing-Van-der-Waals) interactions off by setting the weight to zero: 

   interaction (molecule) (molecule) weights * 1.0 pvdw 0.0 end

If you have other molecules in the asymmetric unit, you have to define the interactions explicitly. For example. 

   interaction (rest) (rest) end
   interaction (rest) (molecule) end
   interaction (molecule) (molecule) weights * 1.0 pvdw 0.0 end

Replace (rest) and (molecule) by the appropriate atom selections. 

The next question is where to put the igroup statement. For example, in minimize.inp or anneal.inp, search for igroup. The
statement you will find is for alternate conformations. Right after the end statement of that igroup block, insert your own igroup statements
as outlined above. 
This will only work if there are no alternate conformations. Otherwise a more complicated sequence of igroup interactions must be
given, which simultaneously take both the alternate conformations and the molecule across the symmetry operation into account. 

Edward Berry wrote:
> Summary of responses to my questions of last week -
> Question 1. What program can positionally refine overlapping sym-related atoms
>         at 0.5 occupancy?
> Bernhard Rupp and Christine Cardin reported that SHELXL can do this.
> Eleanor Dodson said REFMAC will not invoke VDW clashes
>         between symmetry equivs where both occs = 0.5.
> Weiru Wang showed me how to use CNS and modify the selection of atoms
> for which interactions are checked. In the minimize script, well down
> below the line that says:
> {===========================================================================}
> {        things below this line do not normally need to be changed          }
> {===========================================================================}
> you find this section:
> 1    constraints
> 2      interaction ( store1 and not(attr store4 > 0))
> 3                  ( store1 and not(attr store4 > 0))
> 4      evaluate ($alt=1)
> 5      while ( $alt <= $nalt ) loop alcs
> 6        interaction ( store1 and ( attr store4 = $alt or attr store4 = 0 ))
> 7                    ( store1 and ( attr store4 = $alt ))
> 8        evaluate ($alt=$alt+1)
> 9      end loop alcs
> 0    end
> You can modify line 2 to exclude the residue which overlaps with sym-related:
>      interaction ( store1 and not(attr store4 > 0) and not (segid="HHHH" and residue 241 ))
> then you will check interactions of everything except this residue with
> everything including this residue, but will not check interactions between
> the residue and itself. If you have residues in multiple conformations
> (store4 > 0) which interact with the special residue, you might need
> to exclude it in lines 6 or 7.  In my case just changing line 2 seems
> to work. (setting store4=1 for the residue doesn't work- it and its symmetry
> mate are seen as being in the same conformation 1 and clashes occur in 6 and 7)
> =====================================================================================
> Question 2. How can I keep the R-free set valid when expanding to lower symmetry?
> Eleanor Dodson- let CAD expand the Free-R flags together with the data

Edward A. Berry, MailStop 3-250
Lawrence Berkeley National Laboratory
1 Cyclotron Road, Berkeley, CA 94720