[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

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



***  For details on how to be removed from this list visit the  ***
***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***


Hi!

With regards to your first question ---

i had a similar problem with some other ligand of similar kind.
i was also using CNS. ( i did not have mulptiple conformations though)
but i tried a different solution to this, i put off packing VDW
interaction only between the ligand and itself. all other PVDW were left
as usual. I had given 0.5 occupancy to the whole ligand.

i hope this is in effect similar to what u suggested.
The modification script can be had 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.


Only one question, about alternative u suggested.
in the 2 line we mention segid 
interaction ( store1 and not(attr store4 > 0) and not (segid="HHHH"

The whole ligand is one segid or resid , isn't it?

And  it was nice to have the summary, since it gave me  a few more
alternatives to try.

Thanx!
M. Goel







On Tue, 19 Dec 2000, Edward Berry wrote:

> Date: Tue, 19 Dec 2000 21:19:50 -0800
> From: Edward Berry <eaberry@lbl.gov>
> To: ccp4bb@dl.ac.uk
> Subject: Re: [ccp4bb]: refining two conformations related by
>     crystallographic  symmetry
> 
> ***  For details on how to be removed from this list visit the  ***
> ***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***
> 
> Summary of responses to my questions of last week -
> (hope the answers weren't obvious as a pikestaff to everyone but me)
> 
> 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
>