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