[buster-discuss] special position in refine v1.10.0

Dale Tronrud det102 at uoxray.uoregon.edu
Fri Feb 3 18:03:38 CET 2012


   I agree with Peitro.  I don't know of a reason why an atom must be exactly
on the symmetry axis.  Often the density on the axis is not spherical so either
you have anisotropic B's (for a small deviation) or the atom has to shift a
bit off center.

   If a bad contact restraint is pushing the atom away, then the EXCLUDE
statement should do the trick.

Dale Tronrud

On 02/03/12 05:32, Pietro Roversi wrote:
> Dear all,
> 
> I always find that just switching the distance restraints off as Oliver specifies:
> EXCLUDE A|497:MG A|497:MG
> 
> does the job, but perhaps the electron density is weaker in this case
> or the atom tries to fit something in the vicinity?
> 
> Pietro
> 
> ________________________________________
> From: buster-discuss-bounces at globalphasing.com [buster-discuss-bounces at globalphasing.com] On Behalf Of Oliver Smart [osmart at globalphasing.com]
> Sent: 03 February 2012 13:20
> To: wtempel
> Cc: buster-discuss at globalphasing.com
> Subject: Re: [buster-discuss] special position in refine v1.10.0
> 
> On Thu, 2 Feb 2012, wtempel wrote:
> 
>> Hello,
>> I experience problems with a sodium ion on a special position. This
>> special position lies on a two-fold axis and I set the occupancy to
>> 0.5. With or without specifying -constant_dist, the ion will drift
>> away from this position even though it has been placed very close (as
>> precisely as visually possible) to its (special) position. As a
>> workaround I have considered fixing the ion in its position, but do
>> not know how to specify atoms that should remain fixed during
>> refinement. Any ideas out there?
>> Thank you,
>> Wolfram Tempel
> 
> Wolfram,
> 
> Apologies you have come across a missing feature in BUSTER.
> What you need is to be able to specify a distance restraint
> from an atom to a symmetry copy. This has been coded and will be
> included in the next release. So you WILL be able to say in
> a .Gelly file
> 
> EXCLUDE A|497:MG A|497:MG
> NOTE BUSTER_DISTANCE +0.001 0.02  A|497:MG A|497:MG SYMM
> 
> This will mean that the atom is pulled to its symmetry copy with a
> distance restraint that is active if the distance exceed 0.001 angs
> with a sigma of 0.02. If the symmetry is 2-fold the atom is able to move
> freely along the symmetry axis.
> 
> BUT this will not work until the next release, later this year. For now
> the best you can do is to position the atom by hand and then freeze it by
> using "-Gelly freeze.Gelly" with a line like:
> 
> CONSTANT XYZ A|497:MG
> 
> Hope this helps.
> 
> Regards,
> 
> Oliver (for buster-develop).
> 
> 
> | Dr Oliver Smart                             |
> | Global Phasing Ltd., Cambridge UK           |
> | http://www.globalphasing.com/people/osmart/ |
> 
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