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

Pietro Roversi pietro.roversi at path.ox.ac.uk
Fri Feb 3 14:32:50 CET 2012

Dear all,

I always find that just switching the distance restraints off as Oliver specifies:

does the job, but perhaps the electron density is weaker in this case
or the atom tries to fit something in the vicinity?


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


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

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:


Hope this helps.


Oliver (for buster-develop).

| Dr Oliver Smart                             |
| Global Phasing Ltd., Cambridge UK           |
| http://www.globalphasing.com/people/osmart/ |

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