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special positions

Manfred S. Weiss msw at FRANKLIN.MBI.UCLA.EDU
Mon Feb 19 13:24:25 EST 1996

On 19 Feb 1996, Axel T. Brunger wrote:

> > Although special positions are automatically recognized by X-plor,
> > I found it impossible to do any positional refinement afterwards
> > (at least with waters), because the special waters always drifted away
> > from the twofold and got repelled from their symmetry mate. I therefore
> > had to adopt the rather awkward procedure of manually positioning the
> > waters and then fixing their positions. In addition, the file produced
> > is not formally correct because the special waters have full occupancy,
> > instead of half, on third etc., which means that one has to manually
> > correct this if one wants to deposit the coordinates or if one wants to
> > use some other programs.
> >
> > Since the automatic procedure as currently implemented still needs a lot
> > of manual intervention, one might as well explicitly define the special
> > positions in the input file and, instead of reassigning a non-special
> > status once the molecule has drifted a little away, resetting the
> > special coordinates to their exact values.
> >
> This sounds like a problem which occured in older versions of X-PLOR
> (prior to 3.1).  Check the line:
>  XRFILL: #scatt.=    8 #anomalous=  0 #special pos.=  2 occupancies=1
> Does this line display the correct number of special positions?  If not,
> the atom is still not precisely on the special position.
> Fixing the atom at the special position (using CONSTRAINTS FIX) is a good
> idea in any case.
> Axel Brunger
   It would be nicer and much easier if one could fix single coordinates
   using a modified 'CONSTRAINTS FIX' statement. In the case of a water
   oxygen on a twofold along z, only x and y have to be fixed. 
   One of the problems with the current implementation of the 
   CONSTRAINTS FIX statement is, that is constrains all coordinates
   and(!) the temperature factors of the selected atoms. I usually
   have a temperature factor refinement in the same input file as
   the least-squares or slowcool refinement, so I always have to put
   in a nonsense CONSTRAINTS FIX statement to override the first one,
   just before B-factor refinement.

           Manfred Weiss.

* Manfred S. Weiss, PhD                                                      *
* 205 Molecular Biology Institute         | Email: msw at franklin.mbi.ucla.edu *
* University of California at Los Angeles | Phone: x-310-825-1402            *
* Box 951570                              | Fax  : x-310-206-3914            *
* Los Angeles, CA 90095-1570                                                 *
* USA                                                                        *

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