As Garib says - an atom with occupancy 0.00 is treated as a marker - useful
for coot - but is not included in any X-ray refinement at all.. Maybe it
would be more aesthetic to maintain geometry but as crystallographers I
think we should be interested in the fit of model to experiment - right? -
and not in reporting a pseudo fit related to geometric parameters only..
Eleanor
On Mar 24 2012, Garib N Murshudov wrote:
Hi David
Occupancis of input file are very suspicious and not all atoms of resides
are present, some occupancies are zero. In refmac zero occupancy means it
does not exist. It may explain the problem In refinement we could add an
option to make occuancies one if there are no alts but it would be
dangerous thing to do.
Since occupancies are suspect I would check input pdb file carefully.
regards
Garib
On 24 Mar 2012, at 18:39, David Schuller wrote:
CCP4 6.2.0
Refmac_5.6.0117
Scientific Linux 6.1
In my current model, I notice that several sidechains are falling
apart, despite having gone through a few rounds of refinement with
REFMAC5 and model building with COOT. The worst examples were all Glu
and Arg residues.
I tried switch to the REFMAC5 executable on the updates page, which was
Refmac_5.6.0114, with no obvious difference.
Eventually I noticed that these are all residues containing atoms with
occupancy less than 1.00, which must be a carry over from the MR search
model. I set all the occupancies to 1.00 and this seems to have fixed
the problem.
This seems counter-intuitive to me. If the occupancies are set low,
shouldn't the geometry restraints be stronger relative to the density
refinement?
Cheers,
ATOM 1479 N GLU A 7 -51.844 -33.605 37.318 1.00 60.26 N ATOM 1480 CA
GLU A 7 -53.137 -33.849 37.966 1.00 59.28 C ATOM 1481 CB GLU A 7 -52.997
-33.664 39.476 1.00 61.37 C ATOM 1482 CG GLU A 7 -52.799 -32.212 39.905
0.48 60.42 C ATOM 1483 CD GLU A 7 -53.349 -32.573 41.635 0.00 54.47 C
ATOM 1484 OE1 GLU A 7 -52.557 -31.998 42.106 0.83 52.26 O ATOM 1485 OE2
GLU A 7 -55.014 -32.911 42.408 0.68 50.75 O ATOM 1486 C GLU A 7 -54.293
-32.985 37.412 1.00 62.61 C ATOM 1487 O GLU A 7 -55.444 -33.240 37.737
1.00 63.42 O ATOM 3165 N ARG A 77 -46.032 -33.003 26.272 1.00 55.82 N
ATOM 3166 CA ARG A 77 -44.959 -32.368 27.071 1.00 60.92 C ATOM 3167 CB
ARG A 77 -44.050 -31.428 26.231 1.00 54.56 C ATOM 3168 CG ARG A 77
-42.702 -31.102 26.892 1.00 69.21 C ATOM 3169 CD ARG A 77 -42.278
-29.628 26.867 0.46 63.93 C ATOM 3170 NE ARG A 77 -41.587 -29.303 25.625
0.79 61.76 N ATOM 3171 CZ ARG A 77 -41.607 -28.610 24.146 0.00 37.32 C
ATOM 3172 NH1 ARG A 77 -43.177 -26.956 23.467 0.85 60.52 N ATOM 3173 NH2
ARG A 77 -41.267 -28.245 23.427 0.95 58.82 N ATOM 3174 C ARG A 77
-45.585 -31.698 28.281 1.00 64.89 C ATOM 3175 O ARG A 77 -45.949 -32.377
29.262 1.00 77.93 O
--
=======================================================================
All Things Serve the Beam
=======================================================================
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu
Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
--
Professor Eleanor Dodson
YSNL, Dept of Chemistry
University of York
Heslington YO10 5YW
tel: 00 44 1904 328259
Fax: 00 44 1904 328266
