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
>>                               [log in to unmask]
>
>Garib N Murshudov 
>Structural Studies Division
>MRC Laboratory of Molecular Biology
>Hills Road 
>Cambridge 
>CB2 0QH UK
>Email: [log in to unmask] 
>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