On 03/24/12 15:15, Kendall Nettles wrote:
David, how can you justify reducing occupancy of some parts of amino acids?
I don't have to, since I didn't do it. Read again the bit about this
being a carryover from the MR model.
Cheers,
I don't understand this. I can understand deleting stuff that's not there and
reporting it as not modelled. This is factually false. The side chains are not
there at partial occupancy.
Best regards,
Kendall Nettles
On Mar 24, 2012, at 2:39 PM, "David Schuller"<[email protected]> 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
[email protected]
