[sharp-discuss] SOLVE Scaled Data for SHARP
Clemens Vonrhein
vonrhein@globalphasing.com
Thu, 26 Sep 2002 11:35:09 +0100
Hi,
difficult to tell. I could think of several reasons:
- scaling (as you mentioned): if your MAD and SAD data contain the
same scatterers I would assume that SCALEIT might do a better
job. Remember: FHSCAL assumes you scale derivative to native,
where the derivative has additional (heavy) atom contribution.
- scaling (2): by scaling the 3 MAD to the SAD your previous scaling
between the MAD wavelengths get lost. I would rather scale the SAD
to the best MAD wavelegths. This way you don't change a lot
compared to your previous SHAR run.
- scaling (3): you could also just skip any external scaling and add
the SAD wavelength to the end_*.sin SHARP run: by specifying
ESTIMATE for SCAL_K and SCAL_B for the SAD data you start with
reasonable scales and you can refine them.
- indexing? I guess there can't be a problem that the datasets are
indexed differently?
- your coordinates are quite different for your MAD+SAD run: did you
start with the end_*.sin file from the best MAD run and just added
a new crystal?
If you could give a bit more information about data quality,
scatterer and send me some SIN files I might be able to give a few
more suggestions.
Cheers
Clemens
On Tue, Sep 24, 2002 at 09:39:39AM -0500, phubbard@post.its.mcw.edu wrote:
> Hello,
>
> I have managed to phase really well in SHARP using just SAD data (SOLVE did
> a reasonable job), and I have managed to phase even better with SOLVE when I
> combine in-house SAD data with synchrotron MAD data. I have a feeling I can
> phase better still if I use SHARP with the MAD and SAD data; however, it
> keeps getting lost during refinement. I scale the MAD data (3A) to the
> in-house SAD data (2.4A) using FHSCAL. I then set up SHARP as the following:
>
> C-1
> X-1 (MAD DATA)
> W-1
> B-1
> W-2
> B-2
> W-3
> B-3
> X-2 (SAD DATA)
> W-1
> B-1
>
> Below is the output from SHARP (SAD, and MAD + SAD). Has someone ever tried
> converting SOLVE scaled data into an MTZ file for SHARP? I would be grateful
> of any other suggestions.
>
> Thanks
>
> AGS
>
> SHARP SAD OUTPUT
> **************** Cpd Cry Wvl Bat Parameter Old Shift
> New SD
>
> G-SITE-001 X 0.1734 0.0000 0.1733 0.0009
> Y 0.1646 0.0000 0.1646 0.0005
> Z 0.1359 0.0000 0.1359 0.0006
> G-SITE-002 X 0.1781 0.0000 0.1782 0.0008
> Y 0.1617 0.0000 0.1617 0.0004
> Z 0.1633 0.0000 0.1632 0.0004
> G-SITE-003 X 0.1410 0.0000 0.1410 0.0007
> Y 0.1588 0.0000 0.1588 0.0003
> Z 0.1482 0.0000 0.1482 0.0004
> G-SITE-004 X 0.1706 0.0000 0.1705 0.0005
> Y 0.1398 0.0000 0.1398 0.0004
> Z 0.1477 0.0000 0.1477 0.0004
> 001__G-SITE-001 HAT_OCC 1.5764 -0.0045 1.5719 0.1081
> HAT_B 67.9279 -0.1567 67.7713 7.2571
> 001__G-SITE-002 HAT_OCC 1.7385 -0.0023 1.7363 0.0901
> HAT_B 46.0304 -0.1130 45.9174 3.9446
> 001__G-SITE-003 HAT_OCC 1.8967 -0.0012 1.8955 0.0901
> HAT_B 51.5399 0.0029 51.5429 3.7114
> 001__G-SITE-004 HAT_OCC 1.5188 -0.0043 1.5145 0.0698
> HAT_B 36.1583 -0.1484 36.0099 3.0819
> 001_001_001_001 NANO_BGLO 2.3259 -0.0319 2.2940 0.1815
> NANO_CLOC 0.0180 0.0012 0.0191 0.0017
>
> SHARP MAD + SAD OUTPUT
> **********************
>
> Cpd Cry Wvl Bat Parameter Old Shift New SD
>
> G-SITE-001 X 0.1170 -0.0003 0.1167 0.0000
> Y 0.1617 -0.0006 0.1611 0.0000
> Z 0.1242 0.0009 0.1250 0.0000
> G-SITE-002 X 0.1974 0.0015 0.1989 0.0000
> Y 0.1684 -0.0014 0.1670 0.0000
> Z 0.1630 0.0014 0.1644 0.0000
> G-SITE-003 X 0.1457 0.0002 0.1459 0.0000
> Y 0.1591 0.0000 0.1591 0.0000
> Z 0.1530 -0.0001 0.1529 0.0000
> G-SITE-004 X 0.1709 -0.0004 0.1705 0.0000
> Y 0.1345 0.0002 0.1347 0.0000
> Z 0.1532 0.0001 0.1532 0.0000
> 001__G-SITE-001 HAT_OCC -1.6699 -0.2202 -1.8902 0.0016
> HAT_B 29.8155 -3.4500 26.3654 0.0267
> 001__G-SITE-002 HAT_OCC -0.7863 -0.2929 -1.0793 0.0020
> 001__G-SITE-003 HAT_OCC 4.9421 0.3785 5.3206 0.0028
> HAT_B 28.6382 10.4000 39.0382 0.0712
> 001__G-SITE-004 HAT_OCC -8.3488 -0.4515 -8.8003 0.0037
> HAT_B 19.7436 -18.5356 1.2079 0.1247
> 001_001_001_001 NANO_BGLO 1.1126 0.6653 1.7779 0.6784
> | | NANO_CLOC 1.3834 0.6981 2.0816 0.0158
> | \_002_001 SCAL_K 0.8505 0.0001 0.8505 0.0002
> | | SCAL_B -0.3746 0.8976 0.5230 0.0168
> | | NANO_CLOC 5.2297 3.6126 8.8423 0.0982
> | \_003_001 SCAL_K 0.8096 -0.0140 0.7957 0.0004
> | SCAL_B -2.5194 1.4793 -1.0402 0.0334
> | NANO_CLOC 5.2742 2.4323 7.7064 0.0831
> \__G-SITE-001 HAT_OCC 0.6377 0.0926 0.7303 0.0007
> HAT_B 27.0277 11.5754 38.6032 0.0800
> \__G-SITE-002 HAT_OCC -0.7205 -0.1108 -0.8313 0.0008
> HAT_B 32.5326 29.3245 61.8572 0.1972
> \__G-SITE-003 HAT_OCC 3.7357 -0.2510 3.4847 0.0018
> HAT_B 30.9187 -6.8453 24.0734 0.0471
> \__G-SITE-004 HAT_OCC 6.0389 -0.0121 6.0268 0.0016
> HAT_B 29.6765 -6.4903 23.1862 0.0458
> \_002_001_001 SCAL_K 0.7374 -0.0008 0.7366 0.0001
> SCAL_B 2.0742 -0.9987 1.0756 0.0098
> NISO_BGLO 0.0709 0.1067 0.1776 0.0007
> NISO_CLOC 0.0009 -0.0009 0.0000 0.0000
> NANO_CLOC 2.6589 0.5016 3.1606 0.0299
>
>
>
>
>
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