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Re: [ccp4bb]: scaleit on MAD data
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Hi Linda,
I have seen this behavior only once before with SCALEIT, and that was
while scaling anisotropic data with the refine isotropic keyword. In
those cases, scaling anisotropically made things better. However, if
your MAD data were collected on the same crystal at the same source, I
don't understand how this could be the problem in your case.
Regards,
Felix
Linda Hannick wrote:
>
> I'm hoping the community can help me determine if my Selenium MAD data
>
> has a problem. Appened below is a portion of the output from scaleit.
>
> My concern is that the isomorphous differences aren't centered about
> zero.
>
> Is this common to MAD data? Have other people observed this behavior?
>
> Is it indicative of either a data processing or scaling problem?
>
> Background:
> 3 wavelengths of complete and redundant Se MAD data. By redundant, I
> mean at least 2-4 measurements for both I+ and I-, or 4-8 measurements
>
> for I. The data was integrated with Denzo, each wavelength was scaled
>
> using scalepack, and then brought into ccp4 using scalepack2mtz.
> Prior
> to scaleit, the data was passed through sortmtz, truncate, and cad.
> Scaling in scalepack used the 'scale anomalous' card for a few rounds
> of scaling, followed by a final round of 'anomalous'.
>
> The anomalous signal in these data sets is sufficient to find Se sites
>
> via Shake-n-Bake and to be handled well by mlphare. The FOMs for
> centric reflections are much weaker than the acentrics - I suspect
> this
> is a result of the isomorphous differences shown below. A table of
> FOMs
> is also appended.
>
> Electron density maps following solvent flattening and histogram
> matching in dm show obvious solvent channels and reasonable protein
> density. However, the protein density is not readily traceable.
>
> Thanks for any help you can offer,
>
>
> Isomorphous Differences
> -----------------------
> Derivative title: FP= FP_se3a FPH= FP_se1a SIGFP_se1a DANO_se1a
> SIGDANO_se1a
> d -224 -196 -168 -140 -112 -84 -56 -28 0
> 28 56 84 112 140 168 196 224
>
> 18.97 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0
> 10.95 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0
> 8.49 0 0 0 0 0 0 1 15 161
> 401 126 26 2 0 0 0 0
> 7.17 0 0 0 0 0 0 1 33 320
> 700 157 9 1 2 1 0 0
> 6.32 0 0 0 0 0 0 3 42 371
> 783 194 13 1 1 0 0 0
> 5.72 0 0 0 0 1 0 5 40 358
> 807 312 40 1 0 0 0 0
> 5.26 0 0 0 0 0 0 2 27 245
> 722 578 113 15 3 0 0 0
> 4.90 0 0 0 0 0 0 3 25 207
> 586 668 268 84 16 3 1 0
> 4.60 0 0 0 0 0 1 5 44 194
> 491 642 418 141 32 14 1 1
> 4.35 0 0 0 0 0 0 5 42 178
> 443 688 485 186 51 12 4 0
> 4.14 0 0 0 0 0 1 6 52 213
> 504 676 484 206 62 20 2 1
> 3.96 0 0 0 0 0 2 8 72 255
> 514 669 500 213 63 13 1 1
> 3.79 0 0 0 0 1 2 13 105 291
> 531 676 502 221 53 9 1 3
> 3.65 0 0 0 0 1 0 23 99 285
> 553 663 540 250 70 10 2 2
> 3.52 0 0 0 1 3 2 25 102 338
> 598 697 541 228 87 12 5 0
> 3.41 0 0 0 0 0 4 25 114 366
> 575 683 551 265 79 25 2 3
> 3.30 0 0 0 0 1 6 28 118 405
> 680 620 517 263 110 15 4 2
> 3.21 0 0 0 1 0 3 9 103 468
> 777 720 497 230 64 11 4 0
> 3.12 0 0 1 1 0 4 12 112 483
> 922 707 442 181 61 19 3 0
> 3.04 0 0 0 0 0 2 14 112 771 1622
> 1056 460 200 61 18 2 0
>
> Total 0 0 1 3 7 27 188 1257 5909 12209
> 10532 6406 2688 815 182 32 13
>
> Anomolous Differences
> ---------------------
> d -136 -119 -102 -85 -68 -51 -34 -17 0
> 17 34 51 68 85 102 119 136
>
> 18.97 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0
> 10.95 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0
> 8.49 0 0 1 3 8 24 70 141 246
> 131 70 28 8 2 0 0 0
> 7.17 0 0 1 3 15 52 121 217 393
> 233 127 39 21 2 0 0 0
> 6.32 0 0 1 1 15 53 148 287 434
> 276 137 42 12 2 0 0 0
> 5.72 0 0 0 1 12 45 147 288 500
> 354 158 49 8 2 0 0 0
> 5.26 0 0 1 1 14 39 144 386 539
> 362 147 56 14 2 0 0 0
> 4.90 0 1 3 4 15 49 177 403 612
> 392 147 44 11 2 1 0 0
> 4.60 0 0 2 7 19 46 196 393 682
> 434 142 41 14 5 2 0 1
> 4.35 0 2 2 7 26 66 198 413 679
> 444 174 54 18 7 4 0 0
> 4.14 1 0 4 11 39 84 163 457 691
> 461 195 80 24 14 3 0 0
> 3.96 3 4 7 24 43 88 226 418 660
> 452 237 85 42 16 4 2 0
> 3.79 5 3 11 30 55 117 243 442 608
> 436 247 117 40 36 8 6 4
> 3.65 7 10 18 31 66 149 259 422 577
> 410 272 140 71 34 24 4 4
> 3.52 7 7 21 31 89 153 303 419 610
> 422 282 149 79 46 16 4 1
> 3.41 14 11 28 45 103 160 286 427 572
> 418 293 175 83 49 14 11 3
> 3.30 16 16 22 46 96 179 313 430 536
> 422 342 168 97 53 21 10 2
> 3.21 12 11 26 58 103 194 321 463 594
> 464 303 178 90 48 14 3 5
> 3.12 5 11 16 40 99 186 320 488 646
> 477 318 184 91 43 16 7 1
> 3.04 6 12 18 46 115 208 461 814 1081
> 746 414 218 107 40 20 7 5
>
> Total 76 88 182 389 932 1892 4096 7308 10660 7334
> 4005 1847 830 403 147 54 26
>
>
>
> Resolution in angstroms
> 7.90 6.53 5.57 4.85 4.30 3.86 3.50 3.20
>
> Number of Measurements phased
> -ACENTRIC TOTAL
> 2037 1683 2408 3228 4206 5281 6523 7834
> 33200
> Mean Figure of Merit
> 0.5247 0.5885 0.5170 0.4405 0.3459 0.2242 0.1499 0.1017
> 0.2753
>
> Number of Measurements phased
> -CENTRIC TOTAL
> 149 78 98 111 126 143 158
> 177 1040
> Mean Figure of Merit
> 0.3936 0.2989 0.2280 0.1838 0.1644 0.0908 0.0637 0.0394
> 0.1687
>
> Number of Measurements phased
> -ALL TOTAL
> 2186 1761 2506 3339 4332 5424 6681 8011
> 34240
> Mean Figure of Merit
> 0.5158 0.5757 0.5057 0.4320 0.3406 0.2207 0.1479 0.1003
> 0.2720
>
>
> --
> Dr. Linda Hannick, Structural Biology
> National Institute of Allergy and Infectious Diseases
> National Institutes of Health
> 12441 Parklawn Drive 301-496-3792 Voice
> Rockville, MD 20852 301-402-0284 FAX
>
>
--
*****************************************************************
Felix Vajdos ph. 650-225-6113
Postdoctoral Research Fellow fax 650-225-3734
Department of Protein Engineering e-mail vajdos@gene.com
Genentech, Inc.
1 DNA Way
South San Francisco, CA 94080
*****************************************************************