Dear Eugene, This is only in dials.index, and even then it is only in the initial maximum cell estimation that reflections from ice rings are excluded by default. They are included in the basis vector determination and further refinement. If you wish to exclude ice ring reflections from all steps of indexing you need to filter ice rings in dials.find_spots.
For dials.integrate see: http://dials.github.io/documentation/programs/dials_integrate.html The parameter filter.ice_rings=false by default. Cheers, Richard Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE ________________________________ From: Eugene Osipov [[email protected]] Sent: 10 December 2016 17:21 To: Gildea, Richard (DLSLtd,RAL,LSCI) Cc: ccp4bb Subject: Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin Dear RIchard, It is probably my problems with understanding. >From this page: http://dials.sourceforge.net/documentation/programs/dials_index.html I understood that : filter_ice = True is default parameter and by default DIALS will not consider spots at typical ice resolutions. Or it is only true before refinement procedure? 2016-12-10 18:05 GMT+03:00 <[email protected]<mailto:[email protected]>>: "E.g. DIALS by default do not process reflections near ice rings," I'm not sure where you got this information from, but this is not correct - by default DIALS will process all reflections. Cheers, Richard Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE ________________________________ From: CCP4 bulletin board [[email protected]<mailto:[email protected]>] on behalf of Eugene Osipov [[email protected]<mailto:[email protected]>] Sent: 10 December 2016 13:39 To: ccp4bb Subject: Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin E.g. DIALS by default do not process reflections near ice rings, 2016-12-09 21:05 GMT+03:00 Phil Evans <[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>>: For some reason there is no data in that resolution bin Phil > On 9 Dec 2016, at 17:30, Xiao Lei > <[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> > wrote: > > Hi All, > > I have an x ray diffraction dataset of protein and dna complex processed with > pointless and I am trying to get the resolution cut for this data, the result > is below, I do not know why in the N=23 (Dmid=3.68) bin, there is no > statistic of CC(1/2), N_cc, CCfit, etc? The program just put a "-" sign into > it. I guess if this means something bad probably I have to cut the > resolution to 3.7A. > > $TABLE: Mn(I/sigI) and CC(1/2) [in P1] vs. resolution: > $GRAPHS:Resolution estimate 3.89A:0.000213587|0.0981986x0|1:2,4,6,7,9: > $$ > N 1/d^2 Dmid CC(1/2) N_CC CCfit Mn(I/sigI) N (I/sigI)/10 $$ > $$ > 1 0.0018 23.27 0.939 51 0.990 92.43 142 9.243 > 2 0.0051 13.99 0.993 210 0.987 72.33 607 7.233 > 3 0.0084 10.92 0.984 323 0.984 61.77 937 6.177 > 4 0.0116 9.27 0.974 344 0.981 54.77 1030 5.477 > 5 0.0149 8.19 0.969 486 0.976 29.98 1412 2.998 > 6 0.0182 7.42 0.961 491 0.971 13.24 1459 1.324 > 7 0.0214 6.83 0.879 535 0.964 8.75 1558 0.875 > 8 0.0247 6.36 0.885 597 0.956 6.70 1755 0.670 > 9 0.0280 5.98 0.939 693 0.947 7.16 2003 0.716 > 10 0.0312 5.66 0.807 697 0.935 4.97 2042 0.497 > 11 0.0345 5.38 0.815 757 0.921 5.53 2195 0.553 > 12 0.0378 5.15 0.910 878 0.904 6.08 2547 0.608 > 13 0.0410 4.94 0.913 890 0.884 7.49 2582 0.749 > 14 0.0443 4.75 0.906 934 0.861 7.42 2710 0.742 > 15 0.0476 4.58 0.824 976 0.834 5.06 2695 0.506 > 16 0.0508 4.44 0.812 1010 0.802 5.32 2859 0.532 > 17 0.0541 4.30 0.843 1099 0.767 5.25 3126 0.525 > 18 0.0574 4.17 0.862 1030 0.727 4.49 2790 0.449 > 19 0.0606 4.06 0.752 1115 0.683 3.04 2927 0.304 > 20 0.0639 3.96 0.675 439 0.636 2.53 1117 0.253 > 21 0.0672 3.86 0.139 176 0.586 1.64 393 0.164 > 22 0.0704 3.77 0.734 1082 0.534 2.65 2641 0.265 > 23 0.0737 3.68 - - - - - - > 24 0.0770 3.60 0.489 681 0.429 2.20 1633 0.220 > 25 0.0802 3.53 0.358 1430 0.378 1.85 3248 0.185 > 26 0.0835 3.46 -0.428 12 0.330 1.38 22 0.138 > 27 0.0868 3.39 0.390 663 0.285 1.73 1404 0.173 > 28 0.0900 3.33 0.128 1443 0.244 1.39 2946 0.139 > 29 0.0933 3.27 0.149 1372 0.207 1.37 2835 0.137 > 30 0.0966 3.22 0.183 1578 0.175 1.40 3202 0.140 > > Thanks ahead. -- Eugene Osipov Junior Research Scientist Laboratory of Enzyme Engineering A.N. Bach Institute of Biochemistry Russian Academy of Sciences Leninsky pr. 33, 119071 Moscow, Russia e-mail: [email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>> -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom -- Eugene Osipov Junior Research Scientist Laboratory of Enzyme Engineering A.N. Bach Institute of Biochemistry Russian Academy of Sciences Leninsky pr. 33, 119071 Moscow, Russia e-mail: [email protected]<mailto:[email protected]>
