Dear all, thank you for your comments! Also, Dr Gildea, it is not your fault but mine. I used bookmarked page and saved this link some time ago. Google gives correct link to DIALS github page.
2016-12-10 21:01 GMT+03:00 Richard Gildea <richard.gil...@diamond.ac.uk>: > The documentation you linked to is out of date (our fault), the new DIALS > homepage is: > > http://dials.github.io > > The precise behaviour of the dials.index parameter filter_ice is described > more explicitly in the current documentation: > > http://dials.github.io/documentation/programs/dials_index.html > > max_cell_estimation > .expert_level = 1 > { > filter_ice = True > .help = "Filter out reflections at typical ice ring resolutions > before" > "max_cell estimation." > .type = bool > } > > 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 [CCP4BB@JISCMAIL.AC.UK] on behalf of Richard > Gildea [richard.gil...@diamond.ac.uk] > Sent: 10 December 2016 17:56 > To: ccp4bb > Subject: Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; > CCfit...) in certain resolution bin > > 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 [e.m.osi...@gmail.com] > 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 <richard.gil...@diamond.ac.uk<mailto: > richard.gil...@diamond.ac.uk>>: > "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 [CCP4BB@JISCMAIL.AC.UK<mailto: > CCP4BB@JISCMAIL.AC.UK>] on behalf of Eugene Osipov [e.m.osi...@gmail.com > <mailto:e.m.osi...@gmail.com>] > 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 <p...@mrc-lmb.cam.ac.uk<mailto: > p...@mrc-lmb.cam.ac.uk><mailto:p...@mrc-lmb.cam.ac.uk<mailto:p > r...@mrc-lmb.cam.ac.uk>>>: > For some reason there is no data in that resolution bin > > Phil > > > On 9 Dec 2016, at 17:30, Xiao Lei <xiaolei...@gmail.com<mailto:x > iaolei...@gmail.com><mailto:xiaolei...@gmail.com<mailto:xiao > lei...@gmail.com>>> 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: e.m.osi...@gmail.com<mailto:e.m.osi...@gmail.com><mailto:e. > m.osi...@gmail.com<mailto:e.m.osi...@gmail.com>> > > -- > 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: e.m.osi...@gmail.com<mailto:e.m.osi...@gmail.com> > -- 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: e.m.osi...@gmail.com
