Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin
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 :
> The documentation you linked to is out of date (our fault), the new DIALS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>>:
> "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 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 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 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:0.00021
Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin
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
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
mailto:p...@mrc-lmb.cam.ac.uk><mailto:p...@mrc-lmb.cam.ac.uk<mailto:p...@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
> mailto:xiaolei...@gmail.com><mailto:xiaolei...@gmail.com<mailto:xiaolei...@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:
> $$
> N 1/d^2Dmid CC(1/2) N_CC CCfit Mn(I/sigI) N (I/sigI)/10 $$
> $$
> 1 0.0018 23.27 0.939 51 0.990 92.43142 9.243
> 2 0.0051 13.99 0.993210 0.987 72.33607 7.233
> 3 0.0084 10.92 0.984323 0.984 61.77937 6.177
> 4 0.0116 9.27 0.974344 0.981 54.77 1030 5.477
> 5 0.0149 8.19 0.969486 0.976 29.98 1412 2.998
> 6 0.0182 7.42 0.961491 0.971 13.24 1459 1.324
> 7 0.0214 6.83 0.879535 0.9648.75 1558 0.875
> 8 0.0247 6.36 0.885597 0.9566.70 1755 0.670
> 9 0.0280 5.98 0.939693 0.9477.16 2003
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 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 mailto:p...@mrc-lmb.cam.ac.uk><mailto:p...@mrc-lmb.cam.ac.uk<mailto:p...@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 > mailto:xiaolei...@gmail.com><mailto:xiaolei...@gmail.com<mailto:xiaolei...@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^2Dmid CC(1/2) N_CC CCfit Mn(I/sigI) N (I/sigI)/10 $$ > $$ > 1 0.0018 23.27 0.939 51 0.990 92.43142 9.243 > 2 0.0051 13.99 0.993210 0.987 72.33607 7.233 > 3 0.0084 10.92 0.984323 0.984 61.77937 6.177 > 4 0.0116 9.27 0.974344 0.981 54.77 1030 5.477 > 5 0.0149 8.19 0.969486 0.976 29.98 1412 2.998 > 6 0.0182 7.42 0.961491 0.971 13.24 1459 1.324 > 7 0.0214 6.83 0.879535 0.9648.75 1558 0.875 > 8 0.0247 6.36 0.885597 0.9566.70 1755 0.670 > 9 0.0280 5.98 0.939693 0.9477.16 2003 0.716 > 10 0.0312 5.66 0.807697 0.9354.97 2042 0.497 > 11 0.0345 5.38 0.815757 0.9215.53 2195 0.553 > 12 0.0378 5.15 0.910878 0.9046.08 2547 0.608 > 13 0.0410 4.94 0.913890 0.8847.49 2582 0.749 > 14 0.0443 4.75 0.906934 0.8617.42 2710 0.742 > 15 0.0476 4.58 0.824976 0.8345.06 2695 0.506 > 16 0.0508 4.44 0.812 1010 0.8025.32 2859 0.532 > 17 0.0541 4.30 0.843 1099 0.7675.25 3126 0.525 > 18 0.0574 4.17 0.862 1030 0.7274.49 2790 0.449 > 19 0.0606 4.06 0.752 1115 0.6833.04 2927 0.304 > 20 0.0639 3.96 0.675439 0.6362.53 1117 0.253 > 21 0.0672 3.86 0.139176 0.5861.64393 0.164 > 22 0.0704 3.77 0.734 1082 0.5342.65 2641 0.265
Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin
Dear Eugene Yes this is just indexing and refinement Clearly the documentation needed to be more explicit Best wishes Graeme On 10 Dec 2016, at 17:21, Eugene Osipov mailto:e.m.osi...@gmail.com>> wrote: 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 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 mailto:p...@mrc-lmb.cam.ac.uk><mailto:p...@mrc-lmb.cam.ac.uk<mailto:p...@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 > mailto:xiaolei...@gmail.com><mailto:xiaolei...@gmail.com<mailto:xiaolei...@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: > $$ > N 1/d^2Dmid CC(1/2) N_CC CCfit Mn(I/sigI) N (I/sigI)/10 $$ > $$ > 1 0.0018 23.27 0.939 51 0.990 92.43142 9.243 > 2 0.0051 13.99 0.993210 0.987 72.33607 7.233 > 3 0.0084 10.92 0.984323 0.984 61.77937 6.177 > 4 0.0116 9.27 0.974344 0.981 54.77 1030 5.477 > 5 0.0149 8.19 0.969486 0.976 29.98 1412 2.998 > 6 0.0182 7.42 0.961491 0.971 13.24 1459 1.324 > 7 0.0214 6.83 0.879535 0.9648.75 1558 0.875 > 8 0.0247 6.36 0.885597 0.9566.70 1755 0.670 > 9 0.0280 5.98 0.939693 0.9477.16 2003 0.716 > 10 0.0312 5.66 0.807697 0.9354.97 2042 0.497 > 11 0.0345 5.38 0.815757 0.9215.53 2195 0.553 > 12 0.0378 5.15 0.910878 0.9046.08 2547 0.608 > 13 0.0410 4.94 0.913890 0.8847.49 2582 0.749 > 14 0.0443 4.75 0.906934 0.8617.42 2710 0.742 > 15 0.0476 4.58 0.824976 0.8345.06 2695 0.506 > 16 0.0508 4.44 0.812 1010 0.8025.32 2859 0.532 > 17 0.0541 4.30 0.843 1099 0.7675.25 3126 0.525 > 18 0.0574 4.17 0.862 1030 0.7274.49 2790 0.449 > 19 0.0606 4.06 0.752 1115 0.6833.04 2927 0.304 > 20 0.0639 3.96 0.675439 0.6362.53 1117 0.253 > 21 0.0672 3.86 0.139176 0.5861.64393 0.164 > 22 0.0704 3.77 0.734 1082 0.5342.65 2641 0.265 > 23 0.0737 3.68- ----- > 24 0.0770 3.60 0.489681 0.4292.20 1633 0.220 > 25 0.0802 3.53 0.358 1430 0.3781.85 3248 0.185 > 26 0.0835 3.46 -0.428 12 0.3301.38 22 0.138 > 27 0.0868 3.39 0.390663 0.2851.73 1404 0.173 > 28 0.0900 3.33 0.128 1443 0.2441.39 2946 0.139 > 29 0.0933 3.27 0.149 1372 0.2071.37 2835 0.137 > 30 0.0966 3.22 0.183 1578 0.1751.40 3202 0.140 > > Thanks ahead. -- Eugene Osipov Junior Research Scientist Laboratory of Enzyme Engineering A.N. Bach Institute of Bi
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 : > "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] on behalf of Eugene > Osipov [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>>: > For some reason there is no data in that resolution bin > > Phil > > > On 9 Dec 2016, at 17:30, Xiao Lei iaolei...@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^2Dmid CC(1/2) N_CC CCfit Mn(I/sigI) N > (I/sigI)/10 $$ $$ > > 1 0.0018 23.27 0.939 51 0.990 92.43142 9.243 > > 2 0.0051 13.99 0.993210 0.987 72.33607 7.233 > > 3 0.0084 10.92 0.984323 0.984 61.77937 6.177 > > 4 0.0116 9.27 0.974344 0.981 54.77 1030 5.477 > > 5 0.0149 8.19 0.969486 0.976 29.98 1412 2.998 > > 6 0.0182 7.42 0.961491 0.971 13.24 1459 1.324 > > 7 0.0214 6.83 0.879535 0.9648.75 1558 0.875 > > 8 0.0247 6.36 0.885597 0.9566.70 1755 0.670 > > 9 0.0280 5.98 0.939693 0.9477.16 2003 0.716 > > 10 0.0312 5.66 0.807697 0.9354.97 2042 0.497 > > 11 0.0345 5.38 0.815757 0.9215.53 2195 0.553 > > 12 0.0378 5.15 0.910878 0.9046.08 2547 0.608 > > 13 0.0410 4.94 0.913890 0.8847.49 2582 0.749 > > 14 0.0443 4.75 0.906934 0.8617.42 2710 0.742 > > 15 0.0476 4.58 0.824976 0.8345.06 2695 0.506 > > 16 0.0508 4.44 0.812 1010 0.8025.32 2859 0.532 > > 17 0.0541 4.30 0.843 1099 0.7675.25 3126 0.525 > > 18 0.0574 4.17 0.862 1030 0.7274.49 2790 0.449 > > 19 0.0606 4.06 0.752 1115 0.6833.04 2927 0.304 > > 20 0.0639 3.96 0.675439 0.6362.53 1117 0.253 > > 21 0.0672 3.86 0.139176 0.5861.64393 0.164 > > 22 0.0704 3.77 0.734 1082 0.5342.65 2641 0.265 > > 23 0.0737 3.68- ----- > > 24 0.0770 3.60 0.489681 0.4292.20 1633 0.220 > > 25 0.0802 3.53 0.358 1430 0.3781.85 3248 0.185 > > 26 0.0835 3.46 -0.428 12 0.3301.38 22 0.138 > > 27 0.0868 3.39 0.390663 0.2851.73 1404 0.173 > > 28 0.0900 3.33 0.128 1443 0.2441.39 2946 0.139 > > 29 0.0933 3.27 0.149 1372 0.2071.37 2835 0.137 > > 30 0.0966 3.22 0.183 1578 0.1751.40 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.os
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," 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] on behalf of Eugene Osipov [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 mailto:p...@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 > mailto:xiaolei...@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: > $$ > N 1/d^2Dmid CC(1/2) N_CC CCfit Mn(I/sigI) N (I/sigI)/10 $$ > $$ > 1 0.0018 23.27 0.939 51 0.990 92.43142 9.243 > 2 0.0051 13.99 0.993210 0.987 72.33607 7.233 > 3 0.0084 10.92 0.984323 0.984 61.77937 6.177 > 4 0.0116 9.27 0.974344 0.981 54.77 1030 5.477 > 5 0.0149 8.19 0.969486 0.976 29.98 1412 2.998 > 6 0.0182 7.42 0.961491 0.971 13.24 1459 1.324 > 7 0.0214 6.83 0.879535 0.9648.75 1558 0.875 > 8 0.0247 6.36 0.885597 0.9566.70 1755 0.670 > 9 0.0280 5.98 0.939693 0.9477.16 2003 0.716 > 10 0.0312 5.66 0.807697 0.9354.97 2042 0.497 > 11 0.0345 5.38 0.815757 0.9215.53 2195 0.553 > 12 0.0378 5.15 0.910878 0.9046.08 2547 0.608 > 13 0.0410 4.94 0.913890 0.8847.49 2582 0.749 > 14 0.0443 4.75 0.906934 0.8617.42 2710 0.742 > 15 0.0476 4.58 0.824976 0.8345.06 2695 0.506 > 16 0.0508 4.44 0.812 1010 0.8025.32 2859 0.532 > 17 0.0541 4.30 0.843 1099 0.7675.25 3126 0.525 > 18 0.0574 4.17 0.862 1030 0.7274.49 2790 0.449 > 19 0.0606 4.06 0.752 1115 0.6833.04 2927 0.304 > 20 0.0639 3.96 0.675439 0.6362.53 1117 0.253 > 21 0.0672 3.86 0.139176 0.5861.64393 0.164 > 22 0.0704 3.77 0.734 1082 0.5342.65 2641 0.265 > 23 0.0737 3.68- ----- > 24 0.0770 3.60 0.489681 0.4292.20 1633 0.220 > 25 0.0802 3.53 0.358 1430 0.3781.85 3248 0.185 > 26 0.0835 3.46 -0.428 12 0.3301.38 22 0.138 > 27 0.0868 3.39 0.390663 0.2851.73 1404 0.173 > 28 0.0900 3.33 0.128 1443 0.2441.39 2946 0.139 > 29 0.0933 3.27 0.149 1372 0.2071.37 2835 0.137 > 30 0.0966 3.22 0.183 1578 0.1751.40 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> -- 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 v
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 : > For some reason there is no data in that resolution bin > > Phil > > > On 9 Dec 2016, at 17:30, Xiao Lei 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^2Dmid CC(1/2) N_CC CCfit Mn(I/sigI) N > (I/sigI)/10 $$ $$ > > 1 0.0018 23.27 0.939 51 0.990 92.43142 9.243 > > 2 0.0051 13.99 0.993210 0.987 72.33607 7.233 > > 3 0.0084 10.92 0.984323 0.984 61.77937 6.177 > > 4 0.0116 9.27 0.974344 0.981 54.77 1030 5.477 > > 5 0.0149 8.19 0.969486 0.976 29.98 1412 2.998 > > 6 0.0182 7.42 0.961491 0.971 13.24 1459 1.324 > > 7 0.0214 6.83 0.879535 0.9648.75 1558 0.875 > > 8 0.0247 6.36 0.885597 0.9566.70 1755 0.670 > > 9 0.0280 5.98 0.939693 0.9477.16 2003 0.716 > > 10 0.0312 5.66 0.807697 0.9354.97 2042 0.497 > > 11 0.0345 5.38 0.815757 0.9215.53 2195 0.553 > > 12 0.0378 5.15 0.910878 0.9046.08 2547 0.608 > > 13 0.0410 4.94 0.913890 0.8847.49 2582 0.749 > > 14 0.0443 4.75 0.906934 0.8617.42 2710 0.742 > > 15 0.0476 4.58 0.824976 0.8345.06 2695 0.506 > > 16 0.0508 4.44 0.812 1010 0.8025.32 2859 0.532 > > 17 0.0541 4.30 0.843 1099 0.7675.25 3126 0.525 > > 18 0.0574 4.17 0.862 1030 0.7274.49 2790 0.449 > > 19 0.0606 4.06 0.752 1115 0.6833.04 2927 0.304 > > 20 0.0639 3.96 0.675439 0.6362.53 1117 0.253 > > 21 0.0672 3.86 0.139176 0.5861.64393 0.164 > > 22 0.0704 3.77 0.734 1082 0.5342.65 2641 0.265 > > 23 0.0737 3.68- ----- > > 24 0.0770 3.60 0.489681 0.4292.20 1633 0.220 > > 25 0.0802 3.53 0.358 1430 0.3781.85 3248 0.185 > > 26 0.0835 3.46 -0.428 12 0.3301.38 22 0.138 > > 27 0.0868 3.39 0.390663 0.2851.73 1404 0.173 > > 28 0.0900 3.33 0.128 1443 0.2441.39 2946 0.139 > > 29 0.0933 3.27 0.149 1372 0.2071.37 2835 0.137 > > 30 0.0966 3.22 0.183 1578 0.1751.40 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
Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin
For some reason there is no data in that resolution bin Phil > On 9 Dec 2016, at 17:30, Xiao Lei 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: > $$ > N 1/d^2Dmid CC(1/2) N_CC CCfit Mn(I/sigI) N (I/sigI)/10 $$ > $$ > 1 0.0018 23.27 0.939 51 0.990 92.43142 9.243 > 2 0.0051 13.99 0.993210 0.987 72.33607 7.233 > 3 0.0084 10.92 0.984323 0.984 61.77937 6.177 > 4 0.0116 9.27 0.974344 0.981 54.77 1030 5.477 > 5 0.0149 8.19 0.969486 0.976 29.98 1412 2.998 > 6 0.0182 7.42 0.961491 0.971 13.24 1459 1.324 > 7 0.0214 6.83 0.879535 0.9648.75 1558 0.875 > 8 0.0247 6.36 0.885597 0.9566.70 1755 0.670 > 9 0.0280 5.98 0.939693 0.9477.16 2003 0.716 > 10 0.0312 5.66 0.807697 0.9354.97 2042 0.497 > 11 0.0345 5.38 0.815757 0.9215.53 2195 0.553 > 12 0.0378 5.15 0.910878 0.9046.08 2547 0.608 > 13 0.0410 4.94 0.913890 0.8847.49 2582 0.749 > 14 0.0443 4.75 0.906934 0.8617.42 2710 0.742 > 15 0.0476 4.58 0.824976 0.8345.06 2695 0.506 > 16 0.0508 4.44 0.812 1010 0.8025.32 2859 0.532 > 17 0.0541 4.30 0.843 1099 0.7675.25 3126 0.525 > 18 0.0574 4.17 0.862 1030 0.7274.49 2790 0.449 > 19 0.0606 4.06 0.752 1115 0.6833.04 2927 0.304 > 20 0.0639 3.96 0.675439 0.6362.53 1117 0.253 > 21 0.0672 3.86 0.139176 0.5861.64393 0.164 > 22 0.0704 3.77 0.734 1082 0.5342.65 2641 0.265 > 23 0.0737 3.68- ----- > 24 0.0770 3.60 0.489681 0.4292.20 1633 0.220 > 25 0.0802 3.53 0.358 1430 0.3781.85 3248 0.185 > 26 0.0835 3.46 -0.428 12 0.3301.38 22 0.138 > 27 0.0868 3.39 0.390663 0.2851.73 1404 0.173 > 28 0.0900 3.33 0.128 1443 0.2441.39 2946 0.139 > 29 0.0933 3.27 0.149 1372 0.2071.37 2835 0.137 > 30 0.0966 3.22 0.183 1578 0.1751.40 3202 0.140 > > Thanks ahead.
Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin
Ice ring? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Xiao Lei Sent: Friday, December 09, 2016 12:30 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin 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^2Dmid CC(1/2) N_CC CCfit Mn(I/sigI) N (I/sigI)/10 $$ $$ 1 0.0018 23.27 0.939 51 0.990 92.43142 9.243 2 0.0051 13.99 0.993210 0.987 72.33607 7.233 3 0.0084 10.92 0.984323 0.984 61.77937 6.177 4 0.0116 9.27 0.974344 0.981 54.77 1030 5.477 5 0.0149 8.19 0.969486 0.976 29.98 1412 2.998 6 0.0182 7.42 0.961491 0.971 13.24 1459 1.324 7 0.0214 6.83 0.879535 0.9648.75 1558 0.875 8 0.0247 6.36 0.885597 0.9566.70 1755 0.670 9 0.0280 5.98 0.939693 0.9477.16 2003 0.716 10 0.0312 5.66 0.807697 0.9354.97 2042 0.497 11 0.0345 5.38 0.815757 0.9215.53 2195 0.553 12 0.0378 5.15 0.910878 0.9046.08 2547 0.608 13 0.0410 4.94 0.913890 0.8847.49 2582 0.749 14 0.0443 4.75 0.906934 0.8617.42 2710 0.742 15 0.0476 4.58 0.824976 0.8345.06 2695 0.506 16 0.0508 4.44 0.812 1010 0.8025.32 2859 0.532 17 0.0541 4.30 0.843 1099 0.7675.25 3126 0.525 18 0.0574 4.17 0.862 1030 0.7274.49 2790 0.449 19 0.0606 4.06 0.752 1115 0.6833.04 2927 0.304 20 0.0639 3.96 0.675439 0.6362.53 1117 0.253 21 0.0672 3.86 0.139176 0.5861.64393 0.164 22 0.0704 3.77 0.734 1082 0.5342.65 2641 0.265 23 0.0737 3.68- ----- 24 0.0770 3.60 0.489681 0.4292.20 1633 0.220 25 0.0802 3.53 0.358 1430 0.3781.85 3248 0.185 26 0.0835 3.46 -0.428 12 0.3301.38 22 0.138 27 0.0868 3.39 0.390663 0.2851.73 1404 0.173 28 0.0900 3.33 0.128 1443 0.2441.39 2946 0.139 29 0.0933 3.27 0.149 1372 0.2071.37 2835 0.137 30 0.0966 3.22 0.183 1578 0.1751.40 3202 0.140 Thanks ahead.
[ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin
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: $$ N 1/d^2Dmid CC(1/2) N_CC CCfit Mn(I/sigI) N (I/sigI)/10 $$ $$ 1 0.0018 23.27 0.939 51 0.990 92.43142 9.243 2 0.0051 13.99 0.993210 0.987 72.33607 7.233 3 0.0084 10.92 0.984323 0.984 61.77937 6.177 4 0.0116 9.27 0.974344 0.981 54.77 1030 5.477 5 0.0149 8.19 0.969486 0.976 29.98 1412 2.998 6 0.0182 7.42 0.961491 0.971 13.24 1459 1.324 7 0.0214 6.83 0.879535 0.9648.75 1558 0.875 8 0.0247 6.36 0.885597 0.9566.70 1755 0.670 9 0.0280 5.98 0.939693 0.9477.16 2003 0.716 10 0.0312 5.66 0.807697 0.9354.97 2042 0.497 11 0.0345 5.38 0.815757 0.9215.53 2195 0.553 12 0.0378 5.15 0.910878 0.9046.08 2547 0.608 13 0.0410 4.94 0.913890 0.8847.49 2582 0.749 14 0.0443 4.75 0.906934 0.8617.42 2710 0.742 15 0.0476 4.58 0.824976 0.8345.06 2695 0.506 16 0.0508 4.44 0.812 1010 0.8025.32 2859 0.532 17 0.0541 4.30 0.843 1099 0.7675.25 3126 0.525 18 0.0574 4.17 0.862 1030 0.7274.49 2790 0.449 19 0.0606 4.06 0.752 1115 0.6833.04 2927 0.304 20 0.0639 3.96 0.675439 0.6362.53 1117 0.253 21 0.0672 3.86 0.139176 0.5861.64393 0.164 22 0.0704 3.77 0.734 1082 0.5342.65 2641 0.265 23 0.0737 3.68- ----- 24 0.0770 3.60 0.489681 0.4292.20 1633 0.220 25 0.0802 3.53 0.358 1430 0.3781.85 3248 0.185 26 0.0835 3.46 -0.428 12 0.3301.38 22 0.138 27 0.0868 3.39 0.390663 0.2851.73 1404 0.173 28 0.0900 3.33 0.128 1443 0.2441.39 2946 0.139 29 0.0933 3.27 0.149 1372 0.2071.37 2835 0.137 30 0.0966 3.22 0.183 1578 0.1751.40 3202 0.140 Thanks ahead.
