date:20161210

Re: [ccp4bb] Modeling protein tertiary structure

2016-12-10 Thread Ylva Lindqvist

I would recommend Haddock

Prof. em. Ylva Lindqvist

Dept. of Medical Biochemistry & Biophysics
Div. of Molecular Structural Biology
KAROLINSKA INSTITUTET
Tomtebodavägen 6
S-171 77 Stockholm, Sweden

Phone   +46 8 52487695
Mobile +46 708 264356
Fax +46 8 327626

Email: ylva.lindqv...@ki.se
URL: http://www.msb.mbb.ki.se/

Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

2016-12-10 Thread Eugene Osipov

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] Modeling protein tertiary structure

2016-12-10 Thread Stefan Arold

Dear Myeongseon,
my favourites are
SwissModel (especially good for modelling close homologues, since it keeps
conserved side chains & backbone as in the template; very fast (5-50 min),
nice interactive user interface)
RaptorX (good for more remote homologues too, also gives you secondary
structure and disorder predictions, which I found very useful; takes a
couple of hours to run).
I-Tasser (probably the best for more remote homologues, but also slowest,
and you can only submit 1 job at a time online; also predicts ligands, EC
numbers & GO terms).
@TOME (has some nice features for ligands to proteins).
If time is not an issue, I'd just use all those (or more) servers in
parallel. When superimposing the models, you can easily see where all
servers predict the same model, and where they differ. The local rmsd gives
you a good impression of how confident you can be in the model's different
regions.

best wishes
Stefan

On 10 December 2016 at 00:05, Myeongseon Lee (이명선) <
0e01bd27cd0f-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi, all.
>
> Could you anyone recommend me modeling programs for protein tertiary
> structure?
>
> I have 3D strunture of a template protein and amino acid sequence of my
> protein. These two proteins are very close structurally and functionally.
>
> I have done this kind of modeling with template 3D structure and amino
> acid sequence of an unknown structure long time ago for other project. But,
> unfortunately, I could not remember what program I have used at that time.
>
> Have a great day.
>
>
> Sent from my Samsung device
>

Re: [ccp4bb] Modeling protein tertiary structure

2016-12-10 Thread Antony Oliver

Phyre2 absolutely deserves a mention. My 'threader' of choice.

--- Antony W Oliver ---
--- sent from my mobile account ---


On 10 December 2016 at 00:05, Myeongseon Lee (이명선) 
<0e01bd27cd0f-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Hi, all.

Could you anyone recommend me modeling programs for protein tertiary structure?

I have 3D strunture of a template protein and amino acid sequence of my 
protein. These two proteins are very close structurally and functionally.

I have done this kind of modeling with template 3D structure and amino acid 
sequence of an unknown structure long time ago for other project. But, 
unfortunately, I could not remember what program I have used at that time.

Have a great day.


Sent from my Samsung device

Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

2016-12-10 Thread Richard Gildea

"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

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Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

2016-12-10 Thread Eugene Osipov

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.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

Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

2016-12-10 Thread Graeme Winter

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] 
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>

--
This e-mail and any attachments may contain confide

Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

2016-12-10 Thread Richard Gildea

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] 
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

Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

2016-12-10 Thread 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 
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] 
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   0.9

Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

2016-12-10 Thread Eugene Osipov

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
> ]
> 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> 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:
> >  $$
> >   N  1/d^2Dmid CC(1/2)   N_CC   CCfit  Mn(I/sigI)  N
> (I/sigI)/10   $$ $$
> >   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

[ccp4bb] REMINDER, job opportunities in Melbourne, Australia

2016-12-10 Thread Hans Elmlund

Dear All:

The Elmlund laboratory (http://simplecryoem.com), Monash University,
Melbourne, develops methods for single particle electron microscopy and
conducts an integrative structural biology research program, focussing on
Eukaryotic transcription regulation. We study the large but transient
protein-protein and protein-DNA complexes involved using a combination of
techniques, including cryo-EM, mass-spectrometry and biochemical assays. We
still have two positions to fill:

(1) Postdoctoral fellow   (transcription coupled chromatin remodeling)
(2) Scientific programmer (image processing for single-particle cryo-EM)

Monash University is a leading research university in Australia that
received a rank of 67 worldwide in the 2015/16 report from QS world
university rankings. State-of-the-art technology is available to the
Project via Monash’s research platform strategy, with The Clive and Vera
Ramaciotti Centre for Structural Cryo-EM housing a Titan KRIOS with K2
detector, energy filter and Volta phase plate. Extensive computational
infrastructure is available to the project via the MASSIVE3 supercomputer (
https://www.massive.org.au/). The excellent structural biology community
surrounding the facility, the nearby Australian Synchrotron and other major
research programs, such as the ARC Centre of Excellence in Advanced
Molecular Imaging (led from Monash), provides a unique opportunity to
execute the projects.

To find out more about the positions and our research, please visit
http://simplecryoem.com.

We would appreciate if you could share this announcement with suitably
skilled and interested scientists in your network.

Best,

Dominika & Hans Elmlund

-- 
*HANS ELMLUND PhD *
Associate Professor

*ARC Centre of Excellence for Advanced Molecular Imaging*
*Dept. of Biochemistry and Molecular Biology*
Monash University
Room 228, Level 2, Building 77, Clayton Campus
23 Innovation Walk
Clayton VIC 3800
Australia

T: +61 399029310
M: +61 (0)45271213
E: hans.elml...@monash.edu
simplecryoem.com

Re: [ccp4bb] New BUILT of XDS for academic users

2016-12-10 Thread Wei Wang

Dear Kay,

I updated this version and noticed some error message that I haven't
experience before. When I cp latest geometry description over previous one
and rerun integrate & correct, there's a very large chance to get "!!!
ERROR !!! CANNOT OPEN OR WRITE SCRATCH FILE IN "STRONGHKL1"". xds_par then
get paused. I'm using virtualbox ubuntu 16.04 on win 8.1 host. I haven't
test it on other platform though. Rebooting the machine can help to get
around. If someone also see similar error message maybe they can help
verify.

best,

Wei

On Tue, Dec 6, 2016 at 5:30 AM, Kay Diederichs <
kay.diederi...@uni-konstanz.de> wrote:

> Dear all,
>
> there is a new BUILT of the XDS package available for academic users from
> http://xds.mpimf-heidelberg.mpg.de . This fixes a number of problems with
> the VERSION of Nov 1, and all users of that version should update.
>
> We believe that this has a better background treatment in particular for
> low counts; thanks to Alexey Rozov and others for making their data
> available!
>
> If you find any bugs or regression with this latest BUILT of XDS please
> tell us about it.
>
> best wishes,
>
> Kay
>

Re: [ccp4bb] New BUILT of XDS for academic users

2016-12-10 Thread Kay Diederichs

Dear Wei,

I have seen a similar problem with the latest ifort compiler (that I use) but 
thought it didn't occur with the (old) ifort version that is used for the 
production binaries that are on the XDS download server.

Please show me an exact copy of the full error message (more is better). I will 
send you a new binary which hopefully fixes the problem (it has to do with 
omitting the compiler option -assume buffered_io).
If anybody else is getting this error message I'd like to hear about it.

best,

Kay

On Sat, 10 Dec 2016 19:34:04 -0500, Wei Wang  wrote:

>Dear Kay,
>
>I updated this version and noticed some error message that I haven't
>experience before. When I cp latest geometry description over previous one
>and rerun integrate & correct, there's a very large chance to get "!!!
>ERROR !!! CANNOT OPEN OR WRITE SCRATCH FILE IN "STRONGHKL1"". xds_par then
>get paused. I'm using virtualbox ubuntu 16.04 on win 8.1 host. I haven't
>test it on other platform though. Rebooting the machine can help to get
>around. If someone also see similar error message maybe they can help
>verify.
>
>best,
>
>Wei
>
>On Tue, Dec 6, 2016 at 5:30 AM, Kay Diederichs <
>kay.diederi...@uni-konstanz.de> wrote:
>
>> Dear all,
>>
>> there is a new BUILT of the XDS package available for academic users from
>> http://xds.mpimf-heidelberg.mpg.de . This fixes a number of problems with
>> the VERSION of Nov 1, and all users of that version should update.
>>
>> We believe that this has a better background treatment in particular for
>> low counts; thanks to Alexey Rozov and others for making their data
>> available!
>>
>> If you find any bugs or regression with this latest BUILT of XDS please
>> tell us about it.
>>
>> best wishes,
>>
>> Kay
>>
>

Re: [ccp4bb] Modeling protein tertiary structure

Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

Re: [ccp4bb] Modeling protein tertiary structure

Re: [ccp4bb] Modeling protein tertiary structure

Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

[ccp4bb] REMINDER, job opportunities in Melbourne, Australia

Re: [ccp4bb] New BUILT of XDS for academic users

Re: [ccp4bb] New BUILT of XDS for academic users

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