Re: [ccp4bb] Comparing two datasets

2022-07-26 Thread Cygler, Miroslaw 
:and...@mrc-lmb.cam.ac.uk>> wrote:

I think that POINTLESS works with intensities rather than structure factors 
(I’m not sure if this can be changed). Also, SCALEIT gives a much more detailed 
breakdown (R factors as a function of resolution and differences in terms of 
sigmas etc) than POINTLESS WILL.

Cheers,

Andrew

On 26 Jul 2022, at 09:24, LEGRAND Pierre 
mailto:pierre.legr...@synchrotron-soleil.fr>>
 wrote:

Hello Mirek,

A very quick approach for that is offered by pointless:

pointless HKLREF 1_1_aimless.mtz  HKLIN 2_1_aimless.mtz
or
pointless HKLREF 1_1_aimless.mtz  XDSIN XDS_ASCII.HK

You will obtain a table looking like that, taking into account to possible 
reindexing:

Alternative indexing scores relative to reference
  Alternative reindexingLklhd  CC R(E^2)Number 
Cell_deviation
1  [h,k,l]  0.9930.9620.118 19150  0.08
2  [-k,h,l] 0.0070.0780.512 19150  0.87


Best wishes,

Pierre Legrand
PROXIMA-1 Beamline
Synchrotron SOLEIL

De: "Nicolas Foos" mailto:nicf...@embl.fr>>
À: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Envoyé: Mardi 26 Juillet 2022 08:36:35
Objet: Re: [ccp4bb] Comparing two datasets

Hi Mirek,

I am pretty sure XSCALE will do that for you : 
https://xds.mr.mpg.de/html_doc/xscale_program.html

If not, maybe have a look on SHELXC in SIR mode.

Hope this help.

Nicolas

On 25/07/2022 21:52, Cygler, Miroslaw wrote:
Hi,
I would like to calculate the R-merge for Fs from two datasets processed from 
two different crystals. Tried to use Blend but got the message that Blend 
requires R. Downloaded R but do not know how to tell CCP4 where it is located 
on my Mac. Is there another program that would take two mtg files and merge the 
Fs?
Any help would be greatly appreciated.


Mirek





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EMBL Grenoble, McCarthy Team
71 av. des Martyrs,
38000 Grenoble FRANCE

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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Comparing two datasets

2022-07-26 Thread Jessica Bruhn 
On 26 Jul 2022, 12:25, John R Helliwell < jrhelliw...@gmail.com>
> wrote:
> > >
> > > Dear Colleagues,
> > > Scaleit is a terrific program.
> > > Amongst its strengths already listed I would also mention its
> breakdown table with F so that in the strongest F reflections bin any
> systematic errors between the two data sets can show up if the Rfactor is
> greater than about 1%.
> > > Greetings,
> > > John
> > > Emeritus Professor John R Helliwell DSc
> > >
> > >
> > >
> > >
> > >> On 26 Jul 2022, at 11:40, Eleanor Dodson <
> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> > >>
> > >> 
> > >> Not only does SCALEIT do the job - it presented useful plots and an
> informative log file..
> > >> Eleanor
> > >> (You need to run CAD hklin1 Xtal1.mtz hklin2 Xtal2.mtz ...and
> obviously the columns from each Xtal will need different labels..)
> > >>
> > >> On Tue, 26 Jul 2022 at 09:45, Phil Evans 
> wrote:
> > >>> If you give Pointless Fs, it squares them to Is (not correct if the
> Fs have been derived from the truncate procedure, but not too bad). It will
> then give you a comparison. If you give the two datasets to Pointless,
> labelling them as different datasets, you can use Aimless to compare them
> > >>>
> > >>> But as Andrew said, the appropriate CCP4 program is Scaleit: it’s
> old but still works and gives lots of statistics
> > >>>
> > >>> Phil
> > >>>
> > >>> Sent from my iPhone
> > >>>
> > >>>> On 26 Jul 2022, at 09:37, Andrew Leslie - MRC LMB <
> and...@mrc-lmb.cam.ac.uk> wrote:
> > >>>>
> > >>>> I think that POINTLESS works with intensities rather than
> structure factors (I’m not sure if this can be changed). Also, SCALEIT
> gives a much more detailed breakdown (R factors as a function of resolution
> and differences in terms of sigmas etc) than POINTLESS WILL.
> > >>>>
> > >>>> Cheers,
> > >>>>
> > >>>> Andrew
> > >>>>
> > >>>>> On 26 Jul 2022, at 09:24, LEGRAND Pierre <
> pierre.legr...@synchrotron-soleil.fr> wrote:
> > >>>>>
> > >>>>> Hello Mirek,
> > >>>>>
> > >>>>> A very quick approach for that is offered by pointless:
> > >>>>>
> > >>>>> pointless HKLREF 1_1_aimless.mtz  HKLIN 2_1_aimless.mtz
> > >>>>> or
> > >>>>> pointless HKLREF 1_1_aimless.mtz  XDSIN XDS_ASCII.HK
> > >>>>>
> > >>>>> You will obtain a table looking like that, taking into account to
> possible reindexing:
> > >>>>>
> > >>>>> Alternative indexing scores relative to reference
> > >>>>>Alternative reindexingLklhd  CC R(E^2)
> Number Cell_deviation
> > >>>>>  1  [h,k,l]  0.9930.9620.118
>  19150  0.08
> > >>>>>  2  [-k,h,l] 0.0070.0780.512
>  19150  0.87
> > >>>>>
> > >>>>>
> > >>>>> Best wishes,
> > >>>>>
> > >>>>> Pierre Legrand
> > >>>>> PROXIMA-1 Beamline
> > >>>>> Synchrotron SOLEIL
> > >>>>>
> > >>>>> De: "Nicolas Foos" 
> > >>>>> À: CCP4BB@JISCMAIL.AC.UK
> > >>>>> Envoyé: Mardi 26 Juillet 2022 08:36:35
> > >>>>> Objet: Re: [ccp4bb] Comparing two datasets
> > >>>>>
> > >>>>> Hi Mirek,
> > >>>>>
> > >>>>> I am pretty sure XSCALE will do that for you :
> https://xds.mr.mpg.de/html_doc/xscale_program.html
> > >>>>>
> > >>>>> If not, maybe have a look on SHELXC in SIR mode.
> > >>>>>
> > >>>>> Hope this help.
> > >>>>>
> > >>>>> Nicolas
> > >>>>>
> > >>>>> On 25/07/2022 21:52, Cygler, Miroslaw wrote:
> > >>>>> Hi,
> > >>>>> I would like to calculate the R-merge for Fs from two datasets
> processed from two different crystals. Tried to use Blend but got the
> message that Blend requires R. Downloaded R but do not

Re: [ccp4bb] Comparing two datasets

2022-07-26 Thread Clemens Vonrhein 
;>> still works and gives lots of statistics 
> >>> 
> >>> Phil
> >>> 
> >>> Sent from my iPhone
> >>> 
> >>>> On 26 Jul 2022, at 09:37, Andrew Leslie - MRC LMB 
> >>>>  wrote:
> >>>> 
> >>>> I think that POINTLESS works with intensities rather than structure 
> >>>> factors (I’m not sure if this can be changed). Also, SCALEIT gives a 
> >>>> much more detailed breakdown (R factors as a function of resolution and 
> >>>> differences in terms of sigmas etc) than POINTLESS WILL.
> >>>> 
> >>>> Cheers,
> >>>> 
> >>>> Andrew
> >>>> 
> >>>>> On 26 Jul 2022, at 09:24, LEGRAND Pierre 
> >>>>>  wrote:
> >>>>> 
> >>>>> Hello Mirek,
> >>>>> 
> >>>>> A very quick approach for that is offered by pointless:
> >>>>> 
> >>>>> pointless HKLREF 1_1_aimless.mtz  HKLIN 2_1_aimless.mtz
> >>>>> or
> >>>>> pointless HKLREF 1_1_aimless.mtz  XDSIN XDS_ASCII.HK
> >>>>> 
> >>>>> You will obtain a table looking like that, taking into account to 
> >>>>> possible reindexing:
> >>>>> 
> >>>>> Alternative indexing scores relative to reference
> >>>>>Alternative reindexingLklhd  CC R(E^2)Number 
> >>>>> Cell_deviation
> >>>>>  1  [h,k,l]  0.9930.9620.118 19150  
> >>>>> 0.08
> >>>>>  2  [-k,h,l] 0.0070.0780.512 19150  
> >>>>> 0.87
> >>>>> 
> >>>>> 
> >>>>> Best wishes,
> >>>>> 
> >>>>> Pierre Legrand
> >>>>> PROXIMA-1 Beamline
> >>>>> Synchrotron SOLEIL
> >>>>> 
> >>>>> De: "Nicolas Foos" 
> >>>>> À: CCP4BB@JISCMAIL.AC.UK
> >>>>> Envoyé: Mardi 26 Juillet 2022 08:36:35
> >>>>> Objet: Re: [ccp4bb] Comparing two datasets
> >>>>> 
> >>>>> Hi Mirek, 
> >>>>> 
> >>>>> I am pretty sure XSCALE will do that for you : 
> >>>>> https://xds.mr.mpg.de/html_doc/xscale_program.html
> >>>>> 
> >>>>> If not, maybe have a look on SHELXC in SIR mode. 
> >>>>> 
> >>>>> Hope this help. 
> >>>>> 
> >>>>> Nicolas
> >>>>> 
> >>>>> On 25/07/2022 21:52, Cygler, Miroslaw wrote:
> >>>>> Hi,
> >>>>> I would like to calculate the R-merge for Fs from two datasets 
> >>>>> processed from two different crystals. Tried to use Blend but got the 
> >>>>> message that Blend requires R. Downloaded R but do not know how to tell 
> >>>>> CCP4 where it is located on my Mac. Is there another program that would 
> >>>>> take two mtg files and merge the Fs?
> >>>>> Any help would be greatly appreciated. 
> >>>>> 
> >>>>> 
> >>>>> Mirek
> >>>>> 
> >>>>> 
> >>>>> 
> >>>>> 
> >>>>> 
> >>>>> To unsubscribe from the CCP4BB list, click the following link:
> >>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >>>>> 
> >>>>> --
> >>>>> Nicolas Foos PhD - ARISE fellow
> >>>>> https://orcid.org/-0003-2331-8399
> >>>>> 
> >>>>> EMBL Grenoble, McCarthy Team
> >>>>> 71 av. des Martyrs,
> >>>>> 38000 Grenoble FRANCE
> >>>>> 
> >>>>> +33 4 57 42 84 67
> >>>>> 
> >>>>> To unsubscribe from the CCP4BB list, click the following link:
> >>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >>>>> 
> >>>>> 
> >>>>> 
> >>>>> To unsubscribe from the CCP4BB list, click the following link:
> >>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >>>>> 
> >>>> 
> >>>> 
> >>>> To unsubscribe from the CCP4BB list, click the following link:
> >>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >>>> 
> >>> 
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> >>> 
> >> 
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> >> 
> > 
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*--
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* Global Phasing Ltd., Sheraton House, Castle Park 
* Cambridge CB3 0AX, UK   www.globalphasing.com
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Re: [ccp4bb] Comparing two datasets

2022-07-26 Thread Phil Evans 
If you want to merge them then you can use Pointless/Aimless/ctruncate, with 
the warning that the conversion from F to I is not ideal, and ctruncate should 
be set to regenerate F from I just as sqrt ie not apply the truncate procedure 
again. 
Pointless supersedes combat for this conversion 
Again, just for comparison use scaleit

Phil

Sent from my iPhone

> On 26 Jul 2022, at 13:33, Jon Cooper 
> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hello again, as far as I can tell, the question is about two already 
> merged/unique datasets which Mirek wishes to merge into one. As far as I can 
> tell/remember, Scaleit is for scaling datasets side-by-side to get 
> isomorphous differences, etc, and I don't know of a way that you could get it 
> to merge 2 datasets as Mirek requested. Probably I am wrong but Scaleit 
> R-factors are different from R-merge, although the latter might be a bit 
> dubious in the circumstances. Anyway, I think the Combat route is a viable 
> way of achieving what the questioner wants to achieve ;-0 
> 
> 
> Sent from ProtonMail mobile
> 
> 
> 
>  Original Message 
> On 26 Jul 2022, 12:25, John R Helliwell < jrhelliw...@gmail.com> wrote:
> 
> Dear Colleagues,
> Scaleit is a terrific program. 
> Amongst its strengths already listed I would also mention its breakdown table 
> with F so that in the strongest F reflections bin any systematic errors 
> between the two data sets can show up if the Rfactor is greater than about 
> 1%. 
> Greetings,
> John 
> Emeritus Professor John R Helliwell DSc
> 
> 
> 
> 
>> On 26 Jul 2022, at 11:40, Eleanor Dodson 
>> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> 
>> Not only does SCALEIT do the job - it presented useful plots and an 
>> informative log file..
>> Eleanor
>> (You need to run CAD hklin1 Xtal1.mtz hklin2 Xtal2.mtz ...and obviously the 
>> columns from each Xtal will need different labels..)
>> 
>> On Tue, 26 Jul 2022 at 09:45, Phil Evans  wrote:
>>> If you give Pointless Fs, it squares them to Is (not correct if the Fs have 
>>> been derived from the truncate procedure, but not too bad). It will then 
>>> give you a comparison. If you give the two datasets to Pointless, labelling 
>>> them as different datasets, you can use Aimless to compare them
>>> 
>>> But as Andrew said, the appropriate CCP4 program is Scaleit: it’s old but 
>>> still works and gives lots of statistics 
>>> 
>>> Phil
>>> 
>>> Sent from my iPhone
>>> 
>>>> On 26 Jul 2022, at 09:37, Andrew Leslie - MRC LMB 
>>>>  wrote:
>>>> 
>>>> I think that POINTLESS works with intensities rather than structure 
>>>> factors (I’m not sure if this can be changed). Also, SCALEIT gives a much 
>>>> more detailed breakdown (R factors as a function of resolution and 
>>>> differences in terms of sigmas etc) than POINTLESS WILL.
>>>> 
>>>> Cheers,
>>>> 
>>>> Andrew
>>>> 
>>>>> On 26 Jul 2022, at 09:24, LEGRAND Pierre 
>>>>>  wrote:
>>>>> 
>>>>> Hello Mirek,
>>>>> 
>>>>> A very quick approach for that is offered by pointless:
>>>>> 
>>>>> pointless HKLREF 1_1_aimless.mtz  HKLIN 2_1_aimless.mtz
>>>>> or
>>>>> pointless HKLREF 1_1_aimless.mtz  XDSIN XDS_ASCII.HK
>>>>> 
>>>>> You will obtain a table looking like that, taking into account to 
>>>>> possible reindexing:
>>>>> 
>>>>> Alternative indexing scores relative to reference
>>>>>Alternative reindexingLklhd  CC R(E^2)Number 
>>>>> Cell_deviation
>>>>>  1  [h,k,l]  0.9930.9620.118 19150
>>>>>   0.08
>>>>>  2  [-k,h,l] 0.0070.0780.512 19150
>>>>>   0.87
>>>>> 
>>>>> 
>>>>> Best wishes,
>>>>> 
>>>>> Pierre Legrand
>>>>> PROXIMA-1 Beamline
>>>>> Synchrotron SOLEIL
>>>>> 
>>>>> De: "Nicolas Foos" 
>>>>> À: CCP4BB@JISCMAIL.AC.UK
>>>>> Envoyé: Mardi 26 Juillet 2022 08:36:35
>>>>> Objet: Re: [ccp4bb] Comparing two datasets
>>>>> 
>>>>> Hi Mirek, 
>>>>> 
>>>>> I am pretty sure XSCALE will do that for you

Re: [ccp4bb] Comparing two datasets

2022-07-26 Thread Eleanor Dodson 
Indeed Jon you are right.
If you want to know whether to merge two dasta sets, use SCALEIT for
analysis..

If You actually want to merge the data. best to go back to each unmerged
and feed both into pointless/aimless etc, although you can cheat be letting
pointless square the given Fs then merge those two - not good practice but
possible..
Eleanor

On Tue, 26 Jul 2022 at 13:34, Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello again, as far as I can tell, the question is about two already
> merged/unique datasets which Mirek wishes to merge into one. As far as I
> can tell/remember, Scaleit is for scaling datasets side-by-side to get
> isomorphous differences, etc, and I don't know of a way that you could get
> it to merge 2 datasets as Mirek requested. Probably I am wrong but Scaleit
> R-factors are different from R-merge, although the latter might be a bit
> dubious in the circumstances. Anyway, I think the Combat route is a viable
> way of achieving what the questioner wants to achieve ;-0
>
>
> Sent from ProtonMail mobile
>
>
>
>  Original Message 
> On 26 Jul 2022, 12:25, John R Helliwell < jrhelliw...@gmail.com> wrote:
>
>
> Dear Colleagues,
> Scaleit is a terrific program.
> Amongst its strengths already listed I would also mention its breakdown
> table with F so that in the strongest F reflections bin any systematic
> errors between the two data sets can show up if the Rfactor is greater than
> about 1%.
> Greetings,
> John
> Emeritus Professor John R Helliwell DSc
>
>
>
>
> On 26 Jul 2022, at 11:40, Eleanor Dodson <
> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> 
> Not only does SCALEIT do the job - it presented useful plots and an
> informative log file..
> Eleanor
> (You need to run CAD hklin1 Xtal1.mtz hklin2 Xtal2.mtz ...and obviously
> the columns from each Xtal will need different labels..)
>
> On Tue, 26 Jul 2022 at 09:45, Phil Evans  wrote:
>
>> If you give Pointless Fs, it squares them to Is (not correct if the Fs
>> have been derived from the truncate procedure, but not too bad). It will
>> then give you a comparison. If you give the two datasets to Pointless,
>> labelling them as different datasets, you can use Aimless to compare them
>>
>> But as Andrew said, the appropriate CCP4 program is Scaleit: it’s old but
>> still works and gives lots of statistics
>>
>> Phil
>>
>> Sent from my iPhone
>>
>> On 26 Jul 2022, at 09:37, Andrew Leslie - MRC LMB <
>> and...@mrc-lmb.cam.ac.uk> wrote:
>>
>> I think that POINTLESS works with intensities rather than structure
>> factors (I’m not sure if this can be changed). Also, SCALEIT gives a much
>> more detailed breakdown (R factors as a function of resolution and
>> differences in terms of sigmas etc) than POINTLESS WILL.
>>
>> Cheers,
>>
>> Andrew
>>
>> On 26 Jul 2022, at 09:24, LEGRAND Pierre <
>> pierre.legr...@synchrotron-soleil.fr> wrote:
>>
>> Hello Mirek,
>>
>> A very quick approach for that is offered by pointless:
>>
>> pointless HKLREF 1_1_aimless.mtz  HKLIN 2_1_aimless.mtz
>> or
>> pointless HKLREF 1_1_aimless.mtz  XDSIN XDS_ASCII.HK
>>
>> You will obtain a table looking like that, taking into account to
>> possible reindexing:
>>
>> Alternative indexing scores relative to reference
>>Alternative reindexingLklhd  CC R(E^2)Number
>> Cell_deviation
>>  1          [h,k,l]  0.9930.9620.118
>> 19150  0.08
>>  2  [-k,h,l] 0.0070.0780.512
>> 19150  0.87
>>
>>
>> Best wishes,
>>
>> Pierre Legrand
>> PROXIMA-1 Beamline
>> Synchrotron SOLEIL
>>
>> --
>> *De: *"Nicolas Foos" 
>> *À: *CCP4BB@JISCMAIL.AC.UK
>> *Envoyé: *Mardi 26 Juillet 2022 08:36:35
>> *Objet: *Re: [ccp4bb] Comparing two datasets
>>
>> Hi Mirek,
>>
>> I am pretty sure XSCALE will do that for you :
>> https://xds.mr.mpg.de/html_doc/xscale_program.html
>>
>> If not, maybe have a look on SHELXC in SIR mode.
>>
>> Hope this help.
>>
>> Nicolas
>> On 25/07/2022 21:52, Cygler, Miroslaw wrote:
>>
>> Hi,
>> I would like to calculate the R-merge for Fs from two datasets processed
>> from two different crystals. Tried to use Blend but got the message that
>> Blend requires R. Downloaded R but do not know how to tell CCP4 where it is
>> located on my Mac. Is there another program that would take two mtg

Re: [ccp4bb] Comparing two datasets

2022-07-26 Thread Jon Cooper 
Hello again, as far as I can tell, the question is about two already 
merged/unique datasets which Mirek wishes to merge into one. As far as I can 
tell/remember, Scaleit is for scaling datasets side-by-side to get isomorphous 
differences, etc, and I don't know of a way that you could get it to merge 2 
datasets as Mirek requested. Probably I am wrong but Scaleit R-factors are 
different from R-merge, although the latter might be a bit dubious in the 
circumstances. Anyway, I think the Combat route is a viable way of achieving 
what the questioner wants to achieve ;-0

Sent from ProtonMail mobile

 Original Message 
On 26 Jul 2022, 12:25, John R Helliwell wrote:

> Dear Colleagues,
> Scaleit is a terrific program.
> Amongst its strengths already listed I would also mention its breakdown table 
> with F so that in the strongest F reflections bin any systematic errors 
> between the two data sets can show up if the Rfactor is greater than about 1%.
> Greetings,
> John
>
> Emeritus Professor John R Helliwell DSc
>
>> On 26 Jul 2022, at 11:40, Eleanor Dodson 
>> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> 
>> Not only does SCALEIT do the job - it presented useful plots and an 
>> informative log file..
>> Eleanor
>> (You need to run CAD hklin1 Xtal1.mtz hklin2 Xtal2.mtz ...and obviously the 
>> columns from each Xtal will need different labels..)
>>
>> On Tue, 26 Jul 2022 at 09:45, Phil Evans  wrote:
>>
>>> If you give Pointless Fs, it squares them to Is (not correct if the Fs have 
>>> been derived from the truncate procedure, but not too bad). It will then 
>>> give you a comparison. If you give the two datasets to Pointless, labelling 
>>> them as different datasets, you can use Aimless to compare them
>>>
>>> But as Andrew said, the appropriate CCP4 program is Scaleit: it’s old but 
>>> still works and gives lots of statistics
>>>
>>> Phil
>>>
>>> Sent from my iPhone
>>>
>>>> On 26 Jul 2022, at 09:37, Andrew Leslie - MRC LMB 
>>>>  wrote:
>>>
>>>> I think that POINTLESS works with intensities rather than structure 
>>>> factors (I’m not sure if this can be changed). Also, SCALEIT gives a much 
>>>> more detailed breakdown (R factors as a function of resolution and 
>>>> differences in terms of sigmas etc) than POINTLESS WILL.
>>>>
>>>> Cheers,
>>>>
>>>> Andrew
>>>>
>>>>> On 26 Jul 2022, at 09:24, LEGRAND Pierre 
>>>>>  wrote:
>>>>>
>>>>> Hello Mirek,
>>>>>
>>>>> A very quick approach for that is offered by pointless:
>>>>>
>>>>> pointless HKLREF 1_1_aimless.mtz HKLIN 2_1_aimless.mtz
>>>>> or
>>>>> pointless HKLREF 1_1_aimless.mtz XDSIN XDS_ASCII.HK
>>>>>
>>>>> You will obtain a table looking like that, taking into account to 
>>>>> possible reindexing:
>>>>>
>>>>> Alternative indexing scores relative to reference
>>>>> Alternative reindexing Lklhd CC R(E^2) Number Cell_deviation
>>>>> 1 [h,k,l] 0.993 0.962 0.118 19150 0.08
>>>>> 2 [-k,h,l] 0.007 0.078 0.512 19150 0.87
>>>>>
>>>>> Best wishes,
>>>>>
>>>>> Pierre Legrand
>>>>> PROXIMA-1 Beamline
>>>>> Synchrotron SOLEIL
>>>>>
>>>>> ---
>>>>>
>>>>> De: "Nicolas Foos" 
>>>>> À: CCP4BB@JISCMAIL.AC.UK
>>>>> Envoyé: Mardi 26 Juillet 2022 08:36:35
>>>>> Objet: Re: [ccp4bb] Comparing two datasets
>>>>>
>>>>> Hi Mirek,
>>>>>
>>>>> I am pretty sure XSCALE will do that for you : 
>>>>> https://xds.mr.mpg.de/html_doc/xscale_program.html
>>>>>
>>>>> If not, maybe have a look on SHELXC in SIR mode.
>>>>>
>>>>> Hope this help.
>>>>>
>>>>> Nicolas
>>>>>
>>>>> On 25/07/2022 21:52, Cygler, Miroslaw wrote:
>>>>>
>>>>>> Hi,
>>>>>> I would like to calculate the R-merge for Fs from two datasets processed 
>>>>>> from two different crystals. Tried to use Blend but got the message that 
>>>>>> Blend requires R. D

Re: [ccp4bb] Comparing two datasets

2022-07-26 Thread John R Helliwell 
Dear Colleagues,
Scaleit is a terrific program. 
Amongst its strengths already listed I would also mention its breakdown table 
with F so that in the strongest F reflections bin any systematic errors between 
the two data sets can show up if the Rfactor is greater than about 1%. 
Greetings,
John 
Emeritus Professor John R Helliwell DSc




> On 26 Jul 2022, at 11:40, Eleanor Dodson 
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> 
> Not only does SCALEIT do the job - it presented useful plots and an 
> informative log file..
> Eleanor
> (You need to run CAD hklin1 Xtal1.mtz hklin2 Xtal2.mtz ...and obviously the 
> columns from each Xtal will need different labels..)
> 
>> On Tue, 26 Jul 2022 at 09:45, Phil Evans  wrote:
>> If you give Pointless Fs, it squares them to Is (not correct if the Fs have 
>> been derived from the truncate procedure, but not too bad). It will then 
>> give you a comparison. If you give the two datasets to Pointless, labelling 
>> them as different datasets, you can use Aimless to compare them
>> 
>> But as Andrew said, the appropriate CCP4 program is Scaleit: it’s old but 
>> still works and gives lots of statistics 
>> 
>> Phil
>> 
>> Sent from my iPhone
>> 
>>>> On 26 Jul 2022, at 09:37, Andrew Leslie - MRC LMB 
>>>>  wrote:
>>>> 
>>> I think that POINTLESS works with intensities rather than structure 
>>> factors (I’m not sure if this can be changed). Also, SCALEIT gives a much 
>>> more detailed breakdown (R factors as a function of resolution and 
>>> differences in terms of sigmas etc) than POINTLESS WILL.
>>> 
>>> Cheers,
>>> 
>>> Andrew
>>> 
>>>> On 26 Jul 2022, at 09:24, LEGRAND Pierre 
>>>>  wrote:
>>>> 
>>>> Hello Mirek,
>>>> 
>>>> A very quick approach for that is offered by pointless:
>>>> 
>>>> pointless HKLREF 1_1_aimless.mtz  HKLIN 2_1_aimless.mtz
>>>> or
>>>> pointless HKLREF 1_1_aimless.mtz  XDSIN XDS_ASCII.HK
>>>> 
>>>> You will obtain a table looking like that, taking into account to possible 
>>>> reindexing:
>>>> 
>>>> Alternative indexing scores relative to reference
>>>>Alternative reindexingLklhd  CC R(E^2)Number 
>>>> Cell_deviation
>>>>  1  [h,k,l]  0.9930.9620.118 19150 
>>>>  0.08
>>>>  2  [-k,h,l] 0.0070.0780.512 19150 
>>>>  0.87
>>>> 
>>>> 
>>>> Best wishes,
>>>> 
>>>> Pierre Legrand
>>>> PROXIMA-1 Beamline
>>>> Synchrotron SOLEIL
>>>> 
>>>> De: "Nicolas Foos" 
>>>> À: CCP4BB@JISCMAIL.AC.UK
>>>> Envoyé: Mardi 26 Juillet 2022 08:36:35
>>>> Objet: Re: [ccp4bb] Comparing two datasets
>>>> 
>>>> Hi Mirek, 
>>>> 
>>>> I am pretty sure XSCALE will do that for you : 
>>>> https://xds.mr.mpg.de/html_doc/xscale_program.html
>>>> 
>>>> If not, maybe have a look on SHELXC in SIR mode. 
>>>> 
>>>> Hope this help. 
>>>> 
>>>> Nicolas
>>>> 
>>>> On 25/07/2022 21:52, Cygler, Miroslaw wrote:
>>>> Hi,
>>>> I would like to calculate the R-merge for Fs from two datasets processed 
>>>> from two different crystals. Tried to use Blend but got the message that 
>>>> Blend requires R. Downloaded R but do not know how to tell CCP4 where it 
>>>> is located on my Mac. Is there another program that would take two mtg 
>>>> files and merge the Fs?
>>>> Any help would be greatly appreciated. 
>>>> 
>>>> 
>>>> Mirek
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> To unsubscribe from the CCP4BB list, click the following link:
>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>>> 
>>>> -- 
>>>> Nicolas Foos PhD - ARISE fellow
>>>> https://orcid.org/-0003-2331-8399
>>>>
>>>> EMBL Grenoble, McCarthy Team
>>>> 71 av. des Martyrs, 
>>>> 38000 Grenoble FRANCE
>>>>
>>>> +33 4 57 42 84 67
>>>> 
>>>> To unsubscribe from the CCP4BB list, click the following link:
>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>>> 
>>>> 
>>>> 
>>>> To unsubscribe from the CCP4BB list, click the following link:
>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>>> 
>>> 
>>> 
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> 
> 
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Re: [ccp4bb] Comparing two datasets

2022-07-26 Thread Eleanor Dodson 
Not only does SCALEIT do the job - it presented useful plots and an
informative log file..
Eleanor
(You need to run CAD hklin1 Xtal1.mtz hklin2 Xtal2.mtz ...and obviously the
columns from each Xtal will need different labels..)

On Tue, 26 Jul 2022 at 09:45, Phil Evans  wrote:

> If you give Pointless Fs, it squares them to Is (not correct if the Fs
> have been derived from the truncate procedure, but not too bad). It will
> then give you a comparison. If you give the two datasets to Pointless,
> labelling them as different datasets, you can use Aimless to compare them
>
> But as Andrew said, the appropriate CCP4 program is Scaleit: it’s old but
> still works and gives lots of statistics
>
> Phil
>
> Sent from my iPhone
>
> On 26 Jul 2022, at 09:37, Andrew Leslie - MRC LMB <
> and...@mrc-lmb.cam.ac.uk> wrote:
>
> I think that POINTLESS works with intensities rather than structure
> factors (I’m not sure if this can be changed). Also, SCALEIT gives a much
> more detailed breakdown (R factors as a function of resolution and
> differences in terms of sigmas etc) than POINTLESS WILL.
>
> Cheers,
>
> Andrew
>
> On 26 Jul 2022, at 09:24, LEGRAND Pierre <
> pierre.legr...@synchrotron-soleil.fr> wrote:
>
> Hello Mirek,
>
> A very quick approach for that is offered by pointless:
>
> pointless HKLREF 1_1_aimless.mtz  HKLIN 2_1_aimless.mtz
> or
> pointless HKLREF 1_1_aimless.mtz  XDSIN XDS_ASCII.HK
>
> You will obtain a table looking like that, taking into account to possible
> reindexing:
>
> Alternative indexing scores relative to reference
>Alternative reindexingLklhd  CC R(E^2)Number
> Cell_deviation
>  1  [h,k,l]  0.9930.9620.118
> 19150  0.08
>  2  [-k,h,l] 0.0070.0780.512
> 19150  0.87
>
>
> Best wishes,
>
> Pierre Legrand
> PROXIMA-1 Beamline
> Synchrotron SOLEIL
>
> --
> *De: *"Nicolas Foos" 
> *À: *CCP4BB@JISCMAIL.AC.UK
> *Envoyé: *Mardi 26 Juillet 2022 08:36:35
> *Objet: *Re: [ccp4bb] Comparing two datasets
>
> Hi Mirek,
>
> I am pretty sure XSCALE will do that for you :
> https://xds.mr.mpg.de/html_doc/xscale_program.html
>
> If not, maybe have a look on SHELXC in SIR mode.
>
> Hope this help.
>
> Nicolas
> On 25/07/2022 21:52, Cygler, Miroslaw wrote:
>
> Hi,
> I would like to calculate the R-merge for Fs from two datasets processed
> from two different crystals. Tried to use Blend but got the message that
> Blend requires R. Downloaded R but do not know how to tell CCP4 where it is
> located on my Mac. Is there another program that would take two mtg files
> and merge the Fs?
> Any help would be greatly appreciated.
> Mirek
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> --
> Nicolas Foos PhD - ARISE fellowhttps://orcid.org/-0003-2331-8399
>
> EMBL Grenoble, McCarthy Team
> 71 av. des Martyrs,
> 38000 Grenoble FRANCE
>
> +33 4 57 42 84 67
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Comparing two datasets

2022-07-26 Thread Phil Evans 
If you give Pointless Fs, it squares them to Is (not correct if the Fs have 
been derived from the truncate procedure, but not too bad). It will then give 
you a comparison. If you give the two datasets to Pointless, labelling them as 
different datasets, you can use Aimless to compare them

But as Andrew said, the appropriate CCP4 program is Scaleit: it’s old but still 
works and gives lots of statistics 

Phil

Sent from my iPhone

> On 26 Jul 2022, at 09:37, Andrew Leslie - MRC LMB  
> wrote:
> 
> I think that POINTLESS works with intensities rather than structure factors 
> (I’m not sure if this can be changed). Also, SCALEIT gives a much more 
> detailed breakdown (R factors as a function of resolution and differences in 
> terms of sigmas etc) than POINTLESS WILL.
> 
> Cheers,
> 
> Andrew
> 
>> On 26 Jul 2022, at 09:24, LEGRAND Pierre 
>>  wrote:
>> 
>> Hello Mirek,
>> 
>> A very quick approach for that is offered by pointless:
>> 
>> pointless HKLREF 1_1_aimless.mtz  HKLIN 2_1_aimless.mtz
>> or
>> pointless HKLREF 1_1_aimless.mtz  XDSIN XDS_ASCII.HK
>> 
>> You will obtain a table looking like that, taking into account to possible 
>> reindexing:
>> 
>> Alternative indexing scores relative to reference
>>Alternative reindexingLklhd  CC R(E^2)Number 
>> Cell_deviation
>>  1  [h,k,l]  0.9930.9620.118 19150  
>> 0.08
>>  2  [-k,h,l] 0.0070.0780.512 19150  
>> 0.87
>> 
>> 
>> Best wishes,
>> 
>> Pierre Legrand
>> PROXIMA-1 Beamline
>> Synchrotron SOLEIL
>> 
>> De: "Nicolas Foos" 
>> À: CCP4BB@JISCMAIL.AC.UK
>> Envoyé: Mardi 26 Juillet 2022 08:36:35
>> Objet: Re: [ccp4bb] Comparing two datasets
>> 
>> Hi Mirek, 
>> 
>> I am pretty sure XSCALE will do that for you : 
>> https://xds.mr.mpg.de/html_doc/xscale_program.html
>> 
>> If not, maybe have a look on SHELXC in SIR mode. 
>> 
>> Hope this help. 
>> 
>> Nicolas
>> 
>> On 25/07/2022 21:52, Cygler, Miroslaw wrote:
>> Hi,
>> I would like to calculate the R-merge for Fs from two datasets processed 
>> from two different crystals. Tried to use Blend but got the message that 
>> Blend requires R. Downloaded R but do not know how to tell CCP4 where it is 
>> located on my Mac. Is there another program that would take two mtg files 
>> and merge the Fs?
>> Any help would be greatly appreciated. 
>> 
>> 
>> Mirek
>> 
>> 
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> 
>> -- 
>> Nicolas Foos PhD - ARISE fellow
>> https://orcid.org/-0003-2331-8399
>>
>> EMBL Grenoble, McCarthy Team
>> 71 av. des Martyrs, 
>> 38000 Grenoble FRANCE
>>
>> +33 4 57 42 84 67
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



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Re: [ccp4bb] Comparing two datasets

2022-07-26 Thread Andrew Leslie - MRC LMB 
I think that POINTLESS works with intensities rather than structure factors 
(I’m not sure if this can be changed). Also, SCALEIT gives a much more detailed 
breakdown (R factors as a function of resolution and differences in terms of 
sigmas etc) than POINTLESS WILL.

Cheers,

Andrew

> On 26 Jul 2022, at 09:24, LEGRAND Pierre 
>  wrote:
> 
> Hello Mirek,
> 
> A very quick approach for that is offered by pointless:
> 
> pointless HKLREF 1_1_aimless.mtz  HKLIN 2_1_aimless.mtz
> or
> pointless HKLREF 1_1_aimless.mtz  XDSIN XDS_ASCII.HK
> 
> You will obtain a table looking like that, taking into account to possible 
> reindexing:
> 
> Alternative indexing scores relative to reference
>Alternative reindexingLklhd  CC R(E^2)Number 
> Cell_deviation
>  1  [h,k,l]  0.9930.9620.118 19150  
> 0.08
>  2  [-k,h,l] 0.0070.0780.512 19150  
> 0.87
> 
> 
> Best wishes,
> 
> Pierre Legrand
> PROXIMA-1 Beamline
> Synchrotron SOLEIL
> 
> De: "Nicolas Foos" 
> À: CCP4BB@JISCMAIL.AC.UK
> Envoyé: Mardi 26 Juillet 2022 08:36:35
> Objet: Re: [ccp4bb] Comparing two datasets
> 
> Hi Mirek, 
> 
> I am pretty sure XSCALE will do that for you : 
> https://xds.mr.mpg.de/html_doc/xscale_program.html 
> <https://xds.mr.mpg.de/html_doc/xscale_program.html>
> If not, maybe have a look on SHELXC in SIR mode. 
> 
> Hope this help. 
> 
> Nicolas
> 
> On 25/07/2022 21:52, Cygler, Miroslaw wrote:
> Hi,
> I would like to calculate the R-merge for Fs from two datasets processed from 
> two different crystals. Tried to use Blend but got the message that Blend 
> requires R. Downloaded R but do not know how to tell CCP4 where it is located 
> on my Mac. Is there another program that would take two mtg files and merge 
> the Fs?
> Any help would be greatly appreciated. 
> 
> 
> Mirek
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1>
> -- 
> Nicolas Foos PhD - ARISE fellow
> https://orcid.org/-0003-2331-8399 <https://orcid.org/-0003-2331-8399>
>
> EMBL Grenoble, McCarthy Team
> 71 av. des Martyrs, 
> 38000 Grenoble FRANCE
>
> +33 4 57 42 84 67
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1>
> 
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Comparing two datasets

2022-07-26 Thread LEGRAND Pierre 
Hello Mirek, 

A very quick approach for that is offered by pointless: 

pointless HKLREF 1_1_aimless.mtz HKLIN 2_1_aimless.mtz 
or 
pointless HKLREF 1_1_aimless.mtz XDSIN XDS_ASCII.HK 

You will obtain a table looking like that, taking into account to possible 
reindexing: 

Alternative indexing scores relative to reference 
Alternative reindexing Lklhd CC R(E^2) Number Cell_deviation 
1 [h,k,l] 0.993 0.962 0.118 19150 0.08 
2 [-k,h,l] 0.007 0.078 0.512 19150 0.87 


Best wishes, 

Pierre Legrand 
PROXIMA-1 Beamline 
Synchrotron SOLEIL 


De: "Nicolas Foos"  
À: CCP4BB@JISCMAIL.AC.UK 
Envoyé: Mardi 26 Juillet 2022 08:36:35 
Objet: Re: [ccp4bb] Comparing two datasets 



Hi Mirek, 


I am pretty sure XSCALE will do that for you : [ 
https://xds.mr.mpg.de/html_doc/xscale_program.html | 
https://xds.mr.mpg.de/html_doc/xscale_program.html ] 


If not, maybe have a look on SHELXC in SIR mode. 


Hope this help. 


Nicolas 
On 25/07/2022 21:52, Cygler, Miroslaw wrote: 


Hi, 
I would like to calculate the R-merge for Fs from two datasets processed from 
two different crystals. Tried to use Blend but got the message that Blend 
requires R. Downloaded R but do not know how to tell CCP4 where it is located 
on my Mac. Is there another program that would take two mtg files and merge the 
Fs? 
Any help would be greatly appreciated. 
Mirek 








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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 ] 


-- 
Nicolas Foos PhD - ARISE fellow [ https://orcid.org/-0003-2331-8399 | 
https://orcid.org/-0003-2331-8399 ] EMBL Grenoble, McCarthy Team
71 av. des Martyrs, 
38000 Grenoble FRANCE
   
+33 4 57 42 84 67 




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Re: [ccp4bb] Comparing two datasets

2022-07-26 Thread Nicolas Foos 

Hi Mirek,

I am pretty sure XSCALE will do that for you : 
https://xds.mr.mpg.de/html_doc/xscale_program.html


If not, maybe have a look on SHELXC in SIR mode.

Hope this help.

Nicolas

On 25/07/2022 21:52, Cygler, Miroslaw wrote:

Hi,
I would like to calculate the R-merge for Fs from two datasets 
processed from two different crystals. Tried to use Blend but got the 
message that Blend requires R. Downloaded R but do not know how to 
tell CCP4 where it is located on my Mac. Is there another program that 
would take two mtg files and merge the Fs?

Any help would be greatly appreciated.
Mirek







To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 




--
Nicolas Foos PhD - ARISE fellow
https://orcid.org/-0003-2331-8399
   
EMBL Grenoble, McCarthy Team

71 av. des Martyrs,
38000 Grenoble FRANCE
   
+33 4 57 42 84 67




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Re: [ccp4bb] Comparing two datasets

2022-07-25 Thread Jon Cooper 
Hello, I looked thru the program list in ccp4i and Combat caught my eye. Seems 
you can input an MTZ file of amplitudes and output a multirecord MTZ, and you 
can specify a batch number. If you did the same for your second dataset with a 
different batch number you could then append them with Sortmtz and run Scala, 
Pointless, Aimless, etc, to get the usual stats.

If you scaled the F and sigF columns as Andrew suggested, Sftools has a MERGE 
or MERGE AVERAGE option which *might* work!!

Cheers, Jon.C.

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On 25 Jul 2022, 20:52, Cygler, Miroslaw wrote:

> Hi,
> I would like to calculate the R-merge for Fs from two datasets processed from 
> two different crystals. Tried to use Blend but got the message that Blend 
> requires R. Downloaded R but do not know how to tell CCP4 where it is located 
> on my Mac. Is there another program that would take two mtg files and merge 
> the Fs?
> Any help would be greatly appreciated.
>
> Mirek
>
> ---
>
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Re: [ccp4bb] Comparing two datasets

2022-07-25 Thread Andrew Leslie - MRC LMB 
I think that SCALEIT should be able to do this. This was originally designed to 
compare Fs for Native and heavy atom derivate data, but can compare any two 
similar datasets (ie those that can sensibly be scaled together). You will need 
to merge the two mtz files first.

Cheers,

Andrew

> On 25 Jul 2022, at 20:52, Cygler, Miroslaw  wrote:
> 
> Hi,
> I would like to calculate the R-merge for Fs from two datasets processed from 
> two different crystals. Tried to use Blend but got the message that Blend 
> requires R. Downloaded R but do not know how to tell CCP4 where it is located 
> on my Mac. Is there another program that would take two mtg files and merge 
> the Fs?
> Any help would be greatly appreciated. 
> 
> 
> Mirek
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
> 



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