Re: [ccp4bb] XDS questions

[Jan Stransky]

I had some cases, when path INTEGRATE.HKL -> Aimless gave data, from 
which it was not possible to solve structure by Phaser. It looked like 
structure solved, but then I got 45-50% Rwork/free. There were no 
problems with XDS_ASCCI.HKL -> Aimless (Not scale, just merge) path.

Jan

On 11/24/2016 06:44 PM, Nishant Varshney wrote:

Thanks everyone  for your replies.
cheers
Nishant

On Mon, Nov 21, 2016 at 6:03 PM, Wei Wang > wrote:


My personal test shows that the different paths vary little with
each other, as long as the scaling is done only once. Another way
could be what is said on XDSwiki: Minimum I/Sigma=50,
CORRECTIONS=MODULATION, NBATCH=1. Then the XDS_ASCII.HKL is handed
over to Aimless with default settings.

One question raised is that how can I move the 'aliens' with Z>20
to REMOVE.HKL? I didn't find answer yet. Maybe I didn't read
carefully over the documents, but I would appreciate it if someone
can teach me.

Regards,

Wei


On Mon, Nov 21, 2016 at 6:13 AM, Tim Gruene > wrote:

Dear Nishant,

XDS_ASCII.HKL contains corrected, scaled, but not merged
reflections.
You can specifically ask XDS to merge your data, but I would
not do so unless
really necessary - you loose a lot of information.

I would like to offer a different opinion to Graeme's:
You can read XDS_ASCII.HKL into pointless and aimless and
provide aimless with
the option 'onlymerge'. This way aimless merges the data, but
it does not
rescale them.

XDS performs a couple of corrections in the CORRECT step, the
output of which
is XDS_ASCII.HKL. And while XDS is extremely well documented,
I am not sure
aimless takes into account how XDS treats the data. I would
therefore trust
the step of scaling to the same author and continue with
XDS_ASCII.HKL.

Best,
Tim


On Monday, November 21, 2016 11:37:15 AM Nishant Varshney wrote:
> Dear All,
>
> Just to understand more, the XDS_ASCII.HKL file generated
after running XDS
> contains scaled and merged reflections?
>
> Moreover, what happens exactly, if you use XDS_ASCII.HKL
file in AIMLESS
> instead of INTEGRATE.HKL file??
>
> I ran AIMLESS separately, one using already scaled
XDS_ASCII.HKL and
> another using INTEGRATE.HKL and I found that in the run
using XDS_ASCII.HKL
> little lesser total number of observation but marginally
better statistics.
>
> Thanks
> Nishant
>
> On Thu, Nov 17, 2016 at 10:08 PM, Andreas Forster
>
>
> wrote:
> > Dear Wei,
> >
> > if you process your data with XDS, the best is probably to
do the scaling
> > in XDS (CORRECT) and be done with it.  If you want to use
Aimless for
> > merging, you can turn off scaling with the ONLYMERGE
keyword or use SCALES
> > CONSTANT.
> >
> > All best.
> >
> >
> > Andreas
> >
> > On Thu, Nov 17, 2016 at 9:40 PM, Wei Wang
> wrote:
> >> Hi,
> >>
> >> Is there a way to let xds_par use less than all
processors/threads on the
> >> machine? Sometimes I would like to process something else
while XDS is
> >> running.
> >>
> >> Another question is related to the scaling procedure. My
understanding is
> >> that the XDS already does the scaling during correction.
So if I follow
> >> the
> >> XDS-Aimless route, then probably I should let Aimless do
"skip scaling
> >> and
> >> only merge"? Please elucidate me on this issue.
> >>
> >> Regards,
> >>
> >> Wei
>
> --
> Dr. Nishant Kumar Varshney,
> IISc-ICTP Fellow
> XRD2 Beamline, Elettra-Sincrotrone,
> In Area Science Park,
> Basovizza, S.S. 14, Km 163,5,
> 34012 Trieste, Italy
> +39-040-375 8737  (office ESP4 P1 031)
> +39-040-375-8435  (XRD2 beamline)
> +39 3318809798  (Mobile)
--
--
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
Principal Investigator
Biology and Chemistry
OFLC/102
CH-5232 Villigen PSI

Phone: +41 (0)56 310 5297 

GPG Key ID = A46BEE1A





--
Dr. Nishant Kumar Varshney,
IISc-ICTP 

Re: [ccp4bb] XDS questions

[Nishant Varshney]

Thanks everyone  for your replies.
cheers
Nishant

On Mon, Nov 21, 2016 at 6:03 PM, Wei Wang  wrote:

> My personal test shows that the different paths vary little with each
> other, as long as the scaling is done only once. Another way could be what
> is said on XDSwiki: Minimum I/Sigma=50, CORRECTIONS=MODULATION, NBATCH=1.
> Then the XDS_ASCII.HKL is handed over to Aimless with default settings.
>
> One question raised is that how can I move the 'aliens' with Z>20 to
> REMOVE.HKL? I didn't find answer yet. Maybe I didn't read carefully over
> the documents, but I would appreciate it if someone can teach me.
>
> Regards,
>
> Wei
>
>
> On Mon, Nov 21, 2016 at 6:13 AM, Tim Gruene  wrote:
>
>> Dear Nishant,
>>
>> XDS_ASCII.HKL contains corrected, scaled, but not merged reflections.
>> You can specifically ask XDS to merge your data, but I would not do so
>> unless
>> really necessary - you loose a lot of information.
>>
>> I would like to offer a different opinion to Graeme's:
>> You can read XDS_ASCII.HKL into pointless and aimless and provide aimless
>> with
>> the option 'onlymerge'. This way aimless merges the data, but it does not
>> rescale them.
>>
>> XDS performs a couple of corrections in the CORRECT step, the output of
>> which
>> is XDS_ASCII.HKL. And while XDS is extremely well documented, I am not
>> sure
>> aimless takes into account how XDS treats the data. I would therefore
>> trust
>> the step of scaling to the same author and continue with XDS_ASCII.HKL.
>>
>> Best,
>> Tim
>>
>>
>> On Monday, November 21, 2016 11:37:15 AM Nishant Varshney wrote:
>> > Dear All,
>> >
>> > Just to understand more, the XDS_ASCII.HKL file generated after running
>> XDS
>> > contains scaled and merged reflections?
>> >
>> > Moreover, what happens exactly, if you use XDS_ASCII.HKL file in AIMLESS
>> > instead of INTEGRATE.HKL file??
>> >
>> > I ran AIMLESS separately, one using already scaled XDS_ASCII.HKL and
>> > another using INTEGRATE.HKL and I found that in the run using
>> XDS_ASCII.HKL
>> > little lesser total number of observation but marginally better
>> statistics.
>> >
>> > Thanks
>> > Nishant
>> >
>> > On Thu, Nov 17, 2016 at 10:08 PM, Andreas Forster > >
>> >
>> > wrote:
>> > > Dear Wei,
>> > >
>> > > if you process your data with XDS, the best is probably to do the
>> scaling
>> > > in XDS (CORRECT) and be done with it.  If you want to use Aimless for
>> > > merging, you can turn off scaling with the ONLYMERGE keyword or use
>> SCALES
>> > > CONSTANT.
>> > >
>> > > All best.
>> > >
>> > >
>> > > Andreas
>> > >
>> > > On Thu, Nov 17, 2016 at 9:40 PM, Wei Wang 
>> wrote:
>> > >> Hi,
>> > >>
>> > >> Is there a way to let xds_par use less than all processors/threads
>> on the
>> > >> machine? Sometimes I would like to process something else while XDS
>> is
>> > >> running.
>> > >>
>> > >> Another question is related to the scaling procedure. My
>> understanding is
>> > >> that the XDS already does the scaling during correction. So if I
>> follow
>> > >> the
>> > >> XDS-Aimless route, then probably I should let Aimless do "skip
>> scaling
>> > >> and
>> > >> only merge"? Please elucidate me on this issue.
>> > >>
>> > >> Regards,
>> > >>
>> > >> Wei
>> >
>> > --
>> > Dr. Nishant Kumar Varshney,
>> > IISc-ICTP Fellow
>> > XRD2 Beamline, Elettra-Sincrotrone,
>> > In Area Science Park,
>> > Basovizza, S.S. 14, Km 163,5,
>> > 34012 Trieste, Italy
>> > +39-040-375 8737 (office ESP4 P1 031)
>> > +39-040-375-8435 (XRD2 beamline)
>> > +39 3318809798 (Mobile)
>> --
>> --
>> Paul Scherrer Institut
>> Dr. Tim Gruene
>> - persoenlich -
>> Principal Investigator
>> Biology and Chemistry
>> OFLC/102
>> CH-5232 Villigen PSI
>>
>> Phone: +41 (0)56 310 5297
>>
>> GPG Key ID = A46BEE1A
>>
>>
>


-- 
Dr. Nishant Kumar Varshney,
IISc-ICTP Fellow
XRD2 Beamline, Elettra-Sincrotrone,
In Area Science Park,
Basovizza, S.S. 14, Km 163,5,
34012 Trieste, Italy
+39-040-375 8737 (office ESP4 P1 031)
+39-040-375-8435 (XRD2 beamline)
+39 3318809798 (Mobile)

Re: [ccp4bb] XDS questions

[Boaz Shaanan]

Hi,



I do this by editor (and cut / paste). Clumsy but works. Let me know if you find a more elegant way.
Cheers,
Boaz


 Original message 
From: Wei Wang <ww2...@columbia.edu> 
Date: 21/11/2016 19:05 (GMT+02:00) 
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] XDS questions 





My personal test shows that the different paths vary little with each other, as long as the scaling is done only once. Another way could be what is said on XDSwiki: Minimum I/Sigma=50, CORRECTIONS=MODULATION, NBATCH=1. Then the XDS_ASCII.HKL is handed
 over to Aimless with default settings.


One question raised is that how can I move the 'aliens' with Z>20 to REMOVE.HKL? I didn't find answer yet. Maybe I didn't read carefully over the documents, but I would appreciate it if someone can teach me.


Regards,


Wei





On Mon, Nov 21, 2016 at 6:13 AM, Tim Gruene 
<tim.gru...@psi.ch> wrote:

Dear Nishant,

XDS_ASCII.HKL contains corrected, scaled, but not merged reflections.
You can specifically ask XDS to merge your data, but I would not do so unless
really necessary - you loose a lot of information.

I would like to offer a different opinion to Graeme's:
You can read XDS_ASCII.HKL into pointless and aimless and provide aimless with
the option 'onlymerge'. This way aimless merges the data, but it does not
rescale them.

XDS performs a couple of corrections in the CORRECT step, the output of which
is XDS_ASCII.HKL. And while XDS is extremely well documented, I am not sure
aimless takes into account how XDS treats the data. I would therefore trust
the step of scaling to the same author and continue with XDS_ASCII.HKL.

Best,
Tim



On Monday, November 21, 2016 11:37:15 AM Nishant Varshney wrote:
> Dear All,
>
> Just to understand more, the XDS_ASCII.HKL file generated after running XDS
> contains scaled and merged reflections?
>
> Moreover, what happens exactly, if you use XDS_ASCII.HKL file in AIMLESS
> instead of INTEGRATE.HKL file??
>
> I ran AIMLESS separately, one using already scaled XDS_ASCII.HKL and
> another using INTEGRATE.HKL and I found that in the run using XDS_ASCII.HKL
> little lesser total number of observation but marginally better statistics.
>
> Thanks
> Nishant
>
> On Thu, Nov 17, 2016 at 10:08 PM, Andreas Forster <docandr...@gmail.com>
>
> wrote:
> > Dear Wei,
> >
> > if you process your data with XDS, the best is probably to do the scaling
> > in XDS (CORRECT) and be done with it.  If you want to use Aimless for
> > merging, you can turn off scaling with the ONLYMERGE keyword or use SCALES
> > CONSTANT.
> >
> > All best.
> >
> >
> > Andreas
> >
> > On Thu, Nov 17, 2016 at 9:40 PM, Wei Wang <ww2...@columbia.edu> wrote:
> >> Hi,
> >>
> >> Is there a way to let xds_par use less than all processors/threads on the
> >> machine? Sometimes I would like to process something else while XDS is
> >> running.
> >>
> >> Another question is related to the scaling procedure. My understanding is
> >> that the XDS already does the scaling during correction. So if I follow
> >> the
> >> XDS-Aimless route, then probably I should let Aimless do "skip scaling
> >> and
> >> only merge"? Please elucidate me on this issue.
> >>
> >> Regards,
> >>
> >> Wei
>
> --
> Dr. Nishant Kumar Varshney,
> IISc-ICTP Fellow
> XRD2 Beamline, Elettra-Sincrotrone,
> In Area Science Park,
> Basovizza, S.S. 14, Km 163,5,
> 34012 Trieste, Italy
> +39-040-375 8737 (office ESP4 P1 031)
> +39-040-375-8435 (XRD2 beamline)
> +39 3318809798 (Mobile)


--
--
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
Principal Investigator
Biology and Chemistry
OFLC/102
CH-5232 Villigen PSI

Phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A

Re: [ccp4bb] XDS questions

[Wei Wang]

My personal test shows that the different paths vary little with each
other, as long as the scaling is done only once. Another way could be what
is said on XDSwiki: Minimum I/Sigma=50, CORRECTIONS=MODULATION, NBATCH=1.
Then the XDS_ASCII.HKL is handed over to Aimless with default settings.

One question raised is that how can I move the 'aliens' with Z>20 to
REMOVE.HKL? I didn't find answer yet. Maybe I didn't read carefully over
the documents, but I would appreciate it if someone can teach me.

Regards,

Wei

On Mon, Nov 21, 2016 at 6:13 AM, Tim Gruene  wrote:

> Dear Nishant,
>
> XDS_ASCII.HKL contains corrected, scaled, but not merged reflections.
> You can specifically ask XDS to merge your data, but I would not do so
> unless
> really necessary - you loose a lot of information.
>
> I would like to offer a different opinion to Graeme's:
> You can read XDS_ASCII.HKL into pointless and aimless and provide aimless
> with
> the option 'onlymerge'. This way aimless merges the data, but it does not
> rescale them.
>
> XDS performs a couple of corrections in the CORRECT step, the output of
> which
> is XDS_ASCII.HKL. And while XDS is extremely well documented, I am not sure
> aimless takes into account how XDS treats the data. I would therefore trust
> the step of scaling to the same author and continue with XDS_ASCII.HKL.
>
> Best,
> Tim
>
>
> On Monday, November 21, 2016 11:37:15 AM Nishant Varshney wrote:
> > Dear All,
> >
> > Just to understand more, the XDS_ASCII.HKL file generated after running
> XDS
> > contains scaled and merged reflections?
> >
> > Moreover, what happens exactly, if you use XDS_ASCII.HKL file in AIMLESS
> > instead of INTEGRATE.HKL file??
> >
> > I ran AIMLESS separately, one using already scaled XDS_ASCII.HKL and
> > another using INTEGRATE.HKL and I found that in the run using
> XDS_ASCII.HKL
> > little lesser total number of observation but marginally better
> statistics.
> >
> > Thanks
> > Nishant
> >
> > On Thu, Nov 17, 2016 at 10:08 PM, Andreas Forster 
> >
> > wrote:
> > > Dear Wei,
> > >
> > > if you process your data with XDS, the best is probably to do the
> scaling
> > > in XDS (CORRECT) and be done with it.  If you want to use Aimless for
> > > merging, you can turn off scaling with the ONLYMERGE keyword or use
> SCALES
> > > CONSTANT.
> > >
> > > All best.
> > >
> > >
> > > Andreas
> > >
> > > On Thu, Nov 17, 2016 at 9:40 PM, Wei Wang  wrote:
> > >> Hi,
> > >>
> > >> Is there a way to let xds_par use less than all processors/threads on
> the
> > >> machine? Sometimes I would like to process something else while XDS is
> > >> running.
> > >>
> > >> Another question is related to the scaling procedure. My
> understanding is
> > >> that the XDS already does the scaling during correction. So if I
> follow
> > >> the
> > >> XDS-Aimless route, then probably I should let Aimless do "skip scaling
> > >> and
> > >> only merge"? Please elucidate me on this issue.
> > >>
> > >> Regards,
> > >>
> > >> Wei
> >
> > --
> > Dr. Nishant Kumar Varshney,
> > IISc-ICTP Fellow
> > XRD2 Beamline, Elettra-Sincrotrone,
> > In Area Science Park,
> > Basovizza, S.S. 14, Km 163,5,
> > 34012 Trieste, Italy
> > +39-040-375 8737 (office ESP4 P1 031)
> > +39-040-375-8435 (XRD2 beamline)
> > +39 3318809798 (Mobile)
> --
> --
> Paul Scherrer Institut
> Dr. Tim Gruene
> - persoenlich -
> Principal Investigator
> Biology and Chemistry
> OFLC/102
> CH-5232 Villigen PSI
>
> Phone: +41 (0)56 310 5297
>
> GPG Key ID = A46BEE1A
>
>

Re: [ccp4bb] XDS questions

[Phil Evans]

XDS-CORRECT and Aimless use 

1. different scaling models - CORRECT includes a poorly documented correction 
across the detector plane not present in Aimless: this may or may not be a Good 
Thing

2. different outlier rejection algorithms - XDS seems to reject more 
observations

3. different “correction” of the sigma(I) estimates - XDS seems to do a better 
job at this

In practice, the differences are likely to be marginal, and it is hard to 
decide which is better

Phil

> On 21 Nov 2016, at 11:13, Tim Gruene  wrote:
> 
> Dear Nishant,
> 
> XDS_ASCII.HKL contains corrected, scaled, but not merged reflections. 
> You can specifically ask XDS to merge your data, but I would not do so unless 
> really necessary - you loose a lot of information.
> 
> I would like to offer a different opinion to Graeme's:
> You can read XDS_ASCII.HKL into pointless and aimless and provide aimless 
> with 
> the option 'onlymerge'. This way aimless merges the data, but it does not 
> rescale them.
> 
> XDS performs a couple of corrections in the CORRECT step, the output of which 
> is XDS_ASCII.HKL. And while XDS is extremely well documented, I am not sure 
> aimless takes into account how XDS treats the data. I would therefore trust 
> the step of scaling to the same author and continue with XDS_ASCII.HKL.
> 
> Best,
> Tim
> 
> 
> On Monday, November 21, 2016 11:37:15 AM Nishant Varshney wrote:
>> Dear All,
>> 
>> Just to understand more, the XDS_ASCII.HKL file generated after running XDS
>> contains scaled and merged reflections?
>> 
>> Moreover, what happens exactly, if you use XDS_ASCII.HKL file in AIMLESS
>> instead of INTEGRATE.HKL file??
>> 
>> I ran AIMLESS separately, one using already scaled XDS_ASCII.HKL and
>> another using INTEGRATE.HKL and I found that in the run using XDS_ASCII.HKL
>> little lesser total number of observation but marginally better statistics.
>> 
>> Thanks
>> Nishant
>> 
>> On Thu, Nov 17, 2016 at 10:08 PM, Andreas Forster 
>> 
>> wrote:
>>> Dear Wei,
>>> 
>>> if you process your data with XDS, the best is probably to do the scaling
>>> in XDS (CORRECT) and be done with it.  If you want to use Aimless for
>>> merging, you can turn off scaling with the ONLYMERGE keyword or use SCALES
>>> CONSTANT.
>>> 
>>> All best.
>>> 
>>> 
>>> Andreas
>>> 
>>> On Thu, Nov 17, 2016 at 9:40 PM, Wei Wang  wrote:
 Hi,
 
 Is there a way to let xds_par use less than all processors/threads on the
 machine? Sometimes I would like to process something else while XDS is
 running.
 
 Another question is related to the scaling procedure. My understanding is
 that the XDS already does the scaling during correction. So if I follow
 the
 XDS-Aimless route, then probably I should let Aimless do "skip scaling
 and
 only merge"? Please elucidate me on this issue.
 
 Regards,
 
 Wei
>> 
>> --
>> Dr. Nishant Kumar Varshney,
>> IISc-ICTP Fellow
>> XRD2 Beamline, Elettra-Sincrotrone,
>> In Area Science Park,
>> Basovizza, S.S. 14, Km 163,5,
>> 34012 Trieste, Italy
>> +39-040-375 8737 (office ESP4 P1 031)
>> +39-040-375-8435 (XRD2 beamline)
>> +39 3318809798 (Mobile)
> -- 
> --
> Paul Scherrer Institut
> Dr. Tim Gruene
> - persoenlich -
> Principal Investigator
> Biology and Chemistry
> OFLC/102
> CH-5232 Villigen PSI
> 
> Phone: +41 (0)56 310 5297
> 
> GPG Key ID = A46BEE1A
> 

Re: [ccp4bb] XDS questions

[Graeme Winter]

Dear All,

I agree with Tim - what I was getting at was to perform the scaling exactly 
once - i.e. with AIMLESS or XDS CORRECT but not both

The behaviour Tim describes below is exactly what xia2 does :)

Best wishes Graeme

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene
Sent: 21 November 2016 11:14
To: ccp4bb
Subject: Re: [ccp4bb] XDS questions

Dear Nishant,

XDS_ASCII.HKL contains corrected, scaled, but not merged reflections. 
You can specifically ask XDS to merge your data, but I would not do so unless 
really necessary - you loose a lot of information.

I would like to offer a different opinion to Graeme's:
You can read XDS_ASCII.HKL into pointless and aimless and provide aimless with 
the option 'onlymerge'. This way aimless merges the data, but it does not 
rescale them.

XDS performs a couple of corrections in the CORRECT step, the output of which 
is XDS_ASCII.HKL. And while XDS is extremely well documented, I am not sure 
aimless takes into account how XDS treats the data. I would therefore trust the 
step of scaling to the same author and continue with XDS_ASCII.HKL.

Best,
Tim


On Monday, November 21, 2016 11:37:15 AM Nishant Varshney wrote:
> Dear All,
> 
> Just to understand more, the XDS_ASCII.HKL file generated after 
> running XDS contains scaled and merged reflections?
> 
> Moreover, what happens exactly, if you use XDS_ASCII.HKL file in 
> AIMLESS instead of INTEGRATE.HKL file??
> 
> I ran AIMLESS separately, one using already scaled XDS_ASCII.HKL and 
> another using INTEGRATE.HKL and I found that in the run using 
> XDS_ASCII.HKL little lesser total number of observation but marginally better 
> statistics.
> 
> Thanks
> Nishant
> 
> On Thu, Nov 17, 2016 at 10:08 PM, Andreas Forster 
> <docandr...@gmail.com>
> 
> wrote:
> > Dear Wei,
> > 
> > if you process your data with XDS, the best is probably to do the 
> > scaling in XDS (CORRECT) and be done with it.  If you want to use 
> > Aimless for merging, you can turn off scaling with the ONLYMERGE 
> > keyword or use SCALES CONSTANT.
> > 
> > All best.
> > 
> > 
> > Andreas
> > 
> > On Thu, Nov 17, 2016 at 9:40 PM, Wei Wang <ww2...@columbia.edu> wrote:
> >> Hi,
> >> 
> >> Is there a way to let xds_par use less than all processors/threads 
> >> on the machine? Sometimes I would like to process something else 
> >> while XDS is running.
> >> 
> >> Another question is related to the scaling procedure. My 
> >> understanding is that the XDS already does the scaling during 
> >> correction. So if I follow the XDS-Aimless route, then probably I 
> >> should let Aimless do "skip scaling and only merge"? Please 
> >> elucidate me on this issue.
> >> 
> >> Regards,
> >> 
> >> Wei
> 
> --
> Dr. Nishant Kumar Varshney,
> IISc-ICTP Fellow
> XRD2 Beamline, Elettra-Sincrotrone,
> In Area Science Park,
> Basovizza, S.S. 14, Km 163,5,
> 34012 Trieste, Italy
> +39-040-375 8737 (office ESP4 P1 031)
> +39-040-375-8435 (XRD2 beamline)
> +39 3318809798 (Mobile)
--
--
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
Principal Investigator
Biology and Chemistry
OFLC/102
CH-5232 Villigen PSI

Phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A


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Re: [ccp4bb] XDS questions

[Tim Gruene]

Dear Nishant,

XDS_ASCII.HKL contains corrected, scaled, but not merged reflections. 
You can specifically ask XDS to merge your data, but I would not do so unless 
really necessary - you loose a lot of information.

I would like to offer a different opinion to Graeme's:
You can read XDS_ASCII.HKL into pointless and aimless and provide aimless with 
the option 'onlymerge'. This way aimless merges the data, but it does not 
rescale them.

XDS performs a couple of corrections in the CORRECT step, the output of which 
is XDS_ASCII.HKL. And while XDS is extremely well documented, I am not sure 
aimless takes into account how XDS treats the data. I would therefore trust 
the step of scaling to the same author and continue with XDS_ASCII.HKL.

Best,
Tim


On Monday, November 21, 2016 11:37:15 AM Nishant Varshney wrote:
> Dear All,
> 
> Just to understand more, the XDS_ASCII.HKL file generated after running XDS
> contains scaled and merged reflections?
> 
> Moreover, what happens exactly, if you use XDS_ASCII.HKL file in AIMLESS
> instead of INTEGRATE.HKL file??
> 
> I ran AIMLESS separately, one using already scaled XDS_ASCII.HKL and
> another using INTEGRATE.HKL and I found that in the run using XDS_ASCII.HKL
> little lesser total number of observation but marginally better statistics.
> 
> Thanks
> Nishant
> 
> On Thu, Nov 17, 2016 at 10:08 PM, Andreas Forster 
> 
> wrote:
> > Dear Wei,
> > 
> > if you process your data with XDS, the best is probably to do the scaling
> > in XDS (CORRECT) and be done with it.  If you want to use Aimless for
> > merging, you can turn off scaling with the ONLYMERGE keyword or use SCALES
> > CONSTANT.
> > 
> > All best.
> > 
> > 
> > Andreas
> > 
> > On Thu, Nov 17, 2016 at 9:40 PM, Wei Wang  wrote:
> >> Hi,
> >> 
> >> Is there a way to let xds_par use less than all processors/threads on the
> >> machine? Sometimes I would like to process something else while XDS is
> >> running.
> >> 
> >> Another question is related to the scaling procedure. My understanding is
> >> that the XDS already does the scaling during correction. So if I follow
> >> the
> >> XDS-Aimless route, then probably I should let Aimless do "skip scaling
> >> and
> >> only merge"? Please elucidate me on this issue.
> >> 
> >> Regards,
> >> 
> >> Wei
> 
> --
> Dr. Nishant Kumar Varshney,
> IISc-ICTP Fellow
> XRD2 Beamline, Elettra-Sincrotrone,
> In Area Science Park,
> Basovizza, S.S. 14, Km 163,5,
> 34012 Trieste, Italy
> +39-040-375 8737 (office ESP4 P1 031)
> +39-040-375-8435 (XRD2 beamline)
> +39 3318809798 (Mobile)
-- 
--
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
Principal Investigator
Biology and Chemistry
OFLC/102
CH-5232 Villigen PSI

Phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A



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Re: [ccp4bb] XDS questions

[Graeme Winter]

Dear Nishant

Your statistics will be better taking XDS_ASCII because the scaling has been 
performed twice i.e. you have had two goes (with different models) of reducing 
the differences between reflections. This will *always* make the R factors etc 
smaller – whether the data are better or more true is a matter for debate!

Personally I would recommend not doing this however I gather that there are 
folks who feel scaling twice is a good thing, so your mileage may vary. If 
differences are marginal I would suggest taking the most simply treated data 
i.e. INTEGRATE.HKL -> aimless

Best wishes Graeme

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nishant 
Varshney
Sent: 21 November 2016 10:37
To: ccp4bb
Subject: Re: [ccp4bb] XDS questions

Dear All,

Just to understand more, the XDS_ASCII.HKL file generated after running XDS 
contains scaled and merged reflections?

Moreover, what happens exactly, if you use XDS_ASCII.HKL file in AIMLESS 
instead of INTEGRATE.HKL file??

I ran AIMLESS separately, one using already scaled XDS_ASCII.HKL and another 
using INTEGRATE.HKL and I found that in the run using XDS_ASCII.HKL little 
lesser total number of observation but marginally better statistics.

Thanks
Nishant

On Thu, Nov 17, 2016 at 10:08 PM, Andreas Forster 
<docandr...@gmail.com<mailto:docandr...@gmail.com>> wrote:
Dear Wei,

if you process your data with XDS, the best is probably to do the scaling in 
XDS (CORRECT) and be done with it.  If you want to use Aimless for merging, you 
can turn off scaling with the ONLYMERGE keyword or use SCALES CONSTANT.

All best.


Andreas




On Thu, Nov 17, 2016 at 9:40 PM, Wei Wang 
<ww2...@columbia.edu<mailto:ww2...@columbia.edu>> wrote:
Hi,
Is there a way to let xds_par use less than all processors/threads on the 
machine? Sometimes I would like to process something else while XDS is running.
Another question is related to the scaling procedure. My understanding is that 
the XDS already does the scaling during correction. So if I follow the 
XDS-Aimless route, then probably I should let Aimless do "skip scaling and only 
merge"? Please elucidate me on this issue.
Regards,
Wei




--
Dr. Nishant Kumar Varshney,
IISc-ICTP Fellow
XRD2 Beamline, Elettra-Sincrotrone,
In Area Science Park,
Basovizza, S.S. 14, Km 163,5,
34012 Trieste, Italy
+39-040-375 8737 (office ESP4 P1 031)
+39-040-375-8435 (XRD2 beamline)
+39 3318809798 (Mobile)

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Re: [ccp4bb] XDS questions

[Nishant Varshney]

Dear All,

Just to understand more, the XDS_ASCII.HKL file generated after running XDS
contains scaled and merged reflections?

Moreover, what happens exactly, if you use XDS_ASCII.HKL file in AIMLESS
instead of INTEGRATE.HKL file??

I ran AIMLESS separately, one using already scaled XDS_ASCII.HKL and
another using INTEGRATE.HKL and I found that in the run using XDS_ASCII.HKL
little lesser total number of observation but marginally better statistics.

Thanks
Nishant

On Thu, Nov 17, 2016 at 10:08 PM, Andreas Forster 
wrote:

> Dear Wei,
>
> if you process your data with XDS, the best is probably to do the scaling
> in XDS (CORRECT) and be done with it.  If you want to use Aimless for
> merging, you can turn off scaling with the ONLYMERGE keyword or use SCALES
> CONSTANT.
>
> All best.
>
>
> Andreas
>
>
>
>
> On Thu, Nov 17, 2016 at 9:40 PM, Wei Wang  wrote:
>
>> Hi,
>>
>> Is there a way to let xds_par use less than all processors/threads on the
>> machine? Sometimes I would like to process something else while XDS is
>> running.
>>
>> Another question is related to the scaling procedure. My understanding is
>> that the XDS already does the scaling during correction. So if I follow the
>> XDS-Aimless route, then probably I should let Aimless do "skip scaling and
>> only merge"? Please elucidate me on this issue.
>>
>> Regards,
>>
>> Wei
>>
>
>


-- 
Dr. Nishant Kumar Varshney,
IISc-ICTP Fellow
XRD2 Beamline, Elettra-Sincrotrone,
In Area Science Park,
Basovizza, S.S. 14, Km 163,5,
34012 Trieste, Italy
+39-040-375 8737 (office ESP4 P1 031)
+39-040-375-8435 (XRD2 beamline)
+39 3318809798 (Mobile)

Re: [ccp4bb] XDS questions

[Wei Wang]

Thanks everyone for answering the question!

Best,

Wei

On Thu, Nov 17, 2016 at 4:20 PM, Michael Martynowycz <
michael.martynow...@gmail.com> wrote:

> Wei,
>
> You can use the integrated integrated intensities only if you want to go
> the ccp4 route. Sort the integrated reflections, then scale and truncate
> them using:
>
> Pointless xdsin INTEGRATE.HKL hklout sorted.mtz
>
> Aimless hklin sorted.mtz hklout scaled.mtz
>
> Hope that helps.
>
> -Mike
>
> Sent from my iPhone
>
> On Nov 17, 2016, at 4:08 PM, Andreas Forster  > wrote:
>
> Dear Wei,
>
> if you process your data with XDS, the best is probably to do the scaling
> in XDS (CORRECT) and be done with it.  If you want to use Aimless for
> merging, you can turn off scaling with the ONLYMERGE keyword or use SCALES
> CONSTANT.
>
> All best.
>
>
> Andreas
>
>
>
>
> On Thu, Nov 17, 2016 at 9:40 PM, Wei Wang  wrote:
>
>> Hi,
>>
>> Is there a way to let xds_par use less than all processors/threads on the
>> machine? Sometimes I would like to process something else while XDS is
>> running.
>>
>> Another question is related to the scaling procedure. My understanding is
>> that the XDS already does the scaling during correction. So if I follow the
>> XDS-Aimless route, then probably I should let Aimless do "skip scaling and
>> only merge"? Please elucidate me on this issue.
>>
>> Regards,
>>
>> Wei
>>
>
>

Re: [ccp4bb] XDS questions

[Michael Martynowycz]

Wei,

You can use the integrated integrated intensities only if you want to go the 
ccp4 route. Sort the integrated reflections, then scale and truncate them using:

Pointless xdsin INTEGRATE.HKL hklout sorted.mtz

Aimless hklin sorted.mtz hklout scaled.mtz

Hope that helps.

-Mike

Sent from my iPhone

> On Nov 17, 2016, at 4:08 PM, Andreas Forster  wrote:
> 
> Dear Wei,
> 
> if you process your data with XDS, the best is probably to do the scaling in 
> XDS (CORRECT) and be done with it.  If you want to use Aimless for merging, 
> you can turn off scaling with the ONLYMERGE keyword or use SCALES CONSTANT.
> 
> All best.
> 
> 
> Andreas
> 
> 
>  
> 
>> On Thu, Nov 17, 2016 at 9:40 PM, Wei Wang  wrote:
>> Hi,
>> 
>> Is there a way to let xds_par use less than all processors/threads on the 
>> machine? Sometimes I would like to process something else while XDS is 
>> running.
>> 
>> Another question is related to the scaling procedure. My understanding is 
>> that the XDS already does the scaling during correction. So if I follow the 
>> XDS-Aimless route, then probably I should let Aimless do "skip scaling and 
>> only merge"? Please elucidate me on this issue.
>> 
>> Regards,
>> 
>> Wei
> 

Re: [ccp4bb] XDS questions

[Andreas Forster]

Dear Wei,

if you process your data with XDS, the best is probably to do the scaling
in XDS (CORRECT) and be done with it.  If you want to use Aimless for
merging, you can turn off scaling with the ONLYMERGE keyword or use SCALES
CONSTANT.

All best.


Andreas




On Thu, Nov 17, 2016 at 9:40 PM, Wei Wang  wrote:

> Hi,
>
> Is there a way to let xds_par use less than all processors/threads on the
> machine? Sometimes I would like to process something else while XDS is
> running.
>
> Another question is related to the scaling procedure. My understanding is
> that the XDS already does the scaling during correction. So if I follow the
> XDS-Aimless route, then probably I should let Aimless do "skip scaling and
> only merge"? Please elucidate me on this issue.
>
> Regards,
>
> Wei
>

Re: [ccp4bb] XDS questions

[Jim Fairman]

Wei,

The flag MAXIMUM_NUMBER_OF_PROCESSORS=

in XDS.INP should allow you to choose the number of processors you wish to
use.

Cheers, Jim

--
Jim Fairman
C: 1-240-479-6575

On Thu, Nov 17, 2016 at 12:40 PM, Wei Wang  wrote:

> Hi,
>
> Is there a way to let xds_par use less than all processors/threads on the
> machine? Sometimes I would like to process something else while XDS is
> running.
>
> Another question is related to the scaling procedure. My understanding is
> that the XDS already does the scaling during correction. So if I follow the
> XDS-Aimless route, then probably I should let Aimless do "skip scaling and
> only merge"? Please elucidate me on this issue.
>
> Regards,
>
> Wei
>

[ccp4bb] XDS questions

[Wei Wang]

Hi,

Is there a way to let xds_par use less than all processors/threads on the
machine? Sometimes I would like to process something else while XDS is
running.

Another question is related to the scaling procedure. My understanding is
that the XDS already does the scaling during correction. So if I follow the
XDS-Aimless route, then probably I should let Aimless do "skip scaling and
only merge"? Please elucidate me on this issue.

Regards,

Wei