[ccp4bb] Cryo-EM in Australia: group-leader and staff-scientist positions

[Antoine van Oijen]

Dear cryo-EM community,


Two continuing, full time positions are available at the University of 
Wollongong in Australia:


Staff Scientist (Cryo-Electron Microscopy):

http://uow.employment.com.au/jobs/Staff-Scientist--Cryo-Electron-Microscopy-/2487



Senior Lecturer / Associate Professor (Cryo-Electron Microscopy):

http://uow.employment.com.au/jobs/Senior-Lecturer---Associate-Professor/2488


The University of Wollongong is a young, research-focused university on the 
coast of south eastern Australia, an hour from Sydney and surrounded by natural 
beauty. We are looking for technically skilled cryo-electron microscopists with 
experience in structural biology to play a key role in establishing a 
world-class cryo-electron microscopy research group and facility.


Our University is investing $80 million in the establishment of a 
multidisciplinary research institute, Molecular Horizons, focused on the 
visualisation of the molecular mechanisms of life. By co-locating talented 
researchers with backgrounds in the physical, chemical and biological sciences 
and by providing them with cutting-edge infrastructure, the University is 
committed to making an impact in the molecular life sciences. Our initial 
investment in cryo-EM infrastructure includes a Talos Arctica and a Titan Krios.


Best wishes,


Antoine van Oijen

University of Wollongong

vanoi...@uow.edu.au

Re: [ccp4bb] local coordinate uncertainty / SFCHECK questions

[Ethan Merritt]

On Monday, 21 November 2016 11:53:22 PM Seok-Yong Lee wrote:
> Hi All,
> 
> We have recently solved several structures of a membrane protein in slightly 
> different conformations at low resolutions (3.9-4.2 A). We would like to see 
> that these structures reflect truly different conformations and to what 
> extent these structures are discernible. To answer this question, we would 
> need to estimate local and global coordinate uncertainty of these structures 
> to see if the local/global conformational differences of the structures are 
> bigger than the local/global coordinate uncertainty.
> 
> I am wondering if there is any good way/program to show local coordinate 
> uncertainty. I found that using SFCHECK I can get (i) amplitude of 
> displacement of atom from electron density and (ii) correlation coefficient 
> per residue. I have following questions.
> 
>   1)Can we use this amplitude of displacement as local 
> coordinate uncertainly? If not, is there a way to use as this displacement 
> amplitude to get an estimate of the local coordinate error?
> 
>   2)The output regarding this plot in SFCHECK is somewhat difficult 
> to understand, as it shows a bar graph with multiples of sigma per residue. 
> What does it mean by those residues with no sigma? Do these residues have too 
> much or too less errors?
> 
>   3)Is there a way to convert the output as a text file so that I can 
> plot it myself?
> 
>   4)Any recommendation with other programs that can produce local 
> coordinate uncertainty per residue?
> 
>   Any advice would be greatly appreciated.  Thank you in advance. 

I don't think that the uncertainty/error in individual coordinates is a good 
way to
describe or quantify the existence of "truly different conformations", unless 
what
you really meant is "different rotamers" or some other very local property.

Nevertheless, if you want to estimate coordinate error from the available 
refined
quantities, I suggest looking at
Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583–601.
This paper describes an empirical estimate DPI that seems close to what you
are asking for.  A further empirical simplification was suggest by David Blow
Acta Cryst. (2002). D58, 792-797 
https://doi.org/10.1107/S0907444902003931


If the intent is to ask whether a conformation resulting from final refinement 
against
data from one crystal is compatible with the data from a different crystal, I 
suspect
the most powerful and convincing test is to simply try it.  Transfer the 
relevant
piece of the model from crystal A into your working model for crystal B, refine 
a bit
(maybe only B factors or TLS), and see whether the resulting R/Rfree value are 
different
from those you previously had for the crystal B model.   You could then try the
complementary excercise by placing the original model from crystal B into the
context of the current model and data from crystal A.


Ethan Merritt

-- 
mail:   Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

[ccp4bb] local coordinate uncertainty / SFCHECK questions

[Seok-Yong Lee]

Hi All,

We have recently solved several structures of a membrane protein in slightly 
different conformations at low resolutions (3.9-4.2 A). We would like to see 
that these structures reflect truly different conformations and to what extent 
these structures are discernible. To answer this question, we would need to 
estimate local and global coordinate uncertainty of these structures to see if 
the local/global conformational differences of the structures are bigger than 
the local/global coordinate uncertainty.

I am wondering if there is any good way/program to show local coordinate 
uncertainty. I found that using SFCHECK I can get (i) amplitude of displacement 
of atom from electron density and (ii) correlation coefficient per residue. I 
have following questions.

1)Can we use this amplitude of displacement as local coordinate 
uncertainly? If not, is there a way to use as this displacement amplitude to 
get an estimate of the local coordinate error?

2)The output regarding this plot in SFCHECK is somewhat difficult 
to understand, as it shows a bar graph with multiples of sigma per residue. 
What does it mean by those residues with no sigma? Do these residues have too 
much or too less errors?

3)Is there a way to convert the output as a text file so that I can 
plot it myself?

4)Any recommendation with other programs that can produce local 
coordinate uncertainty per residue?

Any advice would be greatly appreciated.  Thank you in advance. 


All the best,

Seok-Yong

Associate Professor of Biochemistry
Duke University School of Medicine
USA

Re: [ccp4bb] Inclusion Bodies

[Amit Meir]

Hi,
Well, sometimes proteins don't express even though they are from the same 
family and their "cousin" behaved very well. 
I found the followings helpful:
1. forget about the concept "this special strain *should* work because it is a 
Rosseta/ pLysS etc." Sometimes it's a long mRNA, sometimes a rare codon, 
sometimes it's an additional disulfide bond. If you are happy with the 
inclusion bodies protocol (and you know your protein is active later), just 
scan additional strains that you have in the lab (I like the BL21 DE3 BLR, 
which are specialized for long mRNA, but I found them useful in "regular" genes 
as well).
2. Scan "high" temperature (37C) in different time scales - maybe your cells 
need overnight expression instead of 3/4/5hrs? Or maybe the protein undergoes 
degradation overnight, so it is better to grow it for 3hrs only?
3. Change the medium to 2XYT or TB, and increase IPTG concentration if you work 
with a pET vector.
4. Try inducing in OD=1 instead of 0.6.
5. Add glucose (0.1%, but you can optimize) to the media to repress leakiness 
of a toxic protein.
6. Look for "autoinduced media" protocol. The additives there can make a 
difference between none to a few milligrams/liter.
7. Some mutations occurred in the expression vector. Re-clone to a fresh 
plasmid (same/ another pET vector/ vector with a different inducer, e.g. 
arabinose).
8. From my experience, sometimes E.coli get along with non-optimized eukaryotic 
genes even better than the optimized sequence. I would go to additional 
optimization as one of the last options.
9. A mammalian homolog? Or try expressing in lower temperature (17/20/23C) to 
get a soluble protein? (I know sometimes this is not an option).


A starting protocol would be several different strains (everything you and your 
neighbors have in the labs, basically), in 2XYT + 0.1% glucose, induction in 
0.5-1mM IPTG, then grow 3hrs/5hrs/overnight in 37C. Alternatively, 
2XYT+autoinduced media + 0.1-0.2mM IPTG when OD=0.6 to "boost" expression even 
further (and different times as well). 

Good luck :)

Amit




Dr. Amit Meir
Institute of Structural and Molecular Biology
Department of Biological Sciences
Birkbeck College
Malet Street
London WC1E 7HX
UK 

[ccp4bb] Inclusion Bodies

[D Bonsor]

We have been expressing a family of human proteins as inclusion bodies in E. 
coli, which we can be refolded and crystallized. However, three members show no 
expression either as inclusion bodies or as soluble proteins. 

The genes were ligated into the pE21d vector with either a His-tag or no 
His-tag.
The genes were codon optimized for E coli. 
They are expressed in BL21(DE3), though I have tried the different strains for 
the non-expressing protein (e.g. Walker cells, Rosetta).

What are the causes for no expression. I am guessing something to do with the 
mRNA. Should I try unoptimized/semi-optimized codons? Or is there something I 
could add to the media to aid in expression of the protein into inclusion 
bodies? Any suggestions?

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  
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 
 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

[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
>
>

[ccp4bb] facility manager position X-ray crystallography and biophysics

[I.Vetter]

** X-ray crystallography and biophysics facility manager **

The Max Planck Institute of Molecular Physiology, Dortmund, Germany, is 
looking for a X-ray crystallography and biophysics facility manager.


The ideal candidate for this position should have a PhD degree in 
macromolecular crystallography and biophysics, as well as strong 
technical and scientific skills, with several years of post-doctoral 
experience.


Responsibilities:
- maintenance and operation of X-ray crystallography equipment, including
   crystallization and visualization robots, X-ray generators and detectors
- user support in the collection and processing of X-ray diffraction 
data, both

   locally and at synchrotrons
-  maintenance of crystallographic software (with support of our IT 
department)
 - user support in crystal structure determination, either directly or 
through

   supervision of students and postdocs
-  contributions to the maintenance and operation of biophysical equipment
   (e.g. ITC, biolayer interferometry, stopped-flow- and CD 
spectroscopy, analytical
   ultracentrifugation) as well as user support in kinetic methods and 
biophysical

   data evaluation.

Payment depends on personal conditions and qualifications according to 
the directives of TVöD. Social benefits correspond to those of the 
public service. After an initial first 2-year appointment, the 
appointment has the potential to become permanent.


Applications should include a letter of motivation, curriculum vitae, 
and the names of three referees. The application deadline is January 15, 
2017. Please send applications by email to Mrs. Antje Peukert 
(antje.peuk...@mpi-dortmund.mpg.de) using ‘X-ray crystallography 
Facility Manager’ as subject.


Please see the full job profile at the following link:
https://www.mpi-dortmund.mpg.de/1880044/stellenangebote

--
Ingrid Vetter
Max-Planck-Institut fuer molekulare Physiologie, Otto-Hahn-Str. 11
D-44227 Dortmund, Germany, Ph: +49-231-1332737, Fax: +49-231-1332797

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 
> 
> 
> 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

[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 
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 
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)