Re: [ccp4bb] aimless outputs mean intensities for friedel pairs

[Kevin Jude]

I've had two more helpful responses to this off-list. My crystal is P43212,
so there are large swaths of centric reflections that I was looking at. And
indeed, {18,1,1} is not the first reflection with anomalous differences if
I look more carefully. Different sorting of the outputs by phenix and
aimless masked that result for me. Thanks to those who responded for the
help and for the chance to dive into the International Tables.

--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431


On Mon, Mar 30, 2020 at 8:20 PM Kevin Jude  wrote:

> Thanks Reza. Changing the rejection criteria didn't have any effect, but I
> tried xdsconv and got what looked like the same result - ie, DANO = 0. That
> got me started looking at more reflections, and if I make it all the way
> down to {18,1,1) there's suddenly a switch and anomalous differences are
> present for the remaining reflections (which are sorted by increasing h, k,
> l). It turns out the same thing was happening in aimless. This seems
> strange since it isn't in accord with what I saw in CORRECT.LP, namely
> significant anomalous signal in the lower resolution shells, and it
> couldn't be explained away by a wedge of missing Friedel mates.
>
> Finally, I decided to see what happens if I used Phenix's reflection file
> editor to convert XDS_ASCII.HKL to mtz, and. . .it seems to work just fine.
> So I suppose my problem of getting from here to there is solved, though the
> puzzle remains.
>
> --
> Kevin Jude, PhD
> Structural Biology Research Specialist, Garcia Lab
> Howard Hughes Medical Institute
> Stanford University School of Medicine
> Beckman B177, 279 Campus Drive, Stanford CA 94305
> Phone: (650) 723-6431
>
>
> On Mon, Mar 30, 2020 at 6:51 PM Rezaul Karim  wrote:
>
>> Hi Kevin,
>> Just a thought, guidance is left to the experts. Since the aimless
>> reports significant anomalous signal default anomalous rejection criteria
>> most likely is too strict for this run. Changing the default "reject 6
>> all -8" value to loosen the rejection criteria might give some clue
>> whether this is the case. Another alternative is xdsconv. Any advantage of
>> using pointless and aimless instead of xdsconv for your purpose?
>>
>> Thanks,
>> Reza
>>
>> Md. Rezaul Karim (Reza)
>> Ph.D. candidate, PhD Program in Integrated Biomedical Sciences
>> Department of Molecular Medicine
>> Morsani College of Medicine
>> *University** of South Florida*
>> Schonbrunn lab, Moffitt Cancer Center
>> Tampa, FL
>> E-mail: reza...@yahoo.com, rez...@usf.edu
>> Phone: +1-954-937-8487
>> ORCID: https://orcid.org/-0002-0424-127X
>> LinkedIn: https://www.linkedin.com/in/reza092
>>
>>
>>
>> On Monday, March 30, 2020, 7:12:33 PM EDT, Kevin Jude 
>> wrote:
>>
>>
>> Hi all,
>> I am trying to merge and convert reflections from XDS_ASCII.HKL to mtz
>> via pointless and aimless. Everything looks good through pointless, as far
>> as I understand:
>> xds reports significant anomalous correlation in CORRECT.LP
>>
>> Inspection of the mtz output from pointless shows that (+) and (-)
>> reflections are recorded using separate ISYM flags (column 4):
>>
>>  LIST OF REFLECTIONS
>>  ===
>>
>> 0   0   71   902  1.68  1.43  0.91   1230.80
>>1155.20423.20  0.04  0.00
>>
>> 0   0   72 2  1.21  1.68  0.90   1231.40
>>1155.10243.20  0.04  0.00
>>
>> 0   0   81   902 88.18  3.70  1.00   1230.70
>>1139.50423.36  0.04  0.00
>>
>> 0   0   82 2 85.93  3.86  0.99   1231.50
>>1139.30243.36  0.04  0.00
>> ...
>>
>> But when I run aimless as:
>>
>> $ aimless hklin ds5_5_E1_pointless.mtz hklout ds5_5_E1_aimless.mtz
>> <> onlymerge
>> anom on
>> reso 2.5
>> end
>> eof
>>
>> the output mtz file has identical values for IMEAN, I(+), and I(-),
>> despite reporting in the logfile that:
>> Anomalous flag switched ON in input, strong anomalous signal found
>> Estimate of the resolution limit for a significant anomalous signal
>>  3.93A, from the point where the fit drops below threshold 0.15
>>
>> Can anybody provide me with some guidance?
>>
>> Best wishes
>> Kevin
>>
>> --
>> Kevin Jude, PhD
>> Structural Biology Research Specialist, Garcia Lab
>> Howard Hughes Medical Institute
>> Stanford University School of Medicine
>> Beckman B177, 279 Campus Drive, Stanford CA 94305
>> Phone: (650) 723-6431
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>



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Re: [ccp4bb] aimless outputs mean intensities for friedel pairs

[Kevin Jude]

Thanks Reza. Changing the rejection criteria didn't have any effect, but I
tried xdsconv and got what looked like the same result - ie, DANO = 0. That
got me started looking at more reflections, and if I make it all the way
down to {18,1,1) there's suddenly a switch and anomalous differences are
present for the remaining reflections (which are sorted by increasing h, k,
l). It turns out the same thing was happening in aimless. This seems
strange since it isn't in accord with what I saw in CORRECT.LP, namely
significant anomalous signal in the lower resolution shells, and it
couldn't be explained away by a wedge of missing Friedel mates.

Finally, I decided to see what happens if I used Phenix's reflection file
editor to convert XDS_ASCII.HKL to mtz, and. . .it seems to work just fine.
So I suppose my problem of getting from here to there is solved, though the
puzzle remains.

--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431


On Mon, Mar 30, 2020 at 6:51 PM Rezaul Karim  wrote:

> Hi Kevin,
> Just a thought, guidance is left to the experts. Since the aimless reports
> significant anomalous signal default anomalous rejection criteria most
> likely is too strict for this run. Changing the default "reject 6 all -8"
> value to loosen the rejection criteria might give some clue whether this
> is the case. Another alternative is xdsconv. Any advantage of using
> pointless and aimless instead of xdsconv for your purpose?
>
> Thanks,
> Reza
>
> Md. Rezaul Karim (Reza)
> Ph.D. candidate, PhD Program in Integrated Biomedical Sciences
> Department of Molecular Medicine
> Morsani College of Medicine
> *University** of South Florida*
> Schonbrunn lab, Moffitt Cancer Center
> Tampa, FL
> E-mail: reza...@yahoo.com, rez...@usf.edu
> Phone: +1-954-937-8487
> ORCID: https://orcid.org/-0002-0424-127X
> LinkedIn: https://www.linkedin.com/in/reza092
>
>
>
> On Monday, March 30, 2020, 7:12:33 PM EDT, Kevin Jude 
> wrote:
>
>
> Hi all,
> I am trying to merge and convert reflections from XDS_ASCII.HKL to mtz via
> pointless and aimless. Everything looks good through pointless, as far as I
> understand:
> xds reports significant anomalous correlation in CORRECT.LP
>
> Inspection of the mtz output from pointless shows that (+) and (-)
> reflections are recorded using separate ISYM flags (column 4):
>
>  LIST OF REFLECTIONS
>  ===
>
> 0   0   71   902  1.68  1.43  0.91   1230.80
>1155.20423.20  0.04  0.00
>
> 0   0   72 2  1.21  1.68  0.90   1231.40
>1155.10243.20  0.04  0.00
>
> 0   0   81   902 88.18  3.70  1.00   1230.70
>1139.50423.36  0.04  0.00
>
> 0   0   82 2 85.93  3.86  0.99   1231.50
>1139.30243.36  0.04  0.00
> ...
>
> But when I run aimless as:
>
> $ aimless hklin ds5_5_E1_pointless.mtz hklout ds5_5_E1_aimless.mtz
> < onlymerge
> anom on
> reso 2.5
> end
> eof
>
> the output mtz file has identical values for IMEAN, I(+), and I(-),
> despite reporting in the logfile that:
> Anomalous flag switched ON in input, strong anomalous signal found
> Estimate of the resolution limit for a significant anomalous signal
>  3.93A, from the point where the fit drops below threshold 0.15
>
> Can anybody provide me with some guidance?
>
> Best wishes
> Kevin
>
> --
> Kevin Jude, PhD
> Structural Biology Research Specialist, Garcia Lab
> Howard Hughes Medical Institute
> Stanford University School of Medicine
> Beckman B177, 279 Campus Drive, Stanford CA 94305
> Phone: (650) 723-6431
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] aimless outputs mean intensities for friedel pairs

[Rezaul Karim]

Hi Kevin,Just a thought, guidance is left to the experts. Since the aimless 
reports significant anomalous signal default anomalous rejection criteria most 
likely is too strict for this run. Changing the default "reject 6 all -8" value 
to loosen the rejection criteria might give some clue whether this is the case. 
Another alternative is xdsconv. Any advantage of using pointless and aimless 
instead of xdsconv for your purpose?
Thanks,Reza

Md. Rezaul Karim (Reza)
Ph.D. candidate, PhD Program in Integrated Biomedical SciencesDepartment of 
Molecular MedicineMorsani College of MedicineUniversity of South Florida
Schonbrunn lab, Moffitt Cancer CenterTampa, FLE-mail: reza...@yahoo.com, 
rezaul@usf.eduPhone: +1-954-937-8487ORCID: https://orcid.org/-0002-0424-127X
LinkedIn: https://www.linkedin.com/in/reza092
 

On Monday, March 30, 2020, 7:12:33 PM EDT, Kevin Jude  
wrote:  
 
 Hi all,I am trying to merge and convert reflections from XDS_ASCII.HKL to mtz 
via pointless and aimless. Everything looks good through pointless, as far as I 
understand:xds reports significant anomalous correlation in CORRECT.LP
Inspection of the mtz output from pointless shows that (+) and (-) reflections 
are recorded using separate ISYM flags (column 4):
 LIST OF REFLECTIONS
 ===

    0   0   7    1   902      1.68      1.43      0.91   1230.80
                           1155.20    423.20      0.04      0.00

    0   0   7    2     2      1.21      1.68      0.90   1231.40
                           1155.10    243.20      0.04      0.00

    0   0   8    1   902     88.18      3.70      1.00   1230.70
                           1139.50    423.36      0.04      0.00

    0   0   8    2     2     85.93      3.86      0.99   1231.50
                           1139.30    243.36      0.04      0.00...
But when I run aimless as:
$ aimless hklin ds5_5_E1_pointless.mtz hklout ds5_5_E1_aimless.mtz 

[ccp4bb] aimless outputs mean intensities for friedel pairs

[Kevin Jude]

Hi all,
I am trying to merge and convert reflections from XDS_ASCII.HKL to mtz via
pointless and aimless. Everything looks good through pointless, as far as I
understand:
xds reports significant anomalous correlation in CORRECT.LP

Inspection of the mtz output from pointless shows that (+) and (-)
reflections are recorded using separate ISYM flags (column 4):

 LIST OF REFLECTIONS
 ===

0   0   71   902  1.68  1.43  0.91   1230.80
   1155.20423.20  0.04  0.00

0   0   72 2  1.21  1.68  0.90   1231.40
   1155.10243.20  0.04  0.00

0   0   81   902 88.18  3.70  1.00   1230.70
   1139.50423.36  0.04  0.00

0   0   82 2 85.93  3.86  0.99   1231.50
   1139.30243.36  0.04  0.00
...

But when I run aimless as:

$ aimless hklin ds5_5_E1_pointless.mtz hklout ds5_5_E1_aimless.mtz

[ccp4bb] Beamtime @ SLS

[Wang Meitian (PSI)]

Dear SLS users,

We hope that this email finds you well and healthy in these uncertain times. We 
would like to update you on the SLS operational status:


  *   We offer general beamtime to keep the research going for the MX community 
in both academia and industry.
  *   We have canceled the Easter shutdown and will operate the SLS five days a 
week until the end of May (Monday for machine startup, and Tuesday - Saturday 
morning for user operation).
  *   We operate the three SLS MX beamlines in 100 % remote mode (i.e., no 
external users allowed on-site).
  *   We cover Dewar shipping costs for European academic users.

  *   The Call for the beamtime proposal for the second half of 2020 is due by 
April 15th.

We look forward to receiving your samples and proposals at the SLS!

Best regards
The MX group at the SLS







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[ccp4bb] off-topic: work opportunities at Enko

[Artem Evdokimov]

Hello!

Sorry (not sorry) for the off-topic post. We have a few jobs posted and I'd
like to re-post them here.

Please see the link for full descriptions >>>
https://www.enkochem.com/careers-enko

-Scientist, Structural Biology & Protein Chemistry
-Senior Scientist, Protein Target Discovery
-Scientist, Enzymology & Protein Chemistry
-Enzymology Research Associate

(may be less relevant to this crowd - below)

-Regulatory Toxicologist
-Analytical Scientist, Biology
-Greenhouse Technician, Biology
-Greenhouse Manager, Biology

Key points:

(1) if you'd like to learn more, informally - please feel free to write me
directly
(2) if you'd like to apply, please write to *care...@enkochem.com*


Artem

VP of Biochemistry/Molecular Biology
Enko



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[ccp4bb] PRACE fights against COVID-19 - fast track call for proposals is open!

[David Waterman]

Posted on behalf of Dr. Marc Baaden:

Dear colleagues,

the Partnership for Advanced Computing in Europe (PRACE) is welcoming
> project proposals requesting computing resources to contribute to the
> mitigation of the impact of the COVID-19 pandemic.
> This call for proposals will follow a fast track review process to provide
> swift feedback to the applicants.
> This call is open until further notice. Applications are evaluated within
> one week and start as soon as possible if awarded.
>
> Please find full details of the call here:
> https://prace-ri.eu/prace-support-to-mitigate-impact-of-covid-19-pandemic/
> <
> https://prace-ri.eu/prace-support-to-mitigate-impact-of-covid-19-pandemic/
> >
>
> Best regards,
> Marc
> --
>  Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
>  mailto:baa...@smplinux.de  -  http://www.baaden.ibpc.fr
>  FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217



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Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Dear all,

John - I sent off list a PDB / DOI map over the weekend

Some rough edges have now been polished however the code is currently not 
_really_ fit for publication. That said, if any other facilities would like to 
get in touch for information about how to do this please do - I would hate to 
see people reinventing the wheel.

Right now I have tools for

 - creating uploads from a collection of files & some metadata
 - updating published records e.g. changing keywords or … fixing typos
 - searching zenodo programmatically e.g. to generate the DOI / PDB reference 
above

So if anyone is interested please drop me a line off list

All the best Graeme

On 28 Mar 2020, at 06:12, Winter, Graeme (DLSLtd,RAL,LSCI) 
mailto:graeme.win...@diamond.ac.uk>> wrote:

Hi John,

Sure, happy to do this, just as soon as I figure how to do this automatically 
;-)

Thank you Gerard for your kind words - as people will note there are a couple 
of rough edges at the moment (as illustrated with typos) - however once these 
are tidied up I’ll circulate the location of the code and dependencies for the 
upload so other facilities can follow suit.

If people find any issues with the uploads then please get in touch (off list)

Best wishes Graeme




On 27 Mar 2020, at 19:56, John Berrisford 
mailto:j...@ebi.ac.uk>> wrote:

HI

This is great news.

Can you let us at the PDB know the DOI's for each dataset so that we can 
associate the raw images with the PDB entry.  We will be able to then show 
links to the raw images from PDB entry pages so that everyone can find them.

Many thanks

John


John Berrisford
PDBe
+44 1223 492529
European Bioinformatics Institute (EMBL-EBI) European Molecular Biology 
Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD 
UK
https://www.pdbe.org
[Facebook][Twitter]
On Mar 27 2020, at 7:26 pm, Gerard Bricogne 
mailto:g...@globalphasing.com>> wrote:
Dear all, It is a pleasure to be able to end the (GMT) week by calling for a 
huge round of applause for the Diamond team, who this afternoon started 
uploading a large collection of sets of raw diffraction images (77 as we write 
but the upload is still ongoing) for PDB entries that were released two days 
ago. Special thanks to Graeme Winter who organised the upload to Zenodo. The 
datasets are collectively accessible via the following link: 
https://zenodo.org/search?page=1=20=keywords:%22SARS-CoV-2%20main%20protease%22
 Graeme asked that "major kudos [be given] to Zenodo developers who have been 
very responsive with helping us do automated downloads". Happy scrutiny and 
reprocessing of these datasets, and re-refinement of the associated structures, 
to all hard-core MX addicts! With best wishes, Clemens & Gerard. -- On Thu, Mar 
19, 2020 at 10:00:11AM +, John Berrisford wrote: > Dear all > > The wwPDB 
OneDep system allows depositors to provide DOIs of raw > diffraction images 
during deposition to the PDB and once again > encourages depositors to provide 
a DOI for raw images when they have > submitted. > > Out of the 9665 X-ray 
entries that were released in 2019 we have DOI's > for raw images in 205 of 
these entries. > > We would encourage depositors to provide the DOI for their 
raw images > when they are available. > > Regards > > John > > > On Mar 19 
2020, at 9:48 am, Joel Sussman wrote: > > > 19-Mar-2020 > > Dear Loes, Peter, 
Clemens & Gerard, > > I concur that it is crucial to preserve the original 
diffraction data > > and make it available to anyone who would like to use it. 
> > As an example, please see the very recent paper by  > > Nachon et al 
(2020). "A second look at the crystal structures of > > Drosophila melanogaster 
acetylcholinesterase in complex with tacrine > > derivatives provides Insights 
concerning catalytic intermediates and > > the design of specific insecticides" 
Molecules 25 pii: E1198  > > [https://www.ncbi.nlm.nih.gov/pubmed/32155891]. > 
> The study reexamines the original data, with modern software tools, > > the 
original data of a paper we published in 2000 (~20 years ago) and > > revealed 
features that had not been noticed. Specifically  > > 1) previously unmodeled 
density in the native active site can be > > interpreted as stable acetylation 
of the catalytic serine.  > > 2) Similarly, a strong density in the DmAChE/ZA 
complex, originally > > attributed to a sulfate ion, is better interpreted as a 
small molecule > > that is covalently bound. The complex is reminiscent of the 
> > carboxylate/BChE complexes observed in crystal structures of hBChE > > 
[Brazzolotto et al, 2012; Nicolet et al, 2003], and demonstrates the > > 
remarkable ability of ChEs to stabilize covalent complexes with 

[ccp4bb] Postdoc position, Sugar Transporting Membrane Proteins (Denmark), repost

[Bjørn Panyella Pedersen]

Dear colleagues,
Repost of our postdoc position. Deadline is in 3 days.
Please pass this along any one who might be interested. Thanks!
/Bjørn


Postdoctoral position in Structure of Sugar Transporting Membrane Proteins at 
Aarhus University, Denmark.

online posting:
http://tiny.cc/MBG_postdoc

We are looking for a highly skilled and motivated postdoc with an interest in 
working on sugar transporting membrane transporters and preferably with a 
proven track record in the area of structural and/or functional analysis of 
membrane proteins.

The position will be open from summer 2020, but starting date is negotiable. 
Funding is available for at least 2 years of employment, with an automatic 
extension possible for up to a total maximum of 4 years.

The position:
The position seeks to strengthen ongoing activities in the laboratory of Bjørn 
P. Pedersen on structure, related to the function and mechanism of 
sugar-transporting membrane proteins (pedersenlab.dk). The laboratory's 
interest is the interplay between structure and function of transmembrane 
transport processes with a focus on metabolite uptake systems, and the methods 
uses are primarily crystallography, cryo-EM and biochemistry. The group is part 
of the Section of Structural Biology at Aarhus University.

The candidate:
A successful candidate has a relevant Ph.D. degree and a solid and documented 
background in structural biology, biochemistry and/or biophysics. Experience 
with membrane protein expression and purification is favored, and the candidate 
must demonstrate an ability and interest to work with membrane proteins with a 
structural aim. Applicants should be ambitious, show strong collaborative 
skills, and be able to take initiatives and responsibility within the work 
environment.

The successful candidate is offered:
- access to a well-developed research infrastructure.
- a research climate inviting lively, open and critical discussion within and 
across different fields of research.
- a working environment with teamwork, close working relations, network 
activities among young scientists and social activities.
- a workplace characterized by professionalism, equality and a healthy 
work-life balance.

The city:
In Aarhus you have easy access to beautiful nature, an exciting culture and 
city life as well as a safe environment for children - a great place for the 
whole family. The city of Aarhus has everything you need: exciting national and 
international jobs, delightful residential areas, a rich cultural life, and 
beautiful surrounding landscape of woods and coastline that make Aarhus a 
wonderful place to live and work.

Deadline:
All applications must be made online (http://tiny.cc/MBG_postdoc) and received 
by 2. apr. 2020.







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