Re: [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

[Dale C]

Hi Paul,

I seemed to have fixed the amino acid dictionary issue by following Nick's 
suggestion to direct Phenix to the new coot.app location in my ccp4 
applications folder.

Though I am still having the issue that Phenix is not connecting to Coot, is 
this a known/common issue? Would you please have any suggestions on how i might 
fix this?

Thanks.

Dale.



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Re: [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

[Dale C]

Hi Nick,

Thanks a lot for that advice, directing Phenix to the new coot.app location 
appears to have fixed the amino acids restraints issue!

Though still having issue with Phenix not connecting to Coot, perhaps i will 
post this issue on the Phenixbb and see what the community has to say.

Dale.



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Re: [ccp4bb] Regarding the correct space group identification

[Sayan Saha]

Dear Sir,

 image1.osc

 image2.osc

The detector-to-crystal distance was 190 mm. The Oscillation range was 1.0
degree. Please find attached two diffraction images.
With best regards,
Sayan Saha.

On Thu, Jul 28, 2022 at 9:41 PM Sayan Saha  wrote:

> Dear Sir,
>
> The detector-to-crystal distance was 190 mm. The Oscillation range was 1.0
> degree. Please find attached two diffraction images.
> With best regards,
> Sayan Saha.
>
>
> On Thu, Jul 28, 2022 at 7:31 PM Kay Diederichs <
> kay.diederi...@uni-konstanz.de> wrote:
>
>> Dear Sayan,
>>
>> On Thu, 28 Jul 2022 15:12:30 +0530, Sayan Saha 
>> wrote:
>>
>> >Dear Sir,
>> >
>> >1. There are no ice-rings. However, diffraction spots seem to be
>> >overlapping. This can be seen during the data processing, as the space
>> >group (C2 or P222) varies even in the consecutive frames.
>>
>> spot overlap results in inaccurate intensity values. Inaccurate
>> intensities result in high Rwork/Rfree.
>>
>> Why do the spots overlap? High mosaicity? Detector distance too small?
>> Oscillation range too high (0.1° is typically adequate)?
>>
>> It would be good to see the data, otherwise we can only speculate.
>>
>> Space group does not change from one frame to the next. If you use XDS, a
>> good guide to decide between higher and lower-symmetry space groups is to
>> compare their ISa values.
>>
>> best,
>> Kay
>>
>> >
>> >2. Crystal packing of C2 and P22121 seem to be similar (please see the
>> >attached images).
>> >
>> >3. Forgot to mention in my previous email that we have already processed
>> >the data in P1 and MR solution could be found only in P1 (Phaser was used
>> >with an option in all possible space groups of that point group).
>> >
>> >Please let me know if any other information is required.
>> >
>> >With best regards,
>> >Sayan Saha.
>> >
>> >
>> >On Thu, Jul 28, 2022 at 1:26 PM Schreuder, Herman /DE <
>> >herman.schreu...@sanofi.com> wrote:
>> >
>> >> Dear Sayan,
>> >>
>> >>
>> >>
>> >> If a subunit is correctly oriented, but the translation is incorrect,
>> >> density for a ligand may still show up in the binding site of the
>> protein.
>> >> It might be that one of the 2-fold axes, you think is
>> crystallographic, is
>> >> in fact non crystallographic and a few Angstroms away from the
>> >> crystallographic position.
>> >>
>> >>
>> >>
>> >> What I would do:
>> >>
>> >>1. Check the images: are there ice-rings or other artifacts that
>> could
>> >>cause scaling problems that would lead to high Rw/Rf values? In
>> that case,
>> >>there is not much you can do.
>> >>2. Compare the C2 and P22121 solutions: do they have the same
>> overall
>> >>crystal packing (CS+NCS), or are they different? Do they have the
>> same
>> >>Rw/Rf values? Can we learn anything from the differences in overall
>> crystal
>> >>packing?
>> >>3. Process, run MR and refine in P1. Do you get lower R-factors? If
>> >>so, then run Zanuda to find out the real space group.
>> >>
>> >>
>> >>
>> >> Best,
>> >>
>> >> Herman
>> >>
>> >>
>> >>
>> >> *Von:* CCP4 bulletin board  *Im Auftrag von
>> *Sayan
>> >> Saha
>> >> *Gesendet:* Donnerstag, 28. Juli 2022 08:15
>> >> *An:* CCP4BB@JISCMAIL.AC.UK
>> >> *Betreff:* [ccp4bb] Regarding the correct space group identification
>> >>
>> >>
>> >>
>> >> Dear All,
>> >>
>> >>
>> >>
>> >> We have collected home-source X-ray intensity data for a protein at 2.6
>> >> Angstrom. The data can be processed in either C2 (a=120, b=80, c=85 and
>> >> beta=115) or P222 (P22121, a=80, b=85, c=110). MR solution can be
>> obtained
>> >> in both the space groups. However, the solution can be refined with an
>> >> Rw/Rf of 29/32% only. The protein is bound to a ligand
>> (co-crystallization)
>> >> for which a clear density can be observed.
>> >>
>> >>
>> >>
>> >> Any help and suggestion in this regard would be very helpful.
>> >>
>> >>
>> >>
>> >> With best regards,
>> >>
>> >> Sayan Saha.
>> >>
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> To unsubscribe from the CCP4BB list, click the following link:
>> >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>> >>
>> >
>> >
>> >
>> >To unsubscribe from the CCP4BB list, click the following link:
>> >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>> >
>> >This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
>> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
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>> >
>>
>> 
>>
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[ccp4bb] Workshop on Big Data Neuroscience Sept 15-16 Austin TX

[Ressl, Susanne]

Dear Colleagues,
We are excited to announce the 7th annual Big Data Neuroscience (BDN) workshop 
organized by the Advanced Computational Neuroscience 
Network. The BDN 
workshop brings together researchers in neuroscience, computer science, 
statistics, computer engineering, structural biology, neuroinformatics, and 
related disciplines. The workshop aims to bring together a transdisciplinary 
set of speakers to educate trainees and faculty on tackling society's biggest 
challenges in critical areas of interdisciplinary strength, including health & 
well-being and technology & society.
The BDN workshop will be held in Austin, Texas, September 15-16, 2022.
We have an exciting line-up of speakers spanning multiple disciplines of 
science and engineering:
James Carson (Kristen  Harris’ NeuroNex, UT Austin), Dan Stanzione (TACC), 
Damian Eke (De Montfort University), Axel Brunger (Stanford University), Martin 
Paulus (Laureate Institute), Jason McLellan (UT Austin), Jingyu Liu (Georgia 
State), Jessica Church-Lang (UT Austin), Chen Yu (UT Austin), Angie Laird 
(Florida International University), Maryann Martone (University of California 
San Diego), Laura Colgin (The University of Texas at Austin), Franco Pestilli 
(UT Austin), Piotr Sliz (Harvard University), Yaroslav Halchenko (Dartmouth), 
Dora Hermes (Mayo Clinic), and David Kennedy (UMass Medical School).
In addition to science and engineering, the workshop will host a panel 
discussion on “Challenges and opportunities for international-scale 
infrastructure to advance data sharing and equity.” with representatives from 
the National Science Foundation, the National Institutes of Health, the Kavli 
Foundation, Nature Publishing Group, and Wellcome Trust.
Registration
You can register for the workshop using this 
form. The deadline is September 1st, 2022.
Call for Posters and Lightning Talks
You can submit your abstract here. The 
deadline is August 18, 2022.
Travel Scholarships
A few travel scholarships for trainees with underrepresented backgrounds and 
diverse geographical locations are available. Use the abstract submission form 
to apply for a travel scholarship. The 
deadline is August 18, 2022.
Please visit www.neurosciencenetwork.org 
for more information.

Best regards,
Susanne

Workshop organizers
Franco Pestilli, The University of Texas at Austin
Susanne Ressl, The University of Texas at Austin
Josiah Leong, University of Arkansas
Sharlene Newman, University of Alabama
Jessica Turner, The Ohio State University
Ivo Dinov, University of Michigan
Ressl, Susanne PhD
Assistant Professor
Department of Neuroscience
The University of Texas at Austin
100 E 24TH ST, NHB 4.336
Austin, TX 78712-1597
512-475-7904
www.ressllab.org




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Re: [ccp4bb] Regarding the correct space group identification

[Andrew Leslie - MRC LMB]

Dear Sayan,

I could be wrong, but perhaps Kay was asking you to provide 
the actual images, rather than jpeg images. One can usually get a lot more 
information by processing the actual images rather than looking at the jpegs.

Best wishes,

Andrew

> On 28 Jul 2022, at 17:11, Sayan Saha  wrote:
> 
> Dear Sir,
> 
> The detector-to-crystal distance was 190 mm. The Oscillation range was 1.0 
> degree. Please find attached two diffraction images.
> With best regards,
> Sayan Saha.
> 
> 
> On Thu, Jul 28, 2022 at 7:31 PM Kay Diederichs 
> mailto:kay.diederi...@uni-konstanz.de>> 
> wrote:
> Dear Sayan,
> 
> On Thu, 28 Jul 2022 15:12:30 +0530, Sayan Saha  > wrote:
> 
> >Dear Sir,
> >
> >1. There are no ice-rings. However, diffraction spots seem to be
> >overlapping. This can be seen during the data processing, as the space
> >group (C2 or P222) varies even in the consecutive frames.
> 
> spot overlap results in inaccurate intensity values. Inaccurate intensities 
> result in high Rwork/Rfree.
> 
> Why do the spots overlap? High mosaicity? Detector distance too small? 
> Oscillation range too high (0.1° is typically adequate)?
> 
> It would be good to see the data, otherwise we can only speculate.
> 
> Space group does not change from one frame to the next. If you use XDS, a 
> good guide to decide between higher and lower-symmetry space groups is to 
> compare their ISa values.
> 
> best,
> Kay
> 
> >
> >2. Crystal packing of C2 and P22121 seem to be similar (please see the
> >attached images).
> >
> >3. Forgot to mention in my previous email that we have already processed
> >the data in P1 and MR solution could be found only in P1 (Phaser was used
> >with an option in all possible space groups of that point group).
> >
> >Please let me know if any other information is required.
> >
> >With best regards,
> >Sayan Saha.
> >
> >
> >On Thu, Jul 28, 2022 at 1:26 PM Schreuder, Herman /DE <
> >herman.schreu...@sanofi.com > wrote:
> >
> >> Dear Sayan,
> >>
> >>
> >>
> >> If a subunit is correctly oriented, but the translation is incorrect,
> >> density for a ligand may still show up in the binding site of the protein.
> >> It might be that one of the 2-fold axes, you think is crystallographic, is
> >> in fact non crystallographic and a few Angstroms away from the
> >> crystallographic position.
> >>
> >>
> >>
> >> What I would do:
> >>
> >>1. Check the images: are there ice-rings or other artifacts that could
> >>cause scaling problems that would lead to high Rw/Rf values? In that 
> >> case,
> >>there is not much you can do.
> >>2. Compare the C2 and P22121 solutions: do they have the same overall
> >>crystal packing (CS+NCS), or are they different? Do they have the same
> >>Rw/Rf values? Can we learn anything from the differences in overall 
> >> crystal
> >>packing?
> >>3. Process, run MR and refine in P1. Do you get lower R-factors? If
> >>so, then run Zanuda to find out the real space group.
> >>
> >>
> >>
> >> Best,
> >>
> >> Herman
> >>
> >>
> >>
> >> *Von:* CCP4 bulletin board  >> > *Im Auftrag von *Sayan
> >> Saha
> >> *Gesendet:* Donnerstag, 28. Juli 2022 08:15
> >> *An:* CCP4BB@JISCMAIL.AC.UK 
> >> *Betreff:* [ccp4bb] Regarding the correct space group identification
> >>
> >>
> >>
> >> Dear All,
> >>
> >>
> >>
> >> We have collected home-source X-ray intensity data for a protein at 2.6
> >> Angstrom. The data can be processed in either C2 (a=120, b=80, c=85 and
> >> beta=115) or P222 (P22121, a=80, b=85, c=110). MR solution can be obtained
> >> in both the space groups. However, the solution can be refined with an
> >> Rw/Rf of 29/32% only. The protein is bound to a ligand (co-crystallization)
> >> for which a clear density can be observed.
> >>
> >>
> >>
> >> Any help and suggestion in this regard would be very helpful.
> >>
> >>
> >>
> >> With best regards,
> >>
> >> Sayan Saha.
> >>
> >>
> >>
> >>
> >> --
> >>
> >> To unsubscribe from the CCP4BB list, click the following link:
> >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 
> >> 
> >>
> >
> >
> >
> >To unsubscribe from the CCP4BB list, click the following link:
> >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 
> >
> >
> >This message was issued to members of www.jiscmail.ac.uk/CCP4BB 
> >, a mailing list hosted by 
> >www.jiscmail.ac.uk , terms & conditions are 
> >available at https://www.jiscmail.ac.uk/policyandsecurity/ 
> >
> >
> 
> #

Re: [ccp4bb] AW: [ccp4bb] Regarding the correct space group identification

[Sayan Saha]

Dear Madam,

The data were processed in C2 and P222 independently from the same
diffraction. There are two protomers in the ASU.

With best regards,
Sayan Saha.



On Thu, Jul 28, 2022 at 7:25 PM Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> I cant see how the C2 cell can be reindexed to the P/mmm one?
> Am I right to assume these are different processing of the same
> diffraction?
> And how many molecules do you have in each cell?
> Eleanor
>
>
>
> On Thu, 28 Jul 2022 at 12:52, Schreuder, Herman /DE <
> herman.schreu...@sanofi.com> wrote:
>
>> Dear Sayan,
>>
>>
>>
>> Thank you for this information. Why are your spots overlapping? The axes
>> of your crystal are not particularly long. Did you put the detector very
>> close to the crystal, or are there multiple diffraction patterns?
>>
>>
>>
>> Did you run Zanuda on your P1 structure? What Rfactors do you get when
>> you complete the refinement in P1?
>>
>>
>>
>> Best regards,
>>
>> Herman
>>
>>
>>
>> *Von:* Sayan Saha 
>> *Gesendet:* Donnerstag, 28. Juli 2022 11:43
>> *An:* Schreuder, Herman /DE 
>> *Cc:* CCP4BB@JISCMAIL.AC.UK
>> *Betreff:* Re: [ccp4bb] Regarding the correct space group identification
>>
>>
>>
>> Dear Sir,
>>
>>
>>
>> 1. There are no ice-rings. However, diffraction spots seem to be
>> overlapping. This can be seen during the data processing, as the space
>> group (C2 or P222) varies even in the consecutive frames.
>>
>>
>>
>> 2. Crystal packing of C2 and P22121 seem to be similar (please see the
>> attached images).
>>
>>
>>
>> 3. Forgot to mention in my previous email that we have already processed
>> the data in P1 and MR solution could be found only in P1 (Phaser was used
>> with an option in all possible space groups of that point group).
>>
>>
>>
>> Please let me know if any other information is required.
>>
>>
>>
>> With best regards,
>>
>> Sayan Saha.
>>
>>
>>
>>
>>
>> On Thu, Jul 28, 2022 at 1:26 PM Schreuder, Herman /DE <
>> herman.schreu...@sanofi.com> wrote:
>>
>> Dear Sayan,
>>
>>
>>
>> If a subunit is correctly oriented, but the translation is incorrect,
>> density for a ligand may still show up in the binding site of the protein.
>> It might be that one of the 2-fold axes, you think is crystallographic, is
>> in fact non crystallographic and a few Angstroms away from the
>> crystallographic position.
>>
>>
>>
>> What I would do:
>>
>>1. Check the images: are there ice-rings or other artifacts that
>>could cause scaling problems that would lead to high Rw/Rf values? In that
>>case, there is not much you can do.
>>2. Compare the C2 and P22121 solutions: do they have the same overall
>>crystal packing (CS+NCS), or are they different? Do they have the same
>>Rw/Rf values? Can we learn anything from the differences in overall 
>> crystal
>>packing?
>>3. Process, run MR and refine in P1. Do you get lower R-factors? If
>>so, then run Zanuda to find out the real space group.
>>
>>
>>
>> Best,
>>
>> Herman
>>
>>
>>
>> *Von:* CCP4 bulletin board  *Im Auftrag von *Sayan
>> Saha
>> *Gesendet:* Donnerstag, 28. Juli 2022 08:15
>> *An:* CCP4BB@JISCMAIL.AC.UK
>> *Betreff:* [ccp4bb] Regarding the correct space group identification
>>
>>
>>
>> Dear All,
>>
>>
>>
>> We have collected home-source X-ray intensity data for a protein at 2.6
>> Angstrom. The data can be processed in either C2 (a=120, b=80, c=85 and
>> beta=115) or P222 (P22121, a=80, b=85, c=110). MR solution can be obtained
>> in both the space groups. However, the solution can be refined with an
>> Rw/Rf of 29/32% only. The protein is bound to a ligand (co-crystallization)
>> for which a clear density can be observed.
>>
>>
>>
>> Any help and suggestion in this regard would be very helpful.
>>
>>
>>
>> With best regards,
>>
>> Sayan Saha.
>>
>>
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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[ccp4bb] job opening: Scientist, X-ray Crystallography - San Diego, CA

[Rui Xu]

*Scientist, X-ray Crystallography - San Diego, CA*

Pharmaceuticals

*Job Description *

Janssen Research & Development, L.L.C., a division of Johnson & Johnson's
Family of Companies is recruiting for a Scientist, X-ray Crystallography,
located in La Jolla, CA!

At the Janssen Pharmaceutical Companies of Johnson & Johnson, we are
working to create a world without disease. Transforming lives by finding
new and better ways to prevent, intercept, treat and cure disease inspires
us. We bring together the best minds and pursue the most promising science.
We are Janssen. We collaborate with the world for the health of everyone in
it. Learn more at www.janssen.com and follow us @JanssenGlobal. Janssen
Research & Development, LLC is part of the Janssen Pharmaceutical
Companies.

The Discovery Technologies and Molecular Pharmacology group is a dynamic,
diverse and critical part of the Discovery Sciences organization in Janssen
R&D. We are committed to the discovery and characterization of high-quality
chemical leads needed for the generation of small molecule clinical
compounds in all five Janssen Therapeutic Areas. This mission requires deep
scientific expertise across broad subject areas including chemistry,
cellular and molecular pharmacology, enzymology, screening, protein
science, and structural biology coupled with an ability to work
collaboratively with internal and external partners. Building on a strong
legacy of success, we are currently seeking an outstanding and motivated
individual to join our team as Scientist, X-ray Crystallography.

*As the Scientist you will:*

   - Be an active member of drug discovery teams, working closely with
   computational and medicinal chemists on structure-based drug design
   approaches for small molecule agent optimization.
   - Be responsible for crystallization of protein-small molecule
   complexes, determination of high-resolution structures by X-ray
   crystallography and communicating these results to the project team.
   - Work closely with protein scientists, biophysicists, protein NMR and
   cryo-EM scientists as part of an integrated structural biology effort.
   - Contribute to multidisciplinary Fragment-Based Lead Discovery (FBLD)
   efforts.
   - Contribute to enhance the structural biology scientific expertise of
   the group by publishing high-impact research papers, and presenting at
   scientific conferences, internalizing impactful technologies and platforms,
   and establishing academic collaborations.
   - Mentor lab scientists and contribute to the strategic planning of the
   Structural Biology group.


*Qualifications*

   - BS degree with at least 12 years of experience, OR MS degree with at
   least 9 years of experience, OR a Ph.D. or equivalent and postdoctoral
   experience in structural biology (X-ray crystallography, biophysics,
   protein engineering) or related field is required
   - Expertise with crystallography software packages
   (Phenix/CCP4/PyMol/Moe) in a mixed Linux/Windows computational environment
   is required
   - Scientific expertise in structural biology, with strong experience in
   both protein crystallization and structure determination is required
   - Strong record of external publications and presentations is required
   - Outstanding written and oral communication skills are required
   - Experience in Structure-Guided Drug Design utilizing X-ray
   crystallography is preferred
   - Research experience in cryo-electron microscopy (Cryo-EM),
   Micro-electron diffraction (Micro-ED), protein NMR or orthogonal structural
   biology technologies is preferred
   - Research experience with other biophysical techniques such as MST,
   ITC, NMR, DSF, SPR is preferred
   - Broad knowledge of biophysics, biochemistry, molecular pharmacology,
   and protein sciences is preferred.
   - Experience in scientific programming (Unix shells, Python) is preferred
   - Expertise in one or more of the following therapeutic areas: Oncology,
   Inflammation, Neuroscience, Cardiovascular, and Infectious Diseases is
   preferred

Johnson & Johnson is an Affirmative Action and Equal Opportunity Employer.
All qualified applicants will receive consideration for employment without
regard to race, color, religion, sex, sexual orientation, gender identity,
age, national origin, or protected veteran status and will not be
discriminated against on the basis of disability.


*Primary Location*
United States-California-San Diego-
*Organization*
Janssen Research & Development, LLC (6084)
*Job Function*
R&D
*Requisition ID*
2005866689W

https://jobs.jnj.com/jobs/2206025987W?lang=en-us&previousLocale=en-US



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h

[ccp4bb] Yes, there are now 214 *million* structures in the AlphaFold Protein Structure Database

[Gerard Kleywegt]

Hi all,

I thought Sameer was burying the lead a tad in his message... :-) So, for 
those of you who -like me- are not on social media:


==> As of today, the AlphaFold Protein Structure Database contains 214 million 
models predicted with AlphaFold, covering almost all of UniProt. <==


So, if your favourite protein was not available in the database before today, 
it's worth checking in again at https://www.alphafold.ebi.ac.uk/ now.


See also:

- EMBL-EBI press release: 
https://www.ebi.ac.uk/about/news/technology-and-innovation/alphafold-200-million/

- Nature news: https://www.nature.com/articles/d41586-022-02083-2

- IUCr J guest editorial about the potential impact of all this on structural 
biologists (shameless plug): https://journals.iucr.org/m/issues/2022/04/00/me6185/index.html



Best wishes,

--Gerard





On Thu, 28 Jul 2022, Sameer Velankar wrote:


Dear All,

You may have seen our announcement today about expanding the AlphaFold Protein 
Structure Database to 214M predicted models. To enable this expansion, we’ve 
updated the Predicted Aligned Error (PAE) JSON format to make it compact (about 
4x smaller):

The PAE JSON numbers are now rounded to the closest integer, giving ~75% 
compressed size reduction. The integer resolution is sufficient for analytical 
purposes.
The indices are not stored anymore since we store the full 2D PAE matrix rather 
than a sparse one, giving ~4% compressed size reduction.
The “distances” field has been renamed to “predicted_aligned_error” and is now 
stored as a 2D array of shape (num_res, num_res) rather than a 1D array. We 
renamed the field on purpose so that existing code breaks rather than 
potentially silently returning wrong values.

For a protein of length num_res, the PAE JSON file has now the following format:

[{
 "predicted_aligned_error": [[0, 1, 4, 7, 9, ...], ...],  # Shape: (num_res, 
num_res).
 "max_predicted_aligned_error": 31.75  # Scalar.
}]

The fields in the JSON file are:
predicted_aligned_error: The PAE value of the residue pair, rounded to the 
closest integer. For PAE value on position (i, j), i is the residue on which 
the structure is aligned for the predicted error, j is the residue on which the 
error is predicted.
max_predicted_aligned_error: A number that denotes the largest possible 
unrounded value of PAE that could occur in the PAE array. The smallest possible 
value of PAE is 0.

The updated PAE format is only available from the AlphaFold Protein Structure 
Database. The PAE format from the AlphaFold Colab notebook is not updated.

If you require support with this change, please email alphaf...@deepmind.com 
 and they may be able to assist.

Best Wishes,

Sameer Velankar


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Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
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of that pizza is equal to pi*z*z*a !
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Re: [ccp4bb] Regarding the correct space group identification

[Kay Diederichs]

Dear Sayan,

On Thu, 28 Jul 2022 15:12:30 +0530, Sayan Saha  wrote:

>Dear Sir,
>
>1. There are no ice-rings. However, diffraction spots seem to be
>overlapping. This can be seen during the data processing, as the space
>group (C2 or P222) varies even in the consecutive frames.

spot overlap results in inaccurate intensity values. Inaccurate intensities 
result in high Rwork/Rfree.

Why do the spots overlap? High mosaicity? Detector distance too small? 
Oscillation range too high (0.1° is typically adequate)?

It would be good to see the data, otherwise we can only speculate.

Space group does not change from one frame to the next. If you use XDS, a good 
guide to decide between higher and lower-symmetry space groups is to compare 
their ISa values.

best,
Kay

>
>2. Crystal packing of C2 and P22121 seem to be similar (please see the
>attached images).
>
>3. Forgot to mention in my previous email that we have already processed
>the data in P1 and MR solution could be found only in P1 (Phaser was used
>with an option in all possible space groups of that point group).
>
>Please let me know if any other information is required.
>
>With best regards,
>Sayan Saha.
>
>
>On Thu, Jul 28, 2022 at 1:26 PM Schreuder, Herman /DE <
>herman.schreu...@sanofi.com> wrote:
>
>> Dear Sayan,
>>
>>
>>
>> If a subunit is correctly oriented, but the translation is incorrect,
>> density for a ligand may still show up in the binding site of the protein.
>> It might be that one of the 2-fold axes, you think is crystallographic, is
>> in fact non crystallographic and a few Angstroms away from the
>> crystallographic position.
>>
>>
>>
>> What I would do:
>>
>>1. Check the images: are there ice-rings or other artifacts that could
>>cause scaling problems that would lead to high Rw/Rf values? In that case,
>>there is not much you can do.
>>2. Compare the C2 and P22121 solutions: do they have the same overall
>>crystal packing (CS+NCS), or are they different? Do they have the same
>>Rw/Rf values? Can we learn anything from the differences in overall 
>> crystal
>>packing?
>>3. Process, run MR and refine in P1. Do you get lower R-factors? If
>>so, then run Zanuda to find out the real space group.
>>
>>
>>
>> Best,
>>
>> Herman
>>
>>
>>
>> *Von:* CCP4 bulletin board  *Im Auftrag von *Sayan
>> Saha
>> *Gesendet:* Donnerstag, 28. Juli 2022 08:15
>> *An:* CCP4BB@JISCMAIL.AC.UK
>> *Betreff:* [ccp4bb] Regarding the correct space group identification
>>
>>
>>
>> Dear All,
>>
>>
>>
>> We have collected home-source X-ray intensity data for a protein at 2.6
>> Angstrom. The data can be processed in either C2 (a=120, b=80, c=85 and
>> beta=115) or P222 (P22121, a=80, b=85, c=110). MR solution can be obtained
>> in both the space groups. However, the solution can be refined with an
>> Rw/Rf of 29/32% only. The protein is bound to a ligand (co-crystallization)
>> for which a clear density can be observed.
>>
>>
>>
>> Any help and suggestion in this regard would be very helpful.
>>
>>
>>
>> With best regards,
>>
>> Sayan Saha.
>>
>>
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
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Re: [ccp4bb] AW: [ccp4bb] Regarding the correct space group identification

[Eleanor Dodson]

I cant see how the C2 cell can be reindexed to the P/mmm one?
Am I right to assume these are different processing of the same
diffraction?
And how many molecules do you have in each cell?
Eleanor



On Thu, 28 Jul 2022 at 12:52, Schreuder, Herman /DE <
herman.schreu...@sanofi.com> wrote:

> Dear Sayan,
>
>
>
> Thank you for this information. Why are your spots overlapping? The axes
> of your crystal are not particularly long. Did you put the detector very
> close to the crystal, or are there multiple diffraction patterns?
>
>
>
> Did you run Zanuda on your P1 structure? What Rfactors do you get when you
> complete the refinement in P1?
>
>
>
> Best regards,
>
> Herman
>
>
>
> *Von:* Sayan Saha 
> *Gesendet:* Donnerstag, 28. Juli 2022 11:43
> *An:* Schreuder, Herman /DE 
> *Cc:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* Re: [ccp4bb] Regarding the correct space group identification
>
>
>
> Dear Sir,
>
>
>
> 1. There are no ice-rings. However, diffraction spots seem to be
> overlapping. This can be seen during the data processing, as the space
> group (C2 or P222) varies even in the consecutive frames.
>
>
>
> 2. Crystal packing of C2 and P22121 seem to be similar (please see the
> attached images).
>
>
>
> 3. Forgot to mention in my previous email that we have already processed
> the data in P1 and MR solution could be found only in P1 (Phaser was used
> with an option in all possible space groups of that point group).
>
>
>
> Please let me know if any other information is required.
>
>
>
> With best regards,
>
> Sayan Saha.
>
>
>
>
>
> On Thu, Jul 28, 2022 at 1:26 PM Schreuder, Herman /DE <
> herman.schreu...@sanofi.com> wrote:
>
> Dear Sayan,
>
>
>
> If a subunit is correctly oriented, but the translation is incorrect,
> density for a ligand may still show up in the binding site of the protein.
> It might be that one of the 2-fold axes, you think is crystallographic, is
> in fact non crystallographic and a few Angstroms away from the
> crystallographic position.
>
>
>
> What I would do:
>
>1. Check the images: are there ice-rings or other artifacts that could
>cause scaling problems that would lead to high Rw/Rf values? In that case,
>there is not much you can do.
>2. Compare the C2 and P22121 solutions: do they have the same overall
>crystal packing (CS+NCS), or are they different? Do they have the same
>Rw/Rf values? Can we learn anything from the differences in overall crystal
>packing?
>3. Process, run MR and refine in P1. Do you get lower R-factors? If
>so, then run Zanuda to find out the real space group.
>
>
>
> Best,
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board  *Im Auftrag von *Sayan
> Saha
> *Gesendet:* Donnerstag, 28. Juli 2022 08:15
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [ccp4bb] Regarding the correct space group identification
>
>
>
> Dear All,
>
>
>
> We have collected home-source X-ray intensity data for a protein at 2.6
> Angstrom. The data can be processed in either C2 (a=120, b=80, c=85 and
> beta=115) or P222 (P22121, a=80, b=85, c=110). MR solution can be obtained
> in both the space groups. However, the solution can be refined with an
> Rw/Rf of 29/32% only. The protein is bound to a ligand (co-crystallization)
> for which a clear density can be observed.
>
>
>
> Any help and suggestion in this regard would be very helpful.
>
>
>
> With best regards,
>
> Sayan Saha.
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] Regarding the correct space group identification

[Harry Powell]

Sorry - meant to add this: I know that (of the “free” programs) Mosflm, DIALS 
and Eval15 can process multiple lattices.

Harry

> On 28 Jul 2022, at 14:36, Harry Powell  wrote:
> 
> Hi Sayan
> 
> If you have multiple lattices showing in your diffraction pattern, it may be 
> worthwhile using one of the programs that can process multiple lattices for 
> your integration. 
> 
> It may also be a good idea to share a few of your images that show the 
> problem with an expert (don’t post the images to ccp4BB!) who may be able to 
> offer you advice.
> 
> Best wishes
> 
> Harry
> 
> 
>> On 28 Jul 2022, at 14:17, Sayan Saha  wrote:
>> 
>> Dear Sir,  
>> The crystal-to-detector distance was set to 190 mm. Yes, multiple 
>> diffractions seem to be present. We have not yet tried Zanuda on the P1 
>> structure. However, the Rw/Rf of P1 structures are little higher (31/34%).
>> 
>> With best regards,
>> Sayan Saha.
>> 
>> On Thu, Jul 28, 2022 at 5:22 PM Schreuder, Herman /DE 
>>  wrote:
>> Dear Sayan,
>> 
>> 
>> 
>> Thank you for this information. Why are your spots overlapping? The axes of 
>> your crystal are not particularly long. Did you put the detector very close 
>> to the crystal, or are there multiple diffraction patterns?
>> 
>> 
>> 
>> Did you run Zanuda on your P1 structure? What Rfactors do you get when you 
>> complete the refinement in P1?
>> 
>> 
>> 
>> Best regards,
>> 
>> Herman
>> 
>> 
>> 
>> Von: Sayan Saha  
>> Gesendet: Donnerstag, 28. Juli 2022 11:43
>> An: Schreuder, Herman /DE 
>> Cc: CCP4BB@JISCMAIL.AC.UK
>> Betreff: Re: [ccp4bb] Regarding the correct space group identification
>> 
>> 
>> 
>> Dear Sir,
>> 
>> 
>> 
>> 1. There are no ice-rings. However, diffraction spots seem to be 
>> overlapping. This can be seen during the data processing, as the space group 
>> (C2 or P222) varies even in the consecutive frames.
>> 
>> 
>> 
>> 2. Crystal packing of C2 and P22121 seem to be similar (please see the 
>> attached images).
>> 
>> 
>> 
>> 3. Forgot to mention in my previous email that we have already processed the 
>> data in P1 and MR solution could be found only in P1 (Phaser was used with 
>> an option in all possible space groups of that point group).
>> 
>> 
>> 
>> Please let me know if any other information is required.
>> 
>> 
>> 
>> With best regards,
>> 
>> Sayan Saha.
>> 
>> 
>> 
>> 
>> 
>> On Thu, Jul 28, 2022 at 1:26 PM Schreuder, Herman /DE 
>>  wrote:
>> 
>> Dear Sayan,
>> 
>> 
>> 
>> If a subunit is correctly oriented, but the translation is incorrect, 
>> density for a ligand may still show up in the binding site of the protein. 
>> It might be that one of the 2-fold axes, you think is crystallographic, is 
>> in fact non crystallographic and a few Angstroms away from the 
>> crystallographic position.
>> 
>> 
>> 
>> What I would do:
>> 
>>  • Check the images: are there ice-rings or other artifacts that could 
>> cause scaling problems that would lead to high Rw/Rf values? In that case, 
>> there is not much you can do.
>>  • Compare the C2 and P22121 solutions: do they have the same overall 
>> crystal packing (CS+NCS), or are they different? Do they have the same Rw/Rf 
>> values? Can we learn anything from the differences in overall crystal 
>> packing?
>>  • Process, run MR and refine in P1. Do you get lower R-factors? If so, 
>> then run Zanuda to find out the real space group.
>> 
>> 
>> Best,
>> 
>> Herman
>> 
>> 
>> 
>> Von: CCP4 bulletin board  Im Auftrag von Sayan Saha
>> Gesendet: Donnerstag, 28. Juli 2022 08:15
>> An: CCP4BB@JISCMAIL.AC.UK
>> Betreff: [ccp4bb] Regarding the correct space group identification
>> 
>> 
>> 
>> Dear All,
>> 
>> 
>> 
>> We have collected home-source X-ray intensity data for a protein at 2.6 
>> Angstrom. The data can be processed in either C2 (a=120, b=80, c=85 and 
>> beta=115) or P222 (P22121, a=80, b=85, c=110). MR solution can be obtained 
>> in both the space groups. However, the solution can be refined with an Rw/Rf 
>> of 29/32% only. The protein is bound to a ligand (co-crystallization) for 
>> which a clear density can be observed.
>> 
>> 
>> 
>> Any help and suggestion in this regard would be very helpful.
>> 
>> 
>> 
>> With best regards,
>> 
>> Sayan Saha.
>> 
>> 
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>> 
> 



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Re: [ccp4bb] Regarding the correct space group identification

[Harry Powell]

Hi Sayan

If you have multiple lattices showing in your diffraction pattern, it may be 
worthwhile using one of the programs that can process multiple lattices for 
your integration. 

It may also be a good idea to share a few of your images that show the problem 
with an expert (don’t post the images to ccp4BB!) who may be able to offer you 
advice.

Best wishes

Harry


> On 28 Jul 2022, at 14:17, Sayan Saha  wrote:
> 
> Dear Sir,  
>  The crystal-to-detector distance was set to 190 mm. Yes, multiple 
> diffractions seem to be present. We have not yet tried Zanuda on the P1 
> structure. However, the Rw/Rf of P1 structures are little higher (31/34%).
> 
> With best regards,
> Sayan Saha.
> 
> On Thu, Jul 28, 2022 at 5:22 PM Schreuder, Herman /DE 
>  wrote:
> Dear Sayan,
> 
>  
> 
> Thank you for this information. Why are your spots overlapping? The axes of 
> your crystal are not particularly long. Did you put the detector very close 
> to the crystal, or are there multiple diffraction patterns?
> 
>  
> 
> Did you run Zanuda on your P1 structure? What Rfactors do you get when you 
> complete the refinement in P1?
> 
>  
> 
> Best regards,
> 
> Herman
> 
>  
> 
> Von: Sayan Saha  
> Gesendet: Donnerstag, 28. Juli 2022 11:43
> An: Schreuder, Herman /DE 
> Cc: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] Regarding the correct space group identification
> 
>  
> 
> Dear Sir,
> 
>  
> 
> 1. There are no ice-rings. However, diffraction spots seem to be overlapping. 
> This can be seen during the data processing, as the space group (C2 or P222) 
> varies even in the consecutive frames.
> 
>  
> 
> 2. Crystal packing of C2 and P22121 seem to be similar (please see the 
> attached images).
> 
>  
> 
> 3. Forgot to mention in my previous email that we have already processed the 
> data in P1 and MR solution could be found only in P1 (Phaser was used with an 
> option in all possible space groups of that point group).
> 
>  
> 
> Please let me know if any other information is required.
> 
>  
> 
> With best regards,
> 
> Sayan Saha.
> 
>  
> 
>  
> 
> On Thu, Jul 28, 2022 at 1:26 PM Schreuder, Herman /DE 
>  wrote:
> 
> Dear Sayan,
> 
>  
> 
> If a subunit is correctly oriented, but the translation is incorrect, density 
> for a ligand may still show up in the binding site of the protein. It might 
> be that one of the 2-fold axes, you think is crystallographic, is in fact non 
> crystallographic and a few Angstroms away from the crystallographic position.
> 
>  
> 
> What I would do:
> 
>   • Check the images: are there ice-rings or other artifacts that could 
> cause scaling problems that would lead to high Rw/Rf values? In that case, 
> there is not much you can do.
>   • Compare the C2 and P22121 solutions: do they have the same overall 
> crystal packing (CS+NCS), or are they different? Do they have the same Rw/Rf 
> values? Can we learn anything from the differences in overall crystal packing?
>   • Process, run MR and refine in P1. Do you get lower R-factors? If so, 
> then run Zanuda to find out the real space group.
>  
> 
> Best,
> 
> Herman
> 
>  
> 
> Von: CCP4 bulletin board  Im Auftrag von Sayan Saha
> Gesendet: Donnerstag, 28. Juli 2022 08:15
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: [ccp4bb] Regarding the correct space group identification
> 
>  
> 
> Dear All,
> 
>  
> 
> We have collected home-source X-ray intensity data for a protein at 2.6 
> Angstrom. The data can be processed in either C2 (a=120, b=80, c=85 and 
> beta=115) or P222 (P22121, a=80, b=85, c=110). MR solution can be obtained in 
> both the space groups. However, the solution can be refined with an Rw/Rf of 
> 29/32% only. The protein is bound to a ligand (co-crystallization) for which 
> a clear density can be observed.
> 
>  
> 
> Any help and suggestion in this regard would be very helpful.
> 
>  
> 
> With best regards,
> 
> Sayan Saha.
> 
>  
> 
>  
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 



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[ccp4bb] AW: [ccp4bb] Regarding the correct space group identification

[Schreuder, Herman /DE]

Dear Sayan,

your options left, as far as I can see, are:

- check if your structure is not twinned, or if not, correct for twinning
- refine using the Zanuda space group.
- try to find a better crystal that does not produce multiple diffraction 
images.

Best,
Herman

Von: Sayan Saha 
Gesendet: Donnerstag, 28. Juli 2022 15:17
An: Schreuder, Herman /DE 
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Regarding the correct space group identification

Dear Sir,
 The crystal-to-detector distance was set to 190 mm. Yes, multiple diffractions 
seem to be present. We have not yet tried Zanuda on the P1 structure. However, 
the Rw/Rf of P1 structures are little higher (31/34%).

With best regards,
Sayan Saha.

On Thu, Jul 28, 2022 at 5:22 PM Schreuder, Herman /DE 
mailto:herman.schreu...@sanofi.com>> wrote:
Dear Sayan,

Thank you for this information. Why are your spots overlapping? The axes of 
your crystal are not particularly long. Did you put the detector very close to 
the crystal, or are there multiple diffraction patterns?

Did you run Zanuda on your P1 structure? What Rfactors do you get when you 
complete the refinement in P1?

Best regards,
Herman

Von: Sayan Saha mailto:ssaha43...@gmail.com>>
Gesendet: Donnerstag, 28. Juli 2022 11:43
An: Schreuder, Herman /DE 
mailto:herman.schreu...@sanofi.com>>
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Regarding the correct space group identification

Dear Sir,

1. There are no ice-rings. However, diffraction spots seem to be overlapping. 
This can be seen during the data processing, as the space group (C2 or P222) 
varies even in the consecutive frames.

2. Crystal packing of C2 and P22121 seem to be similar (please see the attached 
images).

3. Forgot to mention in my previous email that we have already processed the 
data in P1 and MR solution could be found only in P1 (Phaser was used with an 
option in all possible space groups of that point group).

Please let me know if any other information is required.

With best regards,
Sayan Saha.


On Thu, Jul 28, 2022 at 1:26 PM Schreuder, Herman /DE 
mailto:herman.schreu...@sanofi.com>> wrote:
Dear Sayan,

If a subunit is correctly oriented, but the translation is incorrect, density 
for a ligand may still show up in the binding site of the protein. It might be 
that one of the 2-fold axes, you think is crystallographic, is in fact non 
crystallographic and a few Angstroms away from the crystallographic position.

What I would do:

  1.  Check the images: are there ice-rings or other artifacts that could cause 
scaling problems that would lead to high Rw/Rf values? In that case, there is 
not much you can do.
  2.  Compare the C2 and P22121 solutions: do they have the same overall 
crystal packing (CS+NCS), or are they different? Do they have the same Rw/Rf 
values? Can we learn anything from the differences in overall crystal packing?
  3.  Process, run MR and refine in P1. Do you get lower R-factors? If so, then 
run Zanuda to find out the real space group.

Best,
Herman

Von: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
Im Auftrag von Sayan Saha
Gesendet: Donnerstag, 28. Juli 2022 08:15
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Regarding the correct space group identification

Dear All,

We have collected home-source X-ray intensity data for a protein at 2.6 
Angstrom. The data can be processed in either C2 (a=120, b=80, c=85 and 
beta=115) or P222 (P22121, a=80, b=85, c=110). MR solution can be obtained in 
both the space groups. However, the solution can be refined with an Rw/Rf of 
29/32% only. The protein is bound to a ligand (co-crystallization) for which a 
clear density can be observed.

Any help and suggestion in this regard would be very helpful.

With best regards,
Sayan Saha.




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Re: [ccp4bb] Regarding the correct space group identification

[Sayan Saha]

Dear Sir,
 The crystal-to-detector distance was set to 190 mm. Yes, multiple
diffractions seem to be present. We have not yet tried Zanuda on the P1
structure. However, the Rw/Rf of P1 structures are little higher (31/34%).

With best regards,
Sayan Saha.

On Thu, Jul 28, 2022 at 5:22 PM Schreuder, Herman /DE <
herman.schreu...@sanofi.com> wrote:

> Dear Sayan,
>
>
>
> Thank you for this information. Why are your spots overlapping? The axes
> of your crystal are not particularly long. Did you put the detector very
> close to the crystal, or are there multiple diffraction patterns?
>
>
>
> Did you run Zanuda on your P1 structure? What Rfactors do you get when you
> complete the refinement in P1?
>
>
>
> Best regards,
>
> Herman
>
>
>
> *Von:* Sayan Saha 
> *Gesendet:* Donnerstag, 28. Juli 2022 11:43
> *An:* Schreuder, Herman /DE 
> *Cc:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* Re: [ccp4bb] Regarding the correct space group identification
>
>
>
> Dear Sir,
>
>
>
> 1. There are no ice-rings. However, diffraction spots seem to be
> overlapping. This can be seen during the data processing, as the space
> group (C2 or P222) varies even in the consecutive frames.
>
>
>
> 2. Crystal packing of C2 and P22121 seem to be similar (please see the
> attached images).
>
>
>
> 3. Forgot to mention in my previous email that we have already processed
> the data in P1 and MR solution could be found only in P1 (Phaser was used
> with an option in all possible space groups of that point group).
>
>
>
> Please let me know if any other information is required.
>
>
>
> With best regards,
>
> Sayan Saha.
>
>
>
>
>
> On Thu, Jul 28, 2022 at 1:26 PM Schreuder, Herman /DE <
> herman.schreu...@sanofi.com> wrote:
>
> Dear Sayan,
>
>
>
> If a subunit is correctly oriented, but the translation is incorrect,
> density for a ligand may still show up in the binding site of the protein.
> It might be that one of the 2-fold axes, you think is crystallographic, is
> in fact non crystallographic and a few Angstroms away from the
> crystallographic position.
>
>
>
> What I would do:
>
>1. Check the images: are there ice-rings or other artifacts that could
>cause scaling problems that would lead to high Rw/Rf values? In that case,
>there is not much you can do.
>2. Compare the C2 and P22121 solutions: do they have the same overall
>crystal packing (CS+NCS), or are they different? Do they have the same
>Rw/Rf values? Can we learn anything from the differences in overall crystal
>packing?
>3. Process, run MR and refine in P1. Do you get lower R-factors? If
>so, then run Zanuda to find out the real space group.
>
>
>
> Best,
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board  *Im Auftrag von *Sayan
> Saha
> *Gesendet:* Donnerstag, 28. Juli 2022 08:15
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [ccp4bb] Regarding the correct space group identification
>
>
>
> Dear All,
>
>
>
> We have collected home-source X-ray intensity data for a protein at 2.6
> Angstrom. The data can be processed in either C2 (a=120, b=80, c=85 and
> beta=115) or P222 (P22121, a=80, b=85, c=110). MR solution can be obtained
> in both the space groups. However, the solution can be refined with an
> Rw/Rf of 29/32% only. The protein is bound to a ligand (co-crystallization)
> for which a clear density can be observed.
>
>
>
> Any help and suggestion in this regard would be very helpful.
>
>
>
> With best regards,
>
> Sayan Saha.
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
>



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[ccp4bb] AW: [ccp4bb] Regarding the correct space group identification

[Schreuder, Herman /DE]

Dear Sayan,

Thank you for this information. Why are your spots overlapping? The axes of 
your crystal are not particularly long. Did you put the detector very close to 
the crystal, or are there multiple diffraction patterns?

Did you run Zanuda on your P1 structure? What Rfactors do you get when you 
complete the refinement in P1?

Best regards,
Herman

Von: Sayan Saha 
Gesendet: Donnerstag, 28. Juli 2022 11:43
An: Schreuder, Herman /DE 
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Regarding the correct space group identification

Dear Sir,

1. There are no ice-rings. However, diffraction spots seem to be overlapping. 
This can be seen during the data processing, as the space group (C2 or P222) 
varies even in the consecutive frames.

2. Crystal packing of C2 and P22121 seem to be similar (please see the attached 
images).

3. Forgot to mention in my previous email that we have already processed the 
data in P1 and MR solution could be found only in P1 (Phaser was used with an 
option in all possible space groups of that point group).

Please let me know if any other information is required.

With best regards,
Sayan Saha.


On Thu, Jul 28, 2022 at 1:26 PM Schreuder, Herman /DE 
mailto:herman.schreu...@sanofi.com>> wrote:
Dear Sayan,

If a subunit is correctly oriented, but the translation is incorrect, density 
for a ligand may still show up in the binding site of the protein. It might be 
that one of the 2-fold axes, you think is crystallographic, is in fact non 
crystallographic and a few Angstroms away from the crystallographic position.

What I would do:

  1.  Check the images: are there ice-rings or other artifacts that could cause 
scaling problems that would lead to high Rw/Rf values? In that case, there is 
not much you can do.
  2.  Compare the C2 and P22121 solutions: do they have the same overall 
crystal packing (CS+NCS), or are they different? Do they have the same Rw/Rf 
values? Can we learn anything from the differences in overall crystal packing?
  3.  Process, run MR and refine in P1. Do you get lower R-factors? If so, then 
run Zanuda to find out the real space group.

Best,
Herman

Von: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
Im Auftrag von Sayan Saha
Gesendet: Donnerstag, 28. Juli 2022 08:15
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Regarding the correct space group identification

Dear All,

We have collected home-source X-ray intensity data for a protein at 2.6 
Angstrom. The data can be processed in either C2 (a=120, b=80, c=85 and 
beta=115) or P222 (P22121, a=80, b=85, c=110). MR solution can be obtained in 
both the space groups. However, the solution can be refined with an Rw/Rf of 
29/32% only. The protein is bound to a ligand (co-crystallization) for which a 
clear density can be observed.

Any help and suggestion in this regard would be very helpful.

With best regards,
Sayan Saha.




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[ccp4bb] AlphaFold Protein Structure Database update - changes to PAE JSON format

[Sameer Velankar]

Dear All,

You may have seen our announcement today about expanding the AlphaFold Protein 
Structure Database to 214M predicted models. To enable this expansion, we’ve 
updated the Predicted Aligned Error (PAE) JSON format to make it compact (about 
4x smaller):

The PAE JSON numbers are now rounded to the closest integer, giving ~75% 
compressed size reduction. The integer resolution is sufficient for analytical 
purposes.
The indices are not stored anymore since we store the full 2D PAE matrix rather 
than a sparse one, giving ~4% compressed size reduction.
The “distances” field has been renamed to “predicted_aligned_error” and is now 
stored as a 2D array of shape (num_res, num_res) rather than a 1D array. We 
renamed the field on purpose so that existing code breaks rather than 
potentially silently returning wrong values.

For a protein of length num_res, the PAE JSON file has now the following format:

[{
  "predicted_aligned_error": [[0, 1, 4, 7, 9, ...], ...],  # Shape: (num_res, 
num_res).
  "max_predicted_aligned_error": 31.75  # Scalar.
}]

The fields in the JSON file are:
predicted_aligned_error: The PAE value of the residue pair, rounded to the 
closest integer. For PAE value on position (i, j), i is the residue on which 
the structure is aligned for the predicted error, j is the residue on which the 
error is predicted.
max_predicted_aligned_error: A number that denotes the largest possible 
unrounded value of PAE that could occur in the PAE array. The smallest possible 
value of PAE is 0.

The updated PAE format is only available from the AlphaFold Protein Structure 
Database. The PAE format from the AlphaFold Colab notebook is not updated.

If you require support with this change, please email alphaf...@deepmind.com 
 and they may be able to assist.

Best Wishes,

Sameer Velankar


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[ccp4bb] AW: [ccp4bb] Regarding the correct space group identification

[Schreuder, Herman /DE]

Dear Sayan,

If a subunit is correctly oriented, but the translation is incorrect, density 
for a ligand may still show up in the binding site of the protein. It might be 
that one of the 2-fold axes, you think is crystallographic, is in fact non 
crystallographic and a few Angstroms away from the crystallographic position.

What I would do:

  1.  Check the images: are there ice-rings or other artifacts that could cause 
scaling problems that would lead to high Rw/Rf values? In that case, there is 
not much you can do.
  2.  Compare the C2 and P22121 solutions: do they have the same overall 
crystal packing (CS+NCS), or are they different? Do they have the same Rw/Rf 
values? Can we learn anything from the differences in overall crystal packing?
  3.  Process, run MR and refine in P1. Do you get lower R-factors? If so, then 
run Zanuda to find out the real space group.

Best,
Herman

Von: CCP4 bulletin board  Im Auftrag von Sayan Saha
Gesendet: Donnerstag, 28. Juli 2022 08:15
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Regarding the correct space group identification

Dear All,

We have collected home-source X-ray intensity data for a protein at 2.6 
Angstrom. The data can be processed in either C2 (a=120, b=80, c=85 and 
beta=115) or P222 (P22121, a=80, b=85, c=110). MR solution can be obtained in 
both the space groups. However, the solution can be refined with an Rw/Rf of 
29/32% only. The protein is bound to a ligand (co-crystallization) for which a 
clear density can be observed.

Any help and suggestion in this regard would be very helpful.

With best regards,
Sayan Saha.




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



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