Re: [ccp4bb] iNEXT/3D-Bioinfo AI in structural biology workshop announcement

[Jon Agirre]

Dear all,
Just a reminder that there are only 10 days left until abstract submission
closes.

Abstracts will be considered for oral and poster presentations. Please
register and send your abstract before 25 April 2024.



Website:
https://instruct-eric.org/events/ai-approaches-in-structural-biology-and-drug-discovery/


Registration fee: £50 (includes catering)
Venue: EPN campus, Grenoble, France.
Dates: 13-14 May 2024

Best regards,
Jon Agirre on behalf of the organising committee: Jose A. Marquez
(Instruct-ERIC), Magalie Matthieu (Sanofi-Aventis), Rebecca Thompson
(ThermoFisher), Max Nanao (ESRF), Carlos Oscar Sorzano (Instruct-ERIC), Jon
Agirre (Instruct-ERIC/3D-Bioinfo liaison), Sameer Velankar (EMBL-EBI,
3D-Bioinfo), Evangelia Chrysina (ICB-NHRF, Greece).

On Thu, 28 Mar 2024 at 16:35, Jon Agirre  wrote:

> Dear all,
>
> It is our pleasure to announce the joint iNEXT-Discovery and 3D-Bioinfo
> workshop on "AI advances in structural biology and drug discovery", to be
> held in Grenoble on 13-14 May 2024. The rapid advancements in Artificial
> Intelligence (AI) and Machine Learning (ML) have opened up new horizons in
> the field of Structural Biology and Drug Discovery. This workshop is
> addressed to scientists in industry and academia, and aims to bridge the
> gap between the recent developments in AI technologies and experimental
> approaches in translational research. From understanding biological
> structures to accelerating the drug discovery processes, participants will
> gain insights into the latest AI models, as well as high throughput
> experimental techniques. Through a series of invited and selected talks
> (abstract submission will remain open until 25 April 2024), attendees will
> explore the power of combining AI and experimental approaches in
> translational research.
>
>
> Abstracts will be considered for oral and poster presentations. Please
> register and send your abstract before 25 April 2024.
>
>
>
> Website:
> https://instruct-eric.org/events/ai-approaches-in-structural-biology-and-drug-discovery/
>
>
> Registration fee: £50 (includes catering)
> Venue: EPN campus, Grenoble, France.
> Dates: 13-14 May 2024
>
>
> Best regards,
>
>
>
> Jon Agirre, on behalf of the organising committee: Jose A. Marquez
> (Instruct-ERIC), Magalie Matthieu (Sanofi-Aventis), Rebecca Thompson
> (ThermoFisher), Max Nanao (ESRF), Carlos Oscar Sorzano (Instruct-ERIC), Jon
> Agirre (Instruct-ERIC/3D-Bioinfo liaison), Sameer Velankar (EMBL-EBI,
> 3D-Bioinfo), Evangelia Chrysina (ICB-NHRF, Greece).
> --
> Dr Jon Agirre
> Royal Society University Research Fellow (assistant professor)
> Main editor at Acta Crystallographica Section F: Structural Biology
> Communications
> CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo SC (Elixir)
> York Structural Biology Laboratory, Department of Chemistry
> University of York, Heslington, YO10 5DD, York, UK
>


-- 
Dr Jon Agirre (He/Him)
Royal Society University Research Fellow (assistant professor)
Main editor at Acta Crystallographica Section F: Structural Biology
Communications
CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo SC (Elixir)
York Structural Biology Laboratory, Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK



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Re: [ccp4bb] Refmac problem: Validation and Analysis

[Jon Agirre]

Dear Marian,
Thanks for your report. I'm sorry you're having to deal with this problem.
There is nothing wrong with your machine; this is an identified bug and
we're working towards fixing it. In the meantime, the only workaround I can
think of is to roll CCP4 back to a previous update, e.g. 015.
I will keep you posted,
Jon

On Fri, 5 Apr 2024 at 12:54, Marian Oliva  wrote:

> Dear list,
>
>
>
> I have a problem running the Validation and Analysis in Refmac and I would
> really appreciate any feed-back from your side.
>
>
>
> I am using CCP4i2 (CCP4-8.0.018 locally running in Ubuntu 20.04.4).
>
>
>
> Last time I was using Refmac was in November 2023. At the time, I posted
> in the list an error with the CCP4i2 interface (no responding) that I
> solved by turning off the 3D picture in the reports (as kindly suggested by
> Stuart McNicholas).
>
>
>
> Now, despite the 3D picture in the reports is off, I still experience
> ‘some delays’ on the interface response, though this is not a major issue.
>
>
>
> The real problem I’m experiencing is that after a (apparent) normal
> termination of Refmac (no sign of warnings or error messages), I find no
> results from the Multimeric validation.
>
>
>
> Navigating through the jobs folders I have found that in job2 (which I
> guess correspond to the validation) there is:
>
> - no prosmart related files (.out, .pdb, .py).
>
> - the tables_as_csv_files folder is empty.
>
> - there is no molprobity.log file. Instead, there is a log_mtzjoin.txt
> file but it does not highlight any warning or error either.
>
> - the program.xml file only contains the heather but otherwise, it is
> blank (which I guess this is the reason it is not running).
>
> - also, in the param.xml file I found that there are 2 sets of input data
> (instead of one and I don’t know why), where:
>
> -There is no dbFileID for the input F-SIGF data (in any of them)
>
> -In the first one the XYZIN is the XYZIN-coordinated.pdb (instead
> of the xyzout_prosmart_refmac.pdb) and in the second it is the
> xyzout_prosmart_refmac.pdb)
>
>
>
> Checking the terminal while running refmac I saw the following error
> message that appears just after refmac window state ‘The job is finished’.
> This error repeats multiple times, with variations in the
> .WebGL-alphanumerical code, from time to time and ends as follows.
>
>
>
> [3701:3802:0405/112315.960478:ERROR:gles2_cmd_decoder.cc(12701)]
> [.WebGL-0x23e9d90]GL ERROR :GL_INVALID_VALUE : glVertexAttrib4f: index out
> of range
>
> <--- Last few GCs --->
>
> [4500:0xc37]   177121 ms: Scavenge 2518.8 (2529.1) -> 2510.8
> (2529.1) MB, 0.2 / 0.0 ms  (average mu = 0.980, current mu = 0.948)
> allocation failure
> [4500:0xc37]   177148 ms: Scavenge 2518.8 (2529.1) -> 2510.8
> (2529.1) MB, 0.2 / 0.0 ms  (average mu = 0.980, current mu = 0.948)
> allocation failure
> [4500:0xc37]   177175 ms: Scavenge 2518.8 (2529.1) -> 2510.8
> (2529.1) MB, 0.2 / 0.0 ms  (average mu = 0.980, current mu = 0.948)
> allocation failure
>
>
> <--- JS stacktrace --->
>
> [4500:4500:0405/112334.605730:FATAL:memory.cc(38)] Out of memory. size=0
>
>
>
>
>
> Because at the end there is an ‘out of memory’ message, I have increased
> the ram of my computer from 16GB to 32GB but the problem persists. Another
> piece of info is that my computer has 8 CPU but when running CCP4i2 it only
> uses one.
>
>
>
> Does anybody have an idea of which could be the problem?
>
>
>
> Best regards,
>
> Marian
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>


-- 
Dr Jon Agirre (He/Him)
Royal Society University Research Fellow (assistant professor)
Main editor at Acta Crystallographica Section F: Structural Biology
Communications
CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo SC (Elixir)
York Structural Biology Laboratory, Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK



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[ccp4bb] iNEXT/3D-Bioinfo AI in structural biology workshop announcement

[Jon Agirre]

Dear all,

It is our pleasure to announce the joint iNEXT-Discovery and 3D-Bioinfo
workshop on "AI advances in structural biology and drug discovery", to be
held in Grenoble on 13-14 May 2024. The rapid advancements in Artificial
Intelligence (AI) and Machine Learning (ML) have opened up new horizons in
the field of Structural Biology and Drug Discovery. This workshop is
addressed to scientists in industry and academia, and aims to bridge the
gap between the recent developments in AI technologies and experimental
approaches in translational research. From understanding biological
structures to accelerating the drug discovery processes, participants will
gain insights into the latest AI models, as well as high throughput
experimental techniques. Through a series of invited and selected talks
(abstract submission will remain open until 25 April 2024), attendees will
explore the power of combining AI and experimental approaches in
translational research.


Abstracts will be considered for oral and poster presentations. Please
register and send your abstract before 25 April 2024.



Website:
https://instruct-eric.org/events/ai-approaches-in-structural-biology-and-drug-discovery/


Registration fee: £50 (includes catering)
Venue: EPN campus, Grenoble, France.
Dates: 13-14 May 2024


Best regards,



Jon Agirre, on behalf of the organising committee: Jose A. Marquez
(Instruct-ERIC), Magalie Matthieu (Sanofi-Aventis), Rebecca Thompson
(ThermoFisher), Max Nanao (ESRF), Carlos Oscar Sorzano (Instruct-ERIC), Jon
Agirre (Instruct-ERIC/3D-Bioinfo liaison), Sameer Velankar (EMBL-EBI,
3D-Bioinfo), Evangelia Chrysina (ICB-NHRF, Greece).
-- 
Dr Jon Agirre
Royal Society University Research Fellow (assistant professor)
Main editor at Acta Crystallographica Section F: Structural Biology
Communications
CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo SC (Elixir)
York Structural Biology Laboratory, Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK



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Re: [ccp4bb] O-glycans in coot and phenix/refmac

[Jon Agirre]

To the best of my knowledge, there is no o-glycan equivalent of the Coot
glyco plugin. We (as in YSBL, York) are working with others to provide
tools to build all kinds of glycans, but there's nothing you can use at
this point.
I would deal with it like I'd do with other modifications, get monomer,
make the link, repeat. Links are likely to be part of the CCP4 monomer
library already. Also, they are likely to be short-ish glycans, so
hopefully the task won't be too onerous.
One issue depending on the resolution is the identification of the
monosaccharides. But you can have a look at some of the many possibilities
here:
https://www.cell.com/cell/pdf/S0092-8674(18)30053-9.pdf?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867418300539%3Fshowall%3Dtrue
It might help to look at other o-glycosylated structures in the PDB. You
can now do pretty powerful searches on the PDB. Alternatively, I'm sure
someone in my team could provide a list of all o-glycans Privateer can
detect in the PDB.
Hope this helps,
Jon


On Fri, 14 Jul 2023 at 09:03, Jonas Emsley <
8d0668c7d48d-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear All
>
>
>
> We have a crystal structure with O-glycans for the first time attached to
> a Ser and a Thr sidechain
>
>
>
> If anyone can recommend the procedure for adding these in coot and
> refining them in phenix /refmac that would be greatly appreciated
>
>
>
> All the best
>
>
>
> jonas
>
>
>
>
>
>
>
> ##
> Dr Jonas Emsley
> Professor of Macromolecular Crystallography,
> Nottingham Biodiscovery Institute
> School of Pharmacy,
> University of Nottingham,
> University Park,
> Nottingham.
> NG72RD
> Tel: +44 1158467092 <+441158467092>
> Fax: +44 1158468002 <+441158468002>
> email:jonas.ems...@nottingham.ac.uk
> http://www.nottingham.ac.uk/research/groups/structural-biology/index.aspx
>
> *https://orcid.org/-0002-8949-8030
> <https://orcid.org/-0002-8949-8030>*
>
>
>
>
>
>
>
>
>
>
>
> This message and any attachment are intended solely for the addressee
> and may contain confidential information. If you have received this
> message in error, please contact the sender and delete the email and
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>
> Any views or opinions expressed by the author of this email do not
> necessarily reflect the views of the University of Nottingham. Email
> communications with the University of Nottingham may be monitored
> where permitted by law.
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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-- 
Dr Jon Agirre
Royal Society University Research Fellow (assistant professor)
CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo SC (Elixir)
York Structural Biology Laboratory, Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK



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[ccp4bb] CCP4 Summer School 2023: deadline approaching!

[Jon Agirre]

Dear CCP4bb subscribers,

As you may know, the CCP4 Summer School is returning to York after a 4-year
hiatus – this is a continuation of the excellent work done by our
colleagues at St. Andrews pre-2019.

We've got an exciting programme prepared for the students, including
lectures not just on macromolecular crystallography but also Cryo-EM, NMR
and protein fold prediction – please have a look at our website here:
https://www.ccp4.ac.uk/schools/ccp4-summer-school/index.php

There will be a few social events, including a ceilidh and school dinner
in/on a unique venue (!).

As you will see, the BBSRC is generously funding fees for up to 10
students, while the BCA is also providing some bursaries. These bursaries
are meant for UK-based students only, but our school is open to anyone.

*Registration closes on the 5th of July (next week).*
Places are limited.

Many thanks,
Johan Turkenburg, Jon Agirre and Paul Bond
-- 
Dr Jon Agirre
Royal Society University Research Fellow (assistant professor)
CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo SC (Elixir)
York Structural Biology Laboratory, Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK



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[ccp4bb] Postdoctoral position in method development (York Structural Biology Laboratory)

[Jon Agirre]

Dear all,

Applications are invited for a Postdoctoral Research Associate position,
funded by the Royal Society, for up to 30 months to work with Dr Jon Agirre in
the Department of Chemistry. The successful applicant will join a vibrant
team of researchers at the heart of the world-leading York Structural
Biology Laboratory (YSBL). The work of the laboratory over the years has
included the delivery of world-leading methods and experimental
discoveries, training and nurturing hundreds of outstanding scientists in
the process.

Role
The AlphaFold software for protein model prediction has revolutionised
workflows in structural biology. However, while high-accuracy models are
now available for most human proteins of medical relevance, up to 50% of
those proteins are expected to be glycosylated – a modification whose
structure AlphaFold does not predict. Protein glycosylation is greatly
important, with implications for protein folding and molecular recognition
including, as evidenced by the spike glycoprotein of SARS-CoV-2, viral
infection. In collaboration with other scientists, we have extended the
Privateer software to interactively build missing glycosylation onto
precalculated AlphaFold models. In parallel, we have developed analyses
that allow us to get a clear picture of glycans and their interactions,
including H-bonds and XH-Pi interactions. We expect that these methods will
enable us to, based on existing glycobiological knowledge, extend the
Privateer software to automatically complete AlphaFold models with crucial
missing glycosylation components.

We are seeking a person with an interest in both biology and coding, who
can collaborate with others in a very diverse team with a mission to
further our knowledge of glycobiology and seize the opportunities presented
by a deeper understanding of it.

Main duties and responsibilities
To develop and extend the Privateer software to complete AlphaFold models
with the missing glycan components.
To further our existing collaborations with CCP4, CCP-EM, PDB-REDO, the
Protein Data Bank and the AlphaFold Protein Structure Database.

Department
The Department of Chemistry is one of the largest and most successful
departments at York and we are renowned internationally for our research.
As a department, we strive to provide a working environment that allows all
staff and students to contribute fully, to flourish, and to excel. We are
proud of our Athena Swan Gold Award. The Department of Chemistry values all
employees for the qualities and skills they bring to the workplace and aims
to be a diverse and egalitarian community in which all can thrive.

For informal enquiries: please contact Dr Jon Agirre, jon.agi...@york.ac.uk
To apply: https://jobs.york.ac.uk/vacancy/research-associate-529961.html
Deadline for applications: 20 August 2023.

Many thanks for making it this far in the advert!

With best wishes,
Jon
-- 
Dr Jon Agirre
Royal Society University Research Fellow (assistant professor)
CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo SC (Elixir)
York Structural Biology Laboratory, Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK



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[ccp4bb] Save the dates: CCP4-BCA Summer School in York 19-25 August 2023

[Jon Agirre]

Dear all,

It is a great pleasure to announce the return of the CCP4-BCA Summer School
on macromolecular crystallography and associated techniques, to be held at
the University of York on 19-25 August 2023.

Running in-person for the first time since the COVID-19 pandemic, the
school aims to bring together early-career scientists in the UK, Europe and
beyond and train them in the latest advances in structural biology, with a
primary focus on macromolecular crystallography. The school, which was
formerly run at the University of St. Andrews for many years, has trained
hundreds of crystallographers while also providing them with unforgettable
collective memories. The York team aims to capture and continue the essence
and tradition of the school, blending it with the best the City of York has
to offer.

Registration will open soon, but in the meantime feel free to check out our
preliminary programme on our website:
https://www.ccp4.ac.uk/schools/ccp4-summer-school/index.php

The organisers,
Johan Turkenburg, Jon Agirre and Paul Bond
-- 
Dr Jon Agirre
Royal Society University Research Fellow (assistant professor)
CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo (Elixir)
York Structural Biology Laboratory, Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
Office: B/K065 Phone: +44 (0) 1904 32 8252



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Re: [ccp4bb] Alexey Vagin

[Jon Agirre]

I met Alexey at an EMBO course in Gif-sur-Yvette in 2005. I thought he
was impressive and had an incredible sense of humour: from his
friendly competition with Jorge Navaza, to his remarks about making
MOLREP properly automated so he could have 'more time to smoke'.
Back then, his York website was full of hilarious crystallography
memes, long before the explosion of social media. A brilliant guy who
helped make crystallography both fun and interesting.

My condolences,
Jon


On Sun, 26 Mar 2023 at 19:41, James Foadi
<09daa8ec3774-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> I am very sad to hear this! Alexey was one of my favourites when I was in 
> York, and I have had many lovely conversations with him. You are right, 
> Eugene, his contributions have helped and will keep helping many 
> crystallographers and methods developers.
>
> May his soul rest in peace!
>
> James
>
>
> Sent from Yahoo Mail for iPhone
>
> On Sunday, March 26, 2023, 7:29 pm, Eugene Krissinel - STFC UKRI 
> <6fcecdb9c847-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Dear All,
>
> It is with a great sadness that I share with you that Alexey Vagin passed 
> away this Saturday in the Radcliffe Hospital in Oxford after suffering from a 
> heart attack with subsequent complications. He was 78 years old.
>
> Alexey made many developments in methods and software for macromolecular 
> crystallography, to which he devoted his whole life. He is known for his 
> BLANC Suite for structure solution done at the Moscow Institute of 
> Crystallography in the 1980s, as well as for his contributions to Refmac and 
> Monomer Library. Many thousands of researchers have benefited from his work 
> on Molrep and Balbes software for Molecular Replacement. After his retirement 
> in 2010, Alexey developed and actively maintained the MorDA software for MR, 
> which became a monument to his efforts.
>
> Alexey's work will continue to serve generations of researchers through his 
> contributions to CCP4, where we will take the best care of his distinguished 
> legacy.
>
> With sympathy to everyone who knew Alexey personally and for whom this is 
> very sad news,
>
> Eugene
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>
> ____________
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



-- 
Dr Jon Agirre
Royal Society University Research Fellow (assistant professor)
CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo (Elixir)
York Structural Biology Laboratory, Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
Office: B/K065 Phone: +44 (0) 1904 32 8252



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Re: [ccp4bb] To Trim or Not to To Trim

[Jon Agirre]

Are downstream users of models with poorly resolved regions more likely to
spot them if they have huge B-factors or zero occupancy? If the answer is
'neither', then perhaps we need to develop a different solution.

On Fri, 10 Mar 2023 at 16:33, Goldman, Adrian 
wrote:

> Maybe simplest just to trim it back. I do worry that the presence of a
> wrong conformation will lead to inaccurate vdw clashes that could
> negatively affect other atoms.
>
> Sent from my iPhone
>
> > On 10 Mar 2023, at 18:25, Phil Jeffrey  wrote:
> >
> > On 3/10/23 4:05 AM, Julia Griese wrote:
> >> Hi all,
> >> My impression has been that the most common approach these days is to
> “let the B-factors take care of it”, but I might be wrong. Maybe it’s time
> to run another poll?
> >> Personally, I call any other approach R-factor cosmetics. The goal in
> model building is not to achieve the lowest possible R-factors, it’s to
> build the most physically meaningful, most likely to be correct, model.
> >
> > And I could call your approach "model cosmetics".
> >
> > If you can't see the side-chain, you don't know where it is and you
> probably don't even know where the centroid of the distribution is. Only in
> the case of very short side-chains with few rotamers can you make a
> reasonable volume approximation to where the side-chain is and "let the
> B-factors" smear out the density to cover a range of the projected
> conformations.
> >
> > For longer side-chains, if you put it in a single conformation, you are
> very likely NOT coming close to correctly modeling the actual distribution
> of the conformations.  So let's circle back on "most likely to be correct
> model" and ask what we *actually* know about where the atoms are.
> >
> > Put your disordered Arg in with 10 alternate conformations, each with a
> refined relative occupancy, and then let the B-factors smear that lot out,
> and that's your better model.
> >
> > Phil Jeffrey
> > Princeton
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
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-- 
Dr Jon Agirre [image: A button with "Hear my name" text for name playback
in email signature]  <https://www.name-coach.com/jon-agirre>
Royal Society University Research Fellow
CCP4 WG2 co-chair and ED champion | instruct-ERIC representative @
3D-Bioinfo (Elixir)
York Structural Biology Laboratory, Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
Mastodon: @glycojones@mastodon.world



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[ccp4bb] Postdoctoral position in YSBL, University of York

[Jon Agirre]

Dear all,

Applications are invited for a Postdoctoral Research Associate position,
funded by the Royal Society, for up to 30 months to work with Dr Jon Agirre
in the Department of Chemistry. The successful applicant will join a
vibrant team of researchers at the heart of the world-leading York
Structural Biology Laboratory (YSBL). The work of the laboratory over the
years has included the delivery of world-leading methods and experimental
discoveries, training and nurturing hundreds of outstanding scientists in
the process.

Role
In collaboration with Dr. Elisa Fadda (Maynooth University, Ireland), we
have developed proof-of-concept software that models protein glycosylation
into AlphaFold models. This task has been automated and integrated into the
new Python interface of the carbohydrate-specific Privateer software. In
parallel, we have developed infrastructure and analyses that allow us to
get a clear picture of glycans and their interactions. We expect that this
technology will enable the successful applicant to, based on existing
glycobiological knowledge, extend the Privateer software to predict, build
and adapt models of glycans onto AlphaFold models.

Main duties and responsibilities:
- To develop and extend the Privateer software to predict, build and adapt
models of glycans onto AlphaFold models.
- To further our existing collaborations with CCP4, CCP-EM, PDB-REDO, the
Protein Data Bank and the AlphaFold Protein Structure Database.

For informal enquiries: please contact Dr Jon Agirre, jon.agi...@york.ac.uk
To apply: https://jobs.york.ac.uk/vacancy/research-associate-513495.html

Department
The Department of Chemistry is one of the largest and most successful
departments at York and we are renowned internationally for our research.
As a department, we strive to provide a working environment that allows all
staff and students to contribute fully, to flourish, and to excel. We are
proud of our Athena Swan Gold Award. The Department of Chemistry values all
employees for the qualities and skills they bring to the workplace and aims
to be a diverse and egalitarian community in which all can thrive.

Many thanks for making it this far in the advert!
With best wishes,
Jon
-- 
Dr Jon Agirre [image: A button with "Hear my name" text for name playback
in email signature]  <https://www.name-coach.com/jon-agirre>
Royal Society Olga Kennard Research Fellow
CCP4 ED champion | instruct-ERIC representative @ 3D-Bioinfo (Elixir)
York Structural Biology Laboratory, Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
Twitter: @glycojones



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Re: [ccp4bb] Thanks

[Jon Agirre]

Thank you Clare for all your contributions to the community throughout
these 25 years, particularly for bringing the technicians' perspective into
focus, and providing helpful feedback. You will be missed.
Best of luck in your next role,
Jon

On Wed, 9 Feb 2022 at 09:58, Clare Stevenson (JIC) <
clare.steven...@jic.ac.uk> wrote:

> I have subscribed to the CCP4 bulletin board for over 25 years and
> attended many CCP4 meetings. I am changing role shortly and will no longer
> be a crystallographer so will unsubscribe from the board. I just wanted to
> pass on my thanks to everyone who has written posts, contributed to
> discussions and answered questions. It always amazes me just how great the
> crystallography CCP4 community is and it has been great to be involved in
> it.
>
>
>
> Have fun
>
>
>
> Clare
>
>
>
>
>
> Dr Clare E.M. Stevenson
>
> John Innes Centre
>
> Norwich Research Park
>
> Colney Lane
>
> Norwich
>
> NR4 7UH
>
> Tel 01603 450734
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>


-- 
Dr Jon Agirre
Royal Society Olga Kennard Research Fellow
CCP4 ED champion | Instruct representative @ 3D-Bioinfo (Elixir)
York Structural Biology Laboratory, Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
Twitter: @glycojones



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Re: [ccp4bb] [ccp4bb] A "funny" thing related to AlphaFold2 ....

[Jon Agirre]

It might be, because the mmCIF versions work fine with MG.

On Wed, 10 Nov 2021 at 12:16, Harry Powell - CCP4BB <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi folks
>
> Been a while, but I’ve been doing some work on checking that some files
> are valid PDB files and went back to the documentation; as far as I can
> work out, the best solution to this is John Walker’s, because “MODEL 0” is
> not allowed in the standard (maybe it is for mmCIF…) -
>
> > On 27 Aug 2021, at 16:39, John R. Walker 
> wrote:
> >
> > I just change MODEL 0 to MODEL 1 then it works fine.
> >
> > John
>
> As far as I can see (from a small sample of the 150,000 AlphaFold models,
> soon to be a few more...) all the PDB files downloadable from
> alphafold.ebi.ac.uk are non-conformant. The documentation on PDB files
> that I have been able to find easily says -
>
> > Details
> >
> > * This record is used only when more than one model appears in an entry.
> Generally, it is
> > employed only for NMR structures. The chemical connectivity should be
> the same for each model.
> > ATOM, HETATM, SIGATM, SIGUIJ, ANISOU, and TER records for each model
> structure are
> > interspersed as needed between MODEL and ENDMDL records.
> >
> > * The numbering of models is sequential beginning with 1.
>
> Harry
>
> >
> > On Fri, Aug 27, 2021 at 11:03 AM Schreuder, Herman /DE <
> herman.schreu...@sanofi.com> wrote:
> > Dear Nick,
> >
> >
> >
> > I had just looked at a pdb downloaded from the alphafold server without
> problems. However, then I realized that I had looked at the alphafold model
> after I had it superimposed on my own structure. Loading the alphafoldmodel
> directly in coot failed for me as well.
> >
> >
> >
> > By looking into the pdb file, I discovered that the alphafold file has a
> “MODEL” record just before the coordinates and an “ENDMDL” record after the
> coordinates. After deleting these two records, the alphafold pdb loads fine.
> >
> >
> >
> > Hope this helps,
> >
> > Herman
> >
> >
> >
> > Von: CCP4 bulletin board  Im Auftrag von
> Nicholas Keep
> > Gesendet: Freitag, 27. August 2021 16:51
> > An: CCP4BB@JISCMAIL.AC.UK
> > Betreff: Re: [ccp4bb] A "funny" thing related to AlphaFold2 
> >
> >
> >
> > Has anyone made use of an Alpha Fold PDB as opposed to CIF.  On the half
> > dozen or so I have tried to read into CCP4mg or coot the PDB has always
> > failed but the CIF is fine.  I can then write out a PDB if I want.
> >
> > I could add to the conspiracy theories that this is EBI trying to
> > normalise use of CIF format, but I suspect it is something much more
> > mundane, that should be addressed.
> >
> > Best wishes
> >
> > Nick
> >
> > --
> > NOTE NEW PHONE NUMBER JULY 2020
> >
> > I do not work Mondays. For urgent business on a Monday contact Clare
> Woodward (Director of Operations) or Gillian Forrester (Deputy Dean)
> >
> > Prof Nicholas H. Keep
> > Executive Dean of School of Science
> > Professor of Biomolecular Science
> > Crystallography, Institute for Structural and Molecular Biology,
> > Department of Biological Sciences
> > Birkbeck, University of London,
> > Malet Street,
> > Bloomsbury
> > LONDON
> > WC1E 7HX
> >
> > Office G54a
> >
> > Dean Email; scid...@bbk.ac.uk
> > Dept email n.k...@mail.cryst.bbk.ac.uk
> > Telephone 020-3926-3475 (Will contact me at home if working as well as
> my office)
> >
> > If you want to access me in person you have to come to the
> crystallography entrance
> > and ring me or the department office from the internal phone by the door
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
> >
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
>
> #

Re: [ccp4bb] A "funny" thing related to AlphaFold2 ....

[Jon Agirre]

Just get rid of the PDB header minus CRYST1 IIRC and it'll work. Some weird
formatting problem.

On Fri, 27 Aug 2021 at 15:50, Nicholas Keep 
wrote:

> Has anyone made use of an Alpha Fold PDB as opposed to CIF.  On the half
> dozen or so I have tried to read into CCP4mg or coot the PDB has always
> failed but the CIF is fine.  I can then write out a PDB if I want.
>
> I could add to the conspiracy theories that this is EBI trying to
> normalise use of CIF format, but I suspect it is something much more
> mundane, that should be addressed.
>
> Best wishes
>
> Nick
>
> --
> NOTE NEW PHONE NUMBER JULY 2020
>
> I do not work Mondays.  For urgent business on a Monday contact Clare
> Woodward (Director of Operations) or Gillian Forrester (Deputy Dean)
>
> Prof Nicholas H. Keep
> Executive Dean of School of Science
> Professor of Biomolecular Science
> Crystallography, Institute for Structural and Molecular Biology,
> Department of Biological Sciences
> Birkbeck,  University of London,
> Malet Street,
> Bloomsbury
> LONDON
> WC1E 7HX
>
> Office G54a
>
> Dean Email;scid...@bbk.ac.uk
> Dept email n.k...@mail.cryst.bbk.ac.uk
> Telephone 020-3926-3475  (Will contact me at home if working as well as my
> office)
>
> If you want to access me in person you have to come to the crystallography
> entrance
> and ring me or the department office from the internal phone by the door
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
>


-- 
Dr Jon Agirre
Royal Society Olga Kennard Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
Twitter: @glycojones
<https://york.ac.uk/open-research>



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Re: [ccp4bb] Enhanced Validation of Small-Molecule Ligands and Carbohydrates

[Jon Agirre]

gt;
> Email: jasm...@rcsb.rutgers.edu
>
> Phone: (848)445-0103 ext 4920
>
> Fax: (732)445-4320
>
> ===
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> The contents of this e-mail are confidential and may be subject to legal 
> privilege.
>  If you are not the intended recipient you must not use, disseminate, 
> distribute or
>  reproduce all or any part of this e-mail or attachments.  If you have 
> received this
>  e-mail in error, please notify the sender and delete all material pertaining 
> to this
>  e-mail.  Any opinion or views expressed in this e-mail are those of the 
> individual
>  sender and may not represent those of The New Zealand Institute for Plant and
>  Food Research Limited.
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>


-- 
Dr Jon Agirre
Royal Society Olga Kennard Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
Twitter: @glycojones



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[ccp4bb] Deadline extended: First CCP4 Study Weekend illustration competition

[Jon Agirre]

Dear colleagues,

thanks to those of you who have sent entries for this CCP4 Study Weekend
competition. As a number of people have requested it, we have decided to
extend the deadline until Monday 23 December (one week from now).

Looking forward to receiving your entries – see below for the guidelines.

Best wishes,
Jon, Alan, Robbie and Karen

On Mon, 4 Nov 2019 at 11:37, Jon Agirre  wrote:

> Dear colleagues,
>
> We are pleased to announce the opening of the first CCP4 Study Weekend
> illustration competition, made possible by CCP4’s long standing
> collaboration with IUCr Journals.
>
> Getting your science out to the public requires more than good research.
> You need to make it memorable! And what better way to do it than with
> excellent figures? We invite you to make a figure that tells a structural
> biology story in a creative and informative way. The submitted figures will
> be showcased during the Study Weekend at several locations at the
> conference venue.
>
> *Prize*
> The creator of the winning illustration gets to design the cover
> illustration of the Study Weekend’s proceedings to be published early 2021.
> Apart from this commission there may be another (sur)prize.
>
> *Format*
> Illustrations, along with a short description of content and methods used,
> are to be sent to jon.agi...@york.ac.uk before December 15th 2019.
>
> Images must have a resolution of 1920x1080 (16:9) in order to fit the
> format of the screens and main room projector. Any combination of graphics
> and (if any) post-processing software may be used, as long as details are
> given with the submission. The format of the illustration should be PNG.
>
> *Judges*
> As you may know, Dr Jeroen Claus (founder of Phospho Biomedical Animation)
> will give the closing talk at the 2020 edition of the CCP4 Study Weekend.
> He, along with Louise Jones (managing editor of Acta Crystallographica
> sections D & F) will judge the submitted figures based on their graphical
> quality as well as their ability to convey a complex structural message
> clearly.
>
> *Decision*
> The winner will be announced on January 8th at the dinner - before the
> céilidh.
>
> Up to date information and registration:
> http://www.cvent.com/d/fyq0g9/4K?cpc=FCNF5V7H4B4
>
> Looking forward to receiving your images!
>
> Jon Agirre, Alan Roseman, Robbie Joosten and Karen McIntyre
> --
> Dr Jon Agirre
> Royal Society University Research Fellow
> York Structural Biology Laboratory / Department of Chemistry
> University of York, Heslington, YO10 5DD, York, UK
> http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
> Office: /B/K/065 Phone: +44 (0) 1904 32 8252
> Twitter: @glycojones
>


-- 
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
Twitter: @glycojones



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https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] First CCP4 Study Weekend illustration competition

[Jon Agirre]

Dear colleagues,

We are pleased to announce the opening of the first CCP4 Study Weekend
illustration competition, made possible by CCP4’s long standing
collaboration with IUCr Journals.

Getting your science out to the public requires more than good research.
You need to make it memorable! And what better way to do it than with
excellent figures? We invite you to make a figure that tells a structural
biology story in a creative and informative way. The submitted figures will
be showcased during the Study Weekend at several locations at the
conference venue.

*Prize*
The creator of the winning illustration gets to design the cover
illustration of the Study Weekend’s proceedings to be published early 2021.
Apart from this commission there may be another (sur)prize.

*Format*
Illustrations, along with a short description of content and methods used,
are to be sent to jon.agi...@york.ac.uk before December 15th 2019.

Images must have a resolution of 1920x1080 (16:9) in order to fit the
format of the screens and main room projector. Any combination of graphics
and (if any) post-processing software may be used, as long as details are
given with the submission. The format of the illustration should be PNG.

*Judges*
As you may know, Dr Jeroen Claus (founder of Phospho Biomedical Animation)
will give the closing talk at the 2020 edition of the CCP4 Study Weekend.
He, along with Louise Jones (managing editor of Acta Crystallographica
sections D & F) will judge the submitted figures based on their graphical
quality as well as their ability to convey a complex structural message
clearly.

*Decision*
The winner will be announced on January 8th at the dinner - before the
céilidh.

Up to date information and registration:
http://www.cvent.com/d/fyq0g9/4K?cpc=FCNF5V7H4B4

Looking forward to receiving your images!

Jon Agirre, Alan Roseman, Robbie Joosten and Karen McIntyre
-- 
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
Twitter: @glycojones



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https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] CCP4 Study Weekend 2020: registration now open!

[Jon Agirre]

Of course we want everyone to register immediately, but if you insist on
seeing the programme first, please go to
http://www.cvent.com/events/ccp4-study-weekend-2020/event-summary-001c74f5ecfa4987af3e908c7a9d7d60.aspx?fqp=true


Cheers,
Jon, Robbie and Alan

On Wed, 11 Sep 2019 at 10:15, Jon Agirre  wrote:

> Dear colleagues,
>
> We are pleased to announce that the next CCP4 Study Weekend in its 2020
> edition will be devoted to the single most synergic task in structural
> biology: model building. Aside from covering the latest advances in both
> automated and manual procedures, the meeting will offer sessions on related
> topics such as refinement, validation and representation, with a focus on
> helping you produce the best possible model from your experimental data.
> All sessions will have an integrative character, presenting methods and
> approaches that may be indistinctly used with X-ray crystallography, and
> electron cryo-microscopy or diffraction.
>
> This meeting will have a couple of innovations too - more announcements
> will follow in due course. The most important ones will be posted here (as
> always), but for more fluid news, speaker profiles and direct communication
> with the organisers, please use hashtag #CCP4SW on Twitter or give us a
> follow (vide infra).
>
> As in recent editions, the event will be held at the East Midlands
> Conference Centre in Nottingham, from the 7th to the 9th of January 2020.
> We are very much looking forward to welcoming you in Nottingham. And yes,
> there will be a Cèilidh (https://en.wikipedia.org/wiki/Cèilidh).
>
> Registration and programme details: https://tinyurl.com/ccp4sw2020
>
> Best wishes,
>
> Robbie Joosten (@Robbie_Joosten),
> Alan Roseman (@AlanRoseman3),
> Jon Agirre (@glycojones),
> and the rest of CCP4 (@ccp4_mx)
> --
> Dr Jon Agirre
> Royal Society University Research Fellow
> York Structural Biology Laboratory / Department of Chemistry
> University of York, Heslington, YO10 5DD, York, UK
> http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
> Office: /B/K/065 Phone: +44 (0) 1904 32 8252
> Twitter: @glycojones
>


-- 
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
Twitter: @glycojones



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

[ccp4bb] CCP4 Study Weekend 2020: registration now open!

[Jon Agirre]

Dear colleagues,

We are pleased to announce that the next CCP4 Study Weekend in its 2020
edition will be devoted to the single most synergic task in structural
biology: model building. Aside from covering the latest advances in both
automated and manual procedures, the meeting will offer sessions on related
topics such as refinement, validation and representation, with a focus on
helping you produce the best possible model from your experimental data.
All sessions will have an integrative character, presenting methods and
approaches that may be indistinctly used with X-ray crystallography, and
electron cryo-microscopy or diffraction.

This meeting will have a couple of innovations too - more announcements
will follow in due course. The most important ones will be posted here (as
always), but for more fluid news, speaker profiles and direct communication
with the organisers, please use hashtag #CCP4SW on Twitter or give us a
follow (vide infra).

As in recent editions, the event will be held at the East Midlands
Conference Centre in Nottingham, from the 7th to the 9th of January 2020.
We are very much looking forward to welcoming you in Nottingham. And yes,
there will be a Cèilidh (https://en.wikipedia.org/wiki/Cèilidh).

Registration and programme details: https://tinyurl.com/ccp4sw2020

Best wishes,

Robbie Joosten (@Robbie_Joosten),
Alan Roseman (@AlanRoseman3),
Jon Agirre (@glycojones),
and the rest of CCP4 (@ccp4_mx)
-- 
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
Twitter: @glycojones



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Re: [ccp4bb] CCP4mg trouble making movies

[Jon Agirre]

Hi Tassos,

can you try a standalone CCP4 installation? I seem to recall ffmpeg was
missing from the regular CCP4 distro and therefore that bit didn’t work.

Cheers
Jon

On Tue, 2 Jul 2019 at 17:22, Anastassis Perrakis  wrote:

> Dear all,
>
> I am having some trouble with ccp4mg 2.10.10 and making movies on a Mac
> running OSX 10.13.6
>
> I am trying now for a test a single-scene movie of 2sec “rock”. The movie
> previews  fine.
> When I “make movie” the scene directory and the frames are created, and I
> get a window telling me:
> “For movie test / Converting frames to scene movie / and merging scene
> movies”
> However, nothing is happening - no files and my CPU is blissfully idle.
>
> Any hints/clues?
>
> Thanks,
>
> Tassos
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
-- 
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
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Re: [ccp4bb] different residues as alternate occupancy?

[Jon Agirre]

Another relatively frequent case concerns carbohydrates at the reducing end
of a polysaccharide, where both alpha and beta anomeric forms can occur.
Because the PDB gives two different CCD IDs to alpha and beta anomeric
forms of the same monosaccharide – e.g. BGC and GLC for glucopyranose – you
have the same problem described here. See Fig9 in
https://journals.iucr.org/d/issues/2017/02/00/ba5257/ for an example (sorry
for the plug!).

On Tue, 25 Jun 2019 at 16:00, Guenter Fritz <
guenter.fritz.phenix.c...@gmail.com> wrote:

> Dear all,
> thank you all for feedback help.
> Best wishes!
> Guenter
>
> Dear Guenter, yes look at crambin (pdbcode 1EJG).
>
>
> This crashes Coot until you add*
>
>   allow_duplicate_sequence_numbers()
>
> to $HOME/.coot.py in OSX or the appropriate place on Windows. For
> Windows, as there is no $HOME, Coot uses .coot.py or .coot-preferences/
> directory for configuration - these can be found (added to) the
> directory in which Coot was installed (e.g. C:\WinCoot).
>
> To resolve your problem look at
>
> https://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12
>
> example 5
>
> Br, Georg.
>
>
> Am 2019-06-24 um 4:22 PM schrieb Savvas Savvides:
>
> The structure of milk proteins obtained from in vivo-grown crystals from a
> viviparous cockroach could also serve as an interesting case:
>
> http://dx.doi.org/10.1107/S2052252516008903
>
> best wishes
> Savvas
>
>
> On 24 Jun 2019, at 16:03, Holton, James M <
> 270165b9f4cf-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> A classic case of this is crambin.  Residue 25 of 3nir.
>
> -James Holton
> MAD Scientist
>
> On 6/24/2019 1:00 AM, Guenter Fritz wrote:
>
> Dear all,
>
> I am refining a multimer and mass spec data of the sample indicate
> that there is a mixture of two variants which differ in one amino acid
> residue. The density that we see is therefore most likely an average
> of both variants. I have created a pdb file with "alternate residues"
> each with 0.5 occupancy at this position to use it in refinement.
> However, the programs detect this as an error in the pdb file.
>
> Has anyone  faced such a problem previously? Any suggestions are very
> much appreciated.
>
> Thanks a lot and best regards, Guenter
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
>
> --
>
> 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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-- 
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
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Re: [ccp4bb] PDBe-KB ligand centric pages survey

[Jon Agirre]

Thank you all for your help with this - it looks like John's link was being
wiped out from the e-mail by an ad-blocking extension (?). So if you can't
find the link, make sure you try deactivating whatever ad-blocker your
browser is using :)

On Thu, 4 Apr 2019 at 15:56, Jon Agirre  wrote:

> No link to the survey :(
>
> On Thu, 4 Apr 2019 at 15:55, John Berrisford  wrote:
>
>> Dear All,
>>
>>
>>
>> We are in the process of redesigning the ligand pages of PDBe and we
>> would be grateful if you could fill out a short survey to help us
>> understand what information about small molecules / ligands you would find
>> useful. The survey is available at https://bit.ly/2FFmHFG
>>
>>
>>
>> Recently, we have introduced protein-specific aggregated views on the
>> structural data (pdbe-kb.org/proteins) as a part of Protein Data Bank in
>> Europe Knowledge Base (PDBe-KB). We highlight the available information
>> related to structures of specific proteins, including structural and
>> functional annotations, domains, ligand-binding sites and interfaces. In
>> the next step we would like to present a similar aggregated view from a
>> small molecule / ligand perspective.
>>
>>
>>
>> Thank you for your time,
>>
>>
>>
>> John Berrisford
>>
>>
>>
>> --
>>
>> John Berrisford
>>
>> PDBe
>>
>> European Bioinformatics Institute (EMBL-EBI)
>>
>> European Molecular Biology Laboratory
>>
>> Wellcome Trust Genome Campus
>>
>> Hinxton
>>
>> Cambridge CB10 1SD UK
>>
>> Tel: +44 1223 492529
>>
>>
>>
>> http://www.pdbe.org
>>
>> http://www.facebook.com/proteindatabank
>>
>> http://twitter.com/PDBeurope
>>
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>
>
> --
> Dr Jon Agirre
> Royal Society University Research Fellow
> York Structural Biology Laboratory / Department of Chemistry
> University of York, Heslington, YO10 5DD, York, UK
> http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
> Office: /B/K/065 Phone: +44 (0) 1904 32 8252
> Twitter: @glycojones
>


-- 
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
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Re: [ccp4bb] PDBe-KB ligand centric pages survey

[Jon Agirre]

No link to the survey :(

On Thu, 4 Apr 2019 at 15:55, John Berrisford  wrote:

> Dear All,
>
>
>
> We are in the process of redesigning the ligand pages of PDBe and we would
> be grateful if you could fill out a short survey to help us understand what
> information about small molecules / ligands you would find useful. The
> survey is available at https://bit.ly/2FFmHFG
>
>
>
> Recently, we have introduced protein-specific aggregated views on the
> structural data (pdbe-kb.org/proteins) as a part of Protein Data Bank in
> Europe Knowledge Base (PDBe-KB). We highlight the available information
> related to structures of specific proteins, including structural and
> functional annotations, domains, ligand-binding sites and interfaces. In
> the next step we would like to present a similar aggregated view from a
> small molecule / ligand perspective.
>
>
>
> Thank you for your time,
>
>
>
> John Berrisford
>
>
>
> --
>
> John Berrisford
>
> PDBe
>
> European Bioinformatics Institute (EMBL-EBI)
>
> European Molecular Biology Laboratory
>
> Wellcome Trust Genome Campus
>
> Hinxton
>
> Cambridge CB10 1SD UK
>
> Tel: +44 1223 492529
>
>
>
> http://www.pdbe.org
>
> http://www.facebook.com/proteindatabank
>
> http://twitter.com/PDBeurope
>
>
>
> ------
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>


-- 
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
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Re: [ccp4bb] Molprobity "Feature" in ccp4i2 refmac

[Jon Agirre]

Hi Nick,

thanks for your report; I'm on it.

Cheers,
Jon

On Fri, 29 Mar 2019 at 12:18, Nicholas Keep 
wrote:

> I have found a 'feature' in molprobity.  if there are two atoms on top
> of each other (not hard to do by mistake when adding waters in coot),
> then molprobity does not work or at least does not give the outputs
> required to then give the coot molprobity checklist file our of the
> ccp4i2 refmac interface.  A check at some point for this mistake would
> be good to throw out a clear error message.
>
> Best wishes
>
> Nick
>
>
> --
> Prof Nicholas H. Keep
> Executive Dean of School of Science
> Professor of Biomolecular Science
> Crystallography, Institute for Structural and Molecular Biology,
> Department of Biological Sciences
> Birkbeck,  University of London,
> Malet Street,
> Bloomsbury
> LONDON
> WC1E 7HX
>
> email n.k...@mail.cryst.bbk.ac.uk
> Telephone 020-7631-6852  (Room G54a Office)
>020-7631-6800  (Department Office)
> Fax   020-7631-6803
> If you want to access me in person you have to come to the crystallography
> entrance
> and ring me or the department office from the internal phone by the door
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>


-- 
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
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Re: [ccp4bb] fix b-factors/coordinates during refinement

[Jon Agirre]

Hi Nick,

you can refine B-factors while leaving coordinates untouched by using the
'refi bonly' keywords. You can also preset an average (e.g. Wilson B) and
have refmac do coordinate refinement (
http://www.ccp4.ac.uk/html/refmac5/keywords/xray-principal.html#refi).

Cheers,
Jon

On Wed, 20 Feb 2019 at 11:29, Pearce, N.M. (Nick)  wrote:

> Hi all,
>
> Is it possible to fix the B-factors/coordinates of a model in refinement
> with REFMAC?
>
> It’s trivial to do so in phenix.refine (strategy=…), but I can’t find an
> equivalent command line flag in refmac…
>
> Thanks,
> Nick
>
> Post-doctoral Fellow,
> Crystal and Structural Chemistry,
> Utrecht University
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>


-- 
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
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Re: [ccp4bb] 2019 mid-range & high-end LINUX laptops for structural biology

[Jon Agirre]

Dear Domen,

I bought a Lenovo Thinkpad p72 for both MX and cryoEM work last year and I
am generally happy. The Xeon CPUs do get hot from time to time when
governor is set to performance, but the thing is well ventilated and not
too noisy.

The Quadro GPU I have is, performance-wise, equivalent to a GTX 1070, so
good enough for Cuda too. Works well in Ubuntu as soon as you get rid of
the nouveau driver.

Also, if you find a 17” laptop too big for you, there are smaller
alternatives in the same line.

Am no Lenovo fan, but I find this machine offers similar or better
performance than that of a gaming laptop, but without all the flashy skully
flamboyances.

Best wishes,
Jon

On Wed, 13 Feb 2019 at 14:09, Domen Zafred  wrote:

> Dear CCP4 community,
>
> My 8-year-old Dell Inspiron with Ubuntu 10 is waving goodbye and I would
> ask for some help on this bulletin as buying/setting up a new workstation
> is common trouble in our community.
> Has anyone recently set up a laptop for structural work with all the MD,
> docking, etc. *in silico *simulations? Is dual boot Linux/Win still a
> thing, or do you rather run Windows virtually (which VM software)? Are
> there any known issues with Nvidia Quadro P series GPUs or Intel i5
> processors? Has anyone tried Xeon/ECC on a laptop? Does Ubuntu LTS still
> win the hearts of non-enthusiasts?
>
> Any successfully tested laptops (with names and/or listed configuration)
> are very welcome and any answers that include fruits or hamburger names may
> be kindly avoided :)
>
> Thanks a lot,
>
> Domen
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
-- 
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
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Re: [ccp4bb] I used up all CCP4 projects ... seemingly ...

[Jon Agirre]

I would transfer the new project to i2, and keep the ‘legacy’ stuff in i1.
You can access i1 stuff from i2 with the i1 viewer.

Let us know if you need any help with the transition. Happy to receive
feedback and suggestions!

Jon
On Mon, 25 Jun 2018 at 18:27, Antonio Ariza 
wrote:

> Hi all and sorry ... (I thought it best to apologise pre-emptively for
> this rather long question).
>
>
> Ok ... so, I know I should have changed over to CCP4i2 a LNG time ago,
> but a student in my lab had trouble transferring his projects from CCP4i to
> CCP4i2, so I decided to postpone it ... and I kept postponing it ever
> since. I have now run into a problem with the old CCP4i gui, which means I
> might have to change over to CCP4i2.
>
>
> It seems I have run out of projects!
>
>
> Over the last 4 years I have created 251 projects. After I created the
> last one and worked on it for a while, I went and revisited an older
> project. Now I can't access the last project I created from the gui anymore.
>
>
> The last project I created would, alphabetically speaking, also be the
> last project in the list that appears when you press the "Change Project"
> button at the top of the gui. However, the list that appears seems to only
> have enough spaces for 250 project names, which means it shows the first
> 250 projects (alphabetically) and the last project isn't on it. When I
> press the "Directories" button I can see I did indeed create the
> project that I'm looking for and when I check the computer, all the files
> for this project are in their corresponding directory.
>
>
> I guess, if I were to create a 252nd project with a title that would fall
> towards the beginning of the alphabetical project list, the gui would let
> me do that, but I would then lose what is currently the last project I can
> see on the list, which means I would have 2 projects I can't access via the
> gui.
>
>
> If I start using CCP4i2 and copy all my old projects across, will it have
> the same problem? Has anybody else with a large number of projects run into
> this problem?
>
>
> Should I re-create only the 251st project and set up all new projects in
> CCP4i2 and keep the old projects for use in CCP4i instead?
>
>
> Cheers,
>
>
> Tony
>
>
> --
>
>
>
>
>
>
> * Dr. Antonio Ariza University of Oxford Sir William Dunn School of
> Pathology South Parks Road Oxford OX1 3RE*
> *e-mail: *antonio.ar...@path.ox.ac.uk
> *Tel: 00 +44 1865 285655*
>
> *Links to my public profiles:*
> ResearchGate <https://www.researchgate.net/profile/Antonio_Ariza>
> LinkedIn <https://www.linkedin.com/in/antonioariza1>
> GoogleScholar
> <https://scholar.google.co.uk/citations?user=9pAIKV0J=en>
> Twitter <https://twitter.com/DrAntonioAriza?lang=en>
>
> *Check out my latest paper!!!*
> Structural insights into the function of ZRANB3 in replication stress
> response <http://www.nature.com/articles/ncomms15847>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
-- 
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
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[ccp4bb] Acta Cryst F special issue on carbohydrates

[Jon Agirre]

Dear colleagues,

just a quick update regarding the special issue with title 'Crystallography
of glycoproteins and protein-carbohydrate complexes', which Mark van Raaij
and I are co-editing for Acta Crystallographica Section F: Structural
BIology Communications.

We have extended the deadline for independent submissions until the 1st of
February. The URL for submitting papers is:
http://submission.iucr.org/submit/f?Qconf=glycoproteins

We should like to take this opportunity to thank those who have already
submitted their contributions for this issue - they are much appreciated.

Yours sincerely,

Jon & Mark


-- 
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
Twitter: @alwaysonthejazz

[ccp4bb] Acta Cryst F special issue on carbohydrates

[Jon Agirre]

Dear colleagues,

Mark van Raaij and I should like to bring your attention to the special
issue with title "Crystallography of glycoproteins and protein-carbohydrate
complexes" we are co-editing for Acta Crystallographica Section F:
Structural Biology Communications.

Aside from a number of commissioned contributions that are hopefully
underway, we should like to encourage independent, thematic submissions to
this issue, with a proposed limit of ~8,000 words. We shall be more than
happy to handle methodological submissions alongside more traditional ones,
such as structure reports or reviews.

The URL for submitting papers is: http://submission.iucr.org/submit/f?Qconf=
glycoproteins

Tentative deadline: 1st of January.

Yours sincerely,

Jon & Mark
-- 
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
Twitter: @alwaysonthejazz

[ccp4bb] Academic position in cryoEM at The University of York

[Jon Agirre]

The Department of Chemistry at The University of York is seeking to make an
appointment of a Lecturer/Senior Lecturer/Reader/Professor in the area of
Cryo Electron Microscopy, the position being based in the world-renowned
York Structural Biology Laboratory within the Department.

The Department has been awarded >£2M by the Wellcome Trust and Wolfson
Foundation to invest in state-of-the-art equipment and a bespoke building
to house a modern 200 kV cryo-electron microscope, supported by significant
investment from the University and a private donor.

We are now seeking to appoint a high-calibre researcher in cryo-electron
microscopy, with a clear vision to lead their own programme of excellent
research within YSBL <https://www.york.ac.uk/chemistry/research/ysbl/>.
Your research will complement the X-ray crystallography and NMR techniques
currently used in the YSBL, and will bridge the gap between X-ray work and
the optical microscopy in the Biology Technology Facility. The role is
available at any level and we welcome interest from talented academics with
an impressive research profile appropriate to the level of application and
a collegiate approach to their work.

You will be a dynamic research leader with a consistent track record in the
application of cryo-electron microscopy to challenging
biochemical/biological problems. We welcome applications from researchers
with an interest in diverse areas of structural and cell biology, with
particular interest in those working on mammalian systems.

The Department of Chemistry is one of the UK's leading Chemistry
departments and is renowned internationally for its research, having
performed exceptionally strongly in the recent Nature Index 2017 Innovation
Table
<https://www.york.ac.uk/chemistry/news/deptnews/nature-index-2017-innovation-table-high-ranking/>.
Combined with a commitment to high-quality teaching and outstanding student
satisfaction, it is recognised consistently for its family-friendly
policies and is proud of its Athena SWAN Gold Award.

*Key requirements:* (viewed relative to the level of post applied for – see
candidate briefs for more details)

   - PhD in Chemical, Biochemical or Physical Sciences
   - Specialist knowledge in cryo electron microscopy
   - Ability to undertake high-quality research and publish in leading,
   peer-reviewed journals
   - Ability to define, lead, manage and attract funds for research,
   operating across disciplinary boundaries
   - Experience of and commitment to teaching and learning at undergraduate
   level.
   - Demonstrable capacity for creative thinking and planning
   - Substantial recent publication record in leading peer-reviewed journal
   - Evidence of national and/or international collaboration

*Why York?*
We are a dynamic, research-intensive university and have experienced
significant growth over the past ten years, securing national and
international recognition for our academic excellence. Our attractive,
landscaped campus has seen significant development which will continue as
the University continues to develop. Chemistry is a multidisciplinary
department with an international reputation for excellence in research
and teaching. www.york.ac.uk/chemistry

*Salary will be commensurate with experience and grade*
Lecturer: £38,832 to £47,722
Senior Lecturer: £49,149 to £56,950
Reader: £49,149 - £60,410
Professorial: current minimum £62,585

*To apply*
Informal enquiries may be directed to Head of Department Professor Duncan
Bruce (chem-...@york.ac.uk; +44 (0)1904 322500) or the Academic Group
Leader in YSBL Professor Tony Wilkinson (tony.wilkin...@york.ac.uk; +44
(0)1904 328261)

Link:
https://jobs.york.ac.uk/wd/plsql/wd_portal.show_job?p_web_site_id=3885_web_page_id=325077

*Closing date:* 9 October 2017
*Interviews will be held in York on:* 29 November 2017
-- 
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8270
Twitter: @alwaysonthejazz

Re: [ccp4bb] refmac output

[Jon Agirre]

Perhaps a good opportunity for getting rid of (scaled) F and SIGF too?

Certain pipelines need Refmac's phase estimates (Buccaneer and Crank2 off
the top of my head), but I can't see how activating an 'expert mode' or
'developer mode' in order to get them would be a problem for their authors.

Cheers,

Jon


On 31 July 2017 at 16:57, Edwin Pozharski <pozharsk...@gmail.com> wrote:

> I know space is cheap these days, but is there a reason for Refmac to
> generate all those extra columns in the output mtz file?  Refmac (as well
> as phenix.refine and buster-tnt) output mtz file is almost always used for
> only one purpose - look at the map in coot.  You only need 4 columns for
> that, not 14.  Other columns are useful for testing, but why not make them
> optional?
>
> This would certainly be a low priority - one can easily delete extra
> columns using, say, sftools.
>
> Cheers,
>
> Ed.
>
> ---
> Hurry up, before we all come to our senses!
> Julien, King of Lemurs
>
>


-- 
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Twitter: @alwaysonthejazz
+44 (0) 1904 32 8270

Re: [ccp4bb] About weighting factor settings in new ccp4i2

[Jon Agirre]

Dear Xu,

you can input those keywords in the text box under 'Advanced options' in
the 'refinement' task. Just make sure you click somewhere else after you're
done putting the keywords in in order to have the text validated by the
interface.

Best regards,
Jon

On 24 July 2017 at 23:01, Liu, Xu <xu@emory.edu> wrote:

> Hi,
>
> In the new cpp4-7.0.042 (ccp4i2), where can I put in the weighting factor
> for B factor restrain weight (the ‘WBSKAL' setting) and/or x-ray terms
> relative to geometric restrains  (the ‘MATRIX’ setting ) in refmac5?
> Basically I want to plug in those weighting factors from pdbredo into
> REFMAC5 for a few more refinement but cannot find in new ccp4.
>
> Thanks!
>
> 
>
> This e-mail message (including any attachments) is for the sole use of
> the intended recipient(s) and may contain confidential and privileged
> information. If the reader of this message is not the intended
> recipient, you are hereby notified that any dissemination, distribution
> or copying of this message (including any attachments) is strictly
> prohibited.
>
> If you have received this message in error, please contact
> the sender by reply e-mail message and destroy all copies of the
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>



-- 
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Twitter: @alwaysonthejazz
+44 (0) 1904 32 8270

Re: [ccp4bb] CCP4i2 error message manual coot

[Jon Agirre]

Me.

On 7 July 2017 at 10:38, Bernhard Rupp <hofkristall...@gmail.com> wrote:

> Dear ccp4i2 developers,
>
>
>
> I am trying to run manual coot for sugar correction after privateer.
>
> Privateer works fine, but the subsequent manual coot (button)
>
> starts but exits with a short error message and
>
> plenty of error logs I do not completely comprehend.
>
>
>
> Coot itself also works fine.
>
>
>
> Who may I spam with the logs?
>
>
>
> Thx, BR
>
>
>
> --
>
> Bernhard Rupp
>
> CVMO
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429 <(925)%20209-7429>
>
> +43 676 571 0536 <+43%20676%205710536>
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>



-- 
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Twitter: @alwaysonthejazz
+44 (0) 1904 32 8270

Re: [ccp4bb] Parallelization?

[Jon Agirre]

As far as I know, OpenMP only works with C, C++ and Fortran.

In addition to Phaser, there are a few other crystallographic programs
I know are using OpenMP: XDS (Fortran), CCP4mg (surface calculations
in C++), Privateer (C++), Sharp...

Other programs may take advantage of multithreading themselves,
without making use of OpenMP. Buccaneer is a good example.

Jon

> On 9 Feb 2017, at 22:09, Dyda  wrote:
>
> Am I correct that OpenMP parallelized crystallographic software is in Fortran?
>
> While I think there is OpenMP extensions for C and variants, but not so for 
> python.
> Is this correct?
>
> Fred
>  
> [32m***
> Fred Dyda, Ph.D.   Phone:301-402-4496
> Laboratory of Molecular BiologyFax: 301-496-0201
> DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov
> Bldg. 5. Room 303
> Bethesda, MD 20892-0560  URGENT message e-mail: 2022476...@mms.att.net
> Google maps coords: 39.000597, -77.102102
> http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred
> ***
>  [m

[ccp4bb] Academic position in glycoscience at The University of York

[Jon Agirre]

Not to be confused with our previous job posting - please note the earlier
deadline (5th of February) for this one!

The Department of Chemistry at The University of York is seeking to appoint
a high-calibre researcher in glycoscience with a clear vision to lead their
own programme of excellent research, which will complement that of
Professor Gideon Davies, FRS FMedSci and other members of the York
Structural Biology Laboratory (YSBL). The role is available at any level
and we welcome interest from talented academics with an impressive research
profile appropriate to the level of application and a collegiate approach
to their work.

We would particularly welcome applications from researchers with a track
record in chemical biology approaches to mammalian glycoscience; preferably
with biomedical aspects. You will join a department renowned
internationally for its research. Combined with a dedication to
high-quality teaching and excellent student satisfaction, we are recognised
consistently for our family-friendly policies and are proud of our Athena
SWAN Gold Award.

Key Requirements (viewed relative to the level of post applied for – see
candidate briefs for more details):

- PhD in a Chemical or Biochemical Science
- Demonstrated expertise in a field/fields central to glycoscience
- Ability to undertake high-quality research and publish in leading,
peer-reviewed journals
- Ability to define, lead, manage and attract funds for research, operating
across disciplinary boundaries
- Experience of and commitment to teaching and learning at undergraduate
level.
- Demonstrable capacity for creative thinking and planning
- Substantial recent publication record in leading peer-reviewed journal
- Evidence of national and/or international collaboration

More information: https://jobs.york.ac.uk/wd/plsql/wd_portal.show
_job?p_web_site_id=3885_web_page_id=297414
Deadline for applications: 05/02/2017

-- 
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
+44 (0) 1904 32 8270

[ccp4bb] Academic position in cryoEM at The University of York

[Jon Agirre]

The Department of Chemistry at The University of York is seeking to appoint
a high-calibre researcher in cryo-electron microscopy, with a clear vision
to lead their own programme of excellent research within the York
Structural Biology Laboratory (YSBL). Your research will complement the
X-ray crystallography and NMR techniques currently used in the YSBL, and
will bridge the gap between X-ray work and the optical microscopy in the
Biology Technology Facility. The role is available at any level and we
welcome interest from talented academics with an impressive research
profile appropriate to the level of application and a collegiate approach
to their work.

You will be a dynamic research leader with a consistent track record in the
application of cryo-electron microscopy to challenging
biochemical/biological problems. We welcome applications from researchers
with an interest in diverse areas of structural and cell biology, with
particular interest in those working on mammalian systems. You'll join a
department renowned internationally for its research. Combined with a
dedication to high-quality teaching and excellent student satisfaction, we
are recognised consistently for our family-friendly policies and are proud
of our Athena SWAN Gold Award.

Key requirements: (viewed relative to the level of post applied for – see
candidate briefs for more details):

- PhD in Chemical, Biochemical or Physical Sciences
- Specialist knowledge in cryo-electron microscopy
- Ability to undertake high-quality research and publish in leading,
peer-reviewed journals
- Ability to undertake high-quality research and publish in leading,
peer-reviewed journals
- Ability to define, lead, manage and attract funds for research, operating
across disciplinary boundaries
- Experience of and commitment to teaching and learning at undergraduate
level.
- Demonstrable capacity for creative thinking and planning
- Substantial recent publication record in leading peer-reviewed journals
- Evidence of national and/or international collaboration

More information: https://jobs.york.ac.uk/wd/plsql/wd_portal.show
_job?p_web_site_id=3885_web_page_id=297412
Deadline for applications: 12/02/2017

-- 
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
+44 (0) 1904 32 8270

Re: [ccp4bb] How can I refine B-factors only in CCP4 REFMAC?

[Jon Agirre]

Hi,

you want to use these keywords:

REFInement BONLY

Good luck,

Jon

On 23 December 2016 at 06:52, Peng <caopen...@126.com> wrote:

>
> Dear all,
> How can I refine B-factors only in CCP4 REFMAC?
> I do not want to refine the XYZ coordinations.
> Thanks
> Peng
>
>
>
>
>
>



-- 
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
+44 (0) 1904 32 8270

Re: [ccp4bb] {meta} posts with pdfs

[Jon Agirre]

Better.

Article requests can always be dealt with off list, unless they're open
access, in which case providing a link would be a better option for
publishers, authors and uninterested recipients.

I think it's a win-win scenario.

On 13 December 2016 at 13:35, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote:

> Would this mailing list be better or worse if mails with pdfs were blocked?
>



-- 
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
+44 (0) 1904 32 8270

Re: [ccp4bb] edstats

[Jon Agirre]

Dear Peter,

the ccp4i2 EDSTATS task works differently to its ccp4i interface. There are
plenty of differences between ccp4i and ccp4i2 in terms of how interface
logic is handled, and using (internally generated) map coefficients is one
of them. Regrettably, due to a bug it used to be impossible to handle
externally-generated map coefficients (e.g. those from refmac), but I'm
almost sure this is fixed in recent revisions. I'll have a look tomorrow
and get back to you.

Thanks,
Jon

On 15 November 2016 at 19:40, Göttig Peter <peter.goet...@sbg.ac.at> wrote:

> On linux and windows there is a problem with EDSTATS in ccp4i2. I always
> get error messages like cfft failed aso. I tried to read input maps in ccp4
> format and even mtz files with map coefficients, which is not in the
> original description, but apparently required in the ccp4i2 versions (?).
> The Hofkristallrat reported something similar, but this did not help to
> narrow down the problem.
>
> Peter
>
>
> --
>
> *Dr. Peter Goettig*
>
> Arbeitsgruppe Strukturbiologie
>
> Universität Salzburg
>
> Billrothstrasse 11
>
> A-5020 Salzburg, Österreich
> Tel.  +43 662 8044-7283
>
> FAX +43 662 8044-7209
> http://www.uni-salzburg.at/xray
> --
>
>
>



-- 
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
+44 (0) 1904 32 8270

Re: [ccp4bb] how to recover my data

[Jon Agirre]

 The current version of CCP4 does not contain mtzdump.


It surely does on my machine:

$ which mtzdump
/Applications/ccp4-6.5/bin/mtzdump

-- 
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/research/jagirre/
+44 (0) 1904 32 8253

Re: [ccp4bb] checking the functionality of ccp4 for general research

[Jon Agirre]

 My background is computer science and I am working on protein interface
 predictions. The questions that I asked are standard processing steps in
 protein interface predictions. But nobody in my field have used a
 *platform* to calculate and integrate them into different classifiers.
 Different classifiers use different features and have different processing
 details. I just thought it would be convenient, for both development and
 maintenance, to build classifiers on one platform that have all the
 functionalities.


All the tasks you've mentioned can be tackled easily with Clipper (
http://www.ysbl.york.ac.uk/~cowtan/clipper/doc/)
Clipper is distributed as part of CCP4.

However, please make sure that your scientific questions aren't already
answered by existing software. Pisa is the first thing that springs to my
mind when talking about interfaces, and is also accessible within CCP4.

Hope this helps,

Jon
-- 
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/research/jagirre/
+44 (0) 1904 32 8253

Re: [ccp4bb] Unsubscribe

[Jon Agirre]

Contrarily to what popular belief seems to be, there's no such thing as
bulletin board fairies. If you want to unsubscribe from it, you need to
follow the instructions:

http://www.ccp4.ac.uk/ccp4bb.php#subscription

Cheers,

Jon

On 4 March 2015 at 10:10, Claudia Schreiner claudia.schrei...@univie.ac.at
wrote:





-- 
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/research/jagirre/
+44 (0) 1904 32 8253

Re: [ccp4bb] Balbes

[Jon Agirre]

Hi,

the Balbes database is now nearly 3 years old, so obviously it won't use
that structure as template... and as Mark has correctly pointed out, Balbes
is a bit of an overkill for this problem. Just follow his advice and you'll
solve it in no time. MR tools are very automated and easy to use nowadays
:-)

On 27 November 2014 at 20:19, Atul Kumar atulsingh21...@gmail.com wrote:

 Hi all,

 I am trying to solve complex structure of my proteins. Apo protein
 structure is already known. Balbes should take this structure as template
 for MR, whereas, it is taking some random proteins as template. I was
 wondering, whether it is synchronized with pdb or uses its own databank.
 Since structure of this protein deposited in pdb last year, wondering
 whether or not it is updated  in its local databank, in case it is not
 synchronized with pdb. Can somebody help to figure out this problem?

 regards

 Atul




-- 
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/research/jagirre/
+44 (0) 1904 32 8253

Re: [ccp4bb] ccp4 QTMG

[Jon Agirre]

You can create the same selection in CCP4mg, display the map and then,
clicking on the first icon on the left underneath the map's name, use Clip
and choose your atom selection. Then, in Clip Radius you can adjust how
much of the map you want to see.

Hope this helps,
Jon


On 19 August 2014 12:06, PC patrick.coss...@inbox.com wrote:

  Hi,

 I used COOT mask map by atom selection and cut out a fragment of the map,
 then exported it and now I tried to open it in QTMG.

 It displays it as a unit cell,  I want one for a presentation, how can I
 combine it to display one image ?

 Thank you,
 Patrick
 --
  [image: 3D Earth Screensaver Preview] http://www.inbox.com/earth
 *Free 3D Earth Screensaver*
 Watch the Earth right on your desktop! Check it out at www.inbox.com/earth




-- 
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/research/jagirre/
+44 (0) 1904 32 8253

Re: [ccp4bb] Salt!

[Jon Agirre]

Hi Catherine,

first of all, I'm sorry that you're feeling so frustrated.

In addition to the many sensible suggestions that you're surely going to
read here, I would like to point you to a paper I read a while ago in
Nature: In situ proteolysis for protein crystallization and structure
determination, http://www.ncbi.nlm.nih.gov/pubmed/17982461

Sometimes proteases can remove from the target protein just those external
bits that hinder crystallisation. I would try everybody else's suggestions
before attempting this, but here it goes just in case everything else fails.

Good luck,

Jon


On 16 July 2014 16:13, Chris Fage cdf...@gmail.com wrote:

 Hi Catherine,

 If they are indeed salt crystals, have you tried preparing different
 truncations of the gene encoding your target? I've seen a number of
 successes in which, after a codon or two was added to the termini of the
 gene being overexpressed, the target crystallized beautifully.

 Best,
 Chris


 On Wed, Jul 16, 2014 at 9:55 AM, Bishop, Catherine E. cati...@ou.edu
 wrote:

  I have been attempting to obtain a protein crystal of my protein for
 just over 2 years at this point.  We have attempted removing the tag,
 binding the protein to its ligand, removing as much salt as possible
 (crashes at at too low a salt concentration)--this lead us to try reverse
 vapor diffusion--seeding, additive trays, optimization around the
 conditions an ortholog of one of the domains crystallized well in, and a
 plethora of other methods. We do get crystals, but they all diffract as
 salt. Most of these salts are found in wells containing a cation (ie.
 lithium sulfate, nickel chloride, magnesium acetate, cobalt chloride,
 etc.). When crystals are too small to shoot, I do set up optimized trays;
 however, if I get larger crystals, they diffract as salt as well. Most of
 these set ups, at this point, have also been conducted in hands other than
 mine and at other facilities known for their successful crystallization of
 proteins.

 Has anyone else run into this problem and seen light at the other side??
 Any suggestions are appreciated.





-- 
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/research/jagirre/
+44 (0) 1904 32 8253

Re: [ccp4bb] EDS server - R-value

[Jon Agirre]

Dear Jai,

you can find lots of possible explanations in that very same website:
http://eds.bmc.uu.se/eds/eds_help.html#PROB_RFAC


On 4 April 2014 09:07, jai mohan jaimoha...@yahoo.co.in wrote:

 Dear all,
 Sorry for the off-topic Question.
 I just tried to extract files *.* from EDS server for a PDB entry.
 The page tells us that

 There is no map available for this entry (),
 because our automatic script failed to produce an electron density map
 with an *R-value (0.309)* within 5 percentage points of the published one
 (*0.165*).
 If you are the author of this entry and wish to help us remedy this
 situation, please contact use...@xray.bmc.uu.se?subject=R_value_diff_3ah9
 .
 Back to EDS home page http://eds.bmc.uu.se/eds

 The reported R-value for the () PDB entry is 0.16 than how 0.309?
 could anyone please explain about this!
 Sincerely,
 S.M. Jaimohan, Ph. D




-- 
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/research/jagirre/
+44 (0) 1904 32 8253

Re: [ccp4bb] Coot Performance on Intel HD Graphics 5000

[Jon Agirre]

 The OpenGL performance is rather poor on intel HD chips up to and
 including the HD 4600 but with the appearance of HD 5000 series (Iris HD)
 the Cinebench OpenGL score increased dramatically and even challenges many
 nvidia cards in performance. With these kind of intel chips you should be
 able to run Coot and Pymol smoothly and operate a passive 3D screen without
 problems.


I beg to differ too. My experience with Coot running on both HD 4000 and
5000 series couldn't be better. In fact, I generally switch to HD4000 on my
Macbook Pro every time I load Coot, because the slight difference in
performance doesn't justify the massive increase in both temperature and
power consumption.

Presentation software like CCP4mg or pymol are much more resource-hungry
than Coot, and still the HD series hold themselves up quite decently.

Jon
-- 
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/research/jagirre/
+44 (0) 1904 32 8253

Re: [ccp4bb] off-topic Electron density map rendering..

[Jon Agirre]

I believe that has been rendered in O, selecting a different line
drawing mode you could get by hitting 'F3' a couple of times, IIRC.

On 12 February 2014 12:05, Boaz Shaanan bshaa...@bgu.ac.il wrote:
 You're absolutely right Tim, but unfortunately that's very common these days 
 not to mention the rendering program and ignore the efforts of those who 
 developed it.

   Boaz


 Boaz Shaanan, Ph.D.
 Dept. of Life Sciences
 Ben-Gurion University of the Negev
 Beer-Sheva 84105
 Israel

 E-mail: bshaa...@bgu.ac.il
 Phone: 972-8-647-2220  Skype: boaz.shaanan
 Fax:   972-8-647-2992 or 972-8-646-1710





 
 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Tim Gruene 
 [t...@shelx.uni-ac.gwdg.de]
 Sent: Wednesday, February 12, 2014 11:18 AM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] off-topic Electron density map rendering..

 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1


 Appalling if the program name is not mentioned in the manuscript.

 Best,
 Tim

 On 02/12/2014 03:08 AM, Francis Reyes wrote:
 Anyone know the program used to render the electron density maps
 for the fungal FAS in Figure 3c-3h from the paper Mueller, M.,
 Jenni, S.  Ban, N. Strategies for crystallization and structure
 determination of very large macromolecular assemblies. Curr Opin
 Struct Biol 17, 572-579 (2007)..

 The depth cueing is phenomenal.


 I'm thinking O.. I can't seem to get it right in Pymol.

 Thanks!,

 F

 - Francis E. Reyes PhD
 215 UCB University of Colorado at Boulder

 Publications  Citations:
 http://scholar.google.com/citations?user=FW4-CaQJhl=en
 --


 - --
 - --
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen

 GPG Key ID = A46BEE1A

 -BEGIN PGP SIGNATURE-
 Version: GnuPG v1.4.12 (GNU/Linux)
 Comment: Using GnuPG with Icedove - http://www.enigmail.net/

 iD8DBQFS+zxcUxlJ7aRr7hoRArIAAJ9FUnn373PWm3uxef4x5LdivxfhBgCfawkH
 oE12Z6GXrEAAWV2UJKpKDYM=
 =b53q
 -END PGP SIGNATURE-



-- 
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/research/jagirre/
+44 (0) 1904 32 8253

Re: [ccp4bb] TRUNCATE CTRUNCATE issues.

[Jon Agirre]

).  The nice thing
 about this method is one can generalise it to calculate the
 Bayesian-corrected F and I as well as arbitrary moments and get rid of F 
 W's cubic spline interpolation code with the slightly worrying warning (see
 NEGIAS  NEGICS s/rs in TRUNCATE):

 C Accuracy - better than 5 percent  (i think).

 With the PCFs the code becomes both much simpler and much more accurate (to
 REAL*4 precision, so ~ 0.0001% accuracy!).

 I should also say that I believe that CTRUNCATE is not immune from these
 issues: it seems to be a straight translation at least in part from Fortran
 to C++ (though I'm far from being a C++ expert so I'll leave fixing
 CTRUNCATE to those who know what they're doing!).

 Sorry about the length of this: at least you can't say I didn't consult you!

 Cheers

 -- Ian




-- 
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/research/jagirre/
+44 (0) 1904 32 8253

Re: [ccp4bb] how to make protein topology figure based on its structure

[Jon Agirre]

Espript will do. http://espript.ibcp.fr/

Good luck,

Jon
On 9 Mar 2013 11:52, LISA science...@gmail.com wrote:

 Hi all,
 I want to make a topological figure of my protein  with a b-sheet and
 helix based on its crystal structure. Please recommend some online sever of
 software?
 Thank you.

 lisa

Re: [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)

[Jon Agirre]

Dear Fred,

I would say that you're using a buggy gfortran version
(http://lists.debian.org/debian-gcc/2009/03/msg00070.html). You may
want to check your version with 'gfortran --version' in order to be
sure of it. The '-malign-double' switch provides only a slight
optimization and as you have already proven, it may be removed with
very little impact on performance.

Cheers,

Jon

2013/3/6 vellieux frederic.velli...@ibs.fr:
 Dear all,

 By popular request here is an example of some code where gfortran gives run
 time errors. This is at the very beginning of the program, the first write
 statement where a parenthesis is seen as missing at run time: (the first
 hyphens are not within the Fortran code but there to indicate the number of
 spaces before each character, 6 and nothing more or less).

 Also enclosed as part.f herewith (as an attachment)

 [I must admit that, somehow, when modifying a Fortran program using vim on
 this new box, the number of characters at the beginning of Fortran cards
 seems to reset to 8 when there are 6 blanks to start with, I have no idea
 why this is so.]

 Help most welcome, and I'd hate to have to retype every single program...

 Ta,

 Fred.

 --

   ORDER='A'
   NATM=0
   DO 5,I=1,3
  NGRID(2,I)= 9
  NGRID(3,I)=-9
  XMIN(I)= .
  XMAX(I)=-.
   5  CONTINUE
 C
 C   OPEN INPUT FILE
 C
   WRITE (*,10)
10 FORMAT(///,25X,'*',
  . /,25X,'*   *',


 --
 Fred. Vellieux (B.Sc., Ph.D., hdr)
 ouvrier de la recherche
 IBS / ELMA
 41 rue Jules Horowitz
 F-38027 Grenoble Cedex 01
 Tel: +33 438789605
 Fax: +33 438785494




-- 
Jon Agirre, PhD
Unit of Biophysics (CSIC-UPV/EHU)
http://sourceforge.net/projects/projectrecon/
+34656756888

Re: [ccp4bb] the matrix format

[Jon Agirre]

Dear Qixu,

here's an excerpt from the pdbset manual:

TRANSFORM [INVERT] [FRACTIONAL] r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz

I'm not sure what you mean by covert from the pdb file format to
the pdbset format. Please elaborate on this.

Jon

2013/2/25 Qixu Cai caiq...@gmail.com:
 Dear all,

 The matrix formats in different program always confuse me.

 The matrix format of the REMARK 290 SMTRY section of pdb file is:

 r11r12r13tx
 r21r22r23ty
 r31r32r33tz

 What's the matrix format accepted by the transform file keywords of the
 pdbset program?
 is it r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz?
 And how to covert from the pdb file format to the pdbset format?

 What's the matrix format of apply NCS operators in phenix GUI?

 Thanks a lot!

 Qixu Cai



-- 
Jon Agirre, PhD
Unit of Biophysics (CSIC-UPV/EHU)
http://sourceforge.net/projects/projectrecon/
+34656756888

Re: [ccp4bb] the matrix format

[Jon Agirre]

If you just want to generate symm mates from MTRIX records, you may
want to give GK's 'xpand' a go:
http://xray.bmc.uu.se/usf/xpand_man.html

Otherwise, I would follow Fred's advice.

Jon

2013/2/25 vellieux frederic.velli...@ibs.fr:
 Hi,

 Emacs, vi, any (text file) editor ? I wouldn't advise a word processing
 program (Word and the likes).

 Unless you want to do this on many pdb files in which case writing a small
 program or shell script would be required.

 Fred.


 On 25/02/13 14:24, Qixu Cai wrote:

 Dear Jon,

 Thanks for your reply.

 The matrix format in the REMARK 290 section of the pdb file (download from
 rcsb.org) is :
 r11r12r13tx
 r21r22r23ty
 r31r32r33tz

 And I want to extract the matrix information from the pdb file REMARK 290
 section and use the matrix in the pdbset.

 so I have to convert the matrix from
 r11r12r13tx
 r21r22r23ty
 r31r32r33tz

 to r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz.

 How can I do it?

 Thanks.

 Qixu Cai


 Qixu Cai
 Email: caiq...@gmail.com
 School of Life Sciences,
 Xiamen University, Fujian, China


 2013/2/25 Jon Agirre jon.agi...@gmail.com

 Dear Qixu,

 here's an excerpt from the pdbset manual:

 TRANSFORM [INVERT] [FRACTIONAL] r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty
 tz

 I'm not sure what you mean by covert from the pdb file format to
 the pdbset format. Please elaborate on this.

 Jon

 2013/2/25 Qixu Cai caiq...@gmail.com:
  Dear all,
 
  The matrix formats in different program always confuse me.
 
  The matrix format of the REMARK 290 SMTRY section of pdb file is:
 
  r11r12r13tx
  r21r22r23ty
  r31r32r33tz
 
  What's the matrix format accepted by the transform file keywords of
  the
  pdbset program?
  is it r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz?
  And how to covert from the pdb file format to the pdbset format?
 
  What's the matrix format of apply NCS operators in phenix GUI?
 
  Thanks a lot!
 
  Qixu Cai



 --
 Jon Agirre, PhD
 Unit of Biophysics (CSIC-UPV/EHU)
 http://sourceforge.net/projects/projectrecon/
 +34656756888




 --
 Fred. Vellieux (B.Sc., Ph.D., hdr)
 IBS / ELMA
 41 rue Jules Horowitz
 F-38027 Grenoble Cedex 01
 Tel: +33 438789605
 Fax: +33 438785494



-- 
Jon Agirre, PhD
Unit of Biophysics (CSIC-UPV/EHU)
http://sourceforge.net/projects/projectrecon/
+34656756888

Re: [ccp4bb] Mac OS 10.8 Mountain Lion and CCP4?

[Jon Agirre]

 The (on by default) versioning auto save is a PITA if you ever use textedit 
 to edit scripts but apart from that 10.8 is a fairly painless upgrade.

You'll probably know about this trick, but just in case there's
someone else still suffering the autosave feature, here it goes: you
can disable autosave and bring back the good old 'Save as...' command
for a number of apps by executing the following commands:

defaults write com.apple.TextEdit ApplePersistence -bool no
defaults write com.apple.Preview ApplePersistence -bool no
defaults write com.apple.iWork.Pages ApplePersistence -bool no
defaults write com.apple.iWork.Numbers ApplePersistence -bool no
defaults write com.apple.iWork.Keynote ApplePersistence -bool no

Cheers,

Jon

-- 
Jon Agirre, PhD
Unit of Biophysics (CSIC-UPV/EHU)
http://sourceforge.net/projects/projectrecon/
+34656756888

Re: [ccp4bb] Mac OS 10.8 Mountain Lion and CCP4?

[Jon Agirre]

To my knowledge, apps are rendered at a typical 15.4 resolution
(1440x900) and then scaled up at the retina resolution (2880x1800).
Non-retina apps look scaled. It's like watching standard definition
video (say 480p) played in a high-definition screen (1080p or the
sort).

Jon

2013/2/22 Carlos Kikuti kik...@gmail.com:
 Hi all,

 On the same topic, I'd like to know wether the retina display is also
 fine, because I've found complains about X11 (non crystallographic)
 programs appearing ugly in it. Is anybody using it?

 Just for info, I'm also using Mountain lion without problems ( Fink got
 weird but I don't really care).

 Carlos
 De : Huw Jenkins
 Envoyé : 21/02/2013 21:44
 À : CCP4BB@jiscmail.ac.uk
 Objet : Re: [ccp4bb] Mac OS 10.8 Mountain Lion and CCP4?
 All works fine. You'll need to install XQuartz (Apple are no longer
 supplying  their own X11 builds) but that's just a couple of clicks in
 the box that pops up the first time you run an program that needs X.

 The (on by default) versioning auto save is a PITA if you ever use
 textedit to edit scripts but apart from that 10.8 is a fairly painless
 upgrade.

 Huw



-- 
Jon Agirre, PhD
Unit of Biophysics (CSIC-UPV/EHU)
http://sourceforge.net/projects/projectrecon/
+34656756888

Re: [ccp4bb] off topic: DSSP

[Jon Agirre]

Dear Rashmi,

you may want to try this web server instead of compiling  installing it:
http://www.cmbi.ru.nl/hsspsoap/

Otherwise, you'd better follow Tim's advice and give us more clues!

Jon

2013/1/28 Tim Gruene t...@shelx.uni-ac.gwdg.de

 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1

 Dear --
 rashmi,

 if you would kindly let us know what exactly you are thanking for, you
 may actually have a reason for doing so - a good start is a
 cut-and-paste copy of the error message(s) from the terminal where you
 typed 'make' and 'make install'.

 If you get this error only from 'make install' but not from 'make',
 chances are that the compilation worked fine but the Makefile attempts
 to install file to a location you do not have write access to.

 Cheers,
 Tim

 On 01/26/2013 10:11 AM, Rashmi Panigrahi wrote:
  Hi All Apologies for the off topic. Could some one help me in
  installing DSSP in Mac OSX 10.5.8 I tried downloading
  dssp-2.0.3.tbz
  ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.3.tbz
  dssp-2.0.4-linux-amd64
 ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64
 
 
 dssp-2.1.0.tgz ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.1.0.tgz
  from http://swift.cmbi.ru.nl/gv/dssp/ I tried doing make followed
  by make install. I got error on compiling. Thanks in advance

 - --
 - --
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen

 GPG Key ID = A46BEE1A

 -BEGIN PGP SIGNATURE-
 Version: GnuPG v1.4.12 (GNU/Linux)
 Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

 iD8DBQFRBpI8UxlJ7aRr7hoRAu1bAJ9q3TWZbBMAlrOWchZnrPo4Iy42YQCg1K+c
 uo0hlOQ0oTPyTDHmXjM57Bw=
 =dBMv
 -END PGP SIGNATURE-




-- 
Jon Agirre, PhD
Unit of Biophysics (CSIC-UPV/EHU)
http://www.ehu.es/jon.agirre
http://sourceforge.net/projects/projectrecon/
+34656756888

Re: [ccp4bb] Coot 0.7 Saving Dialog opens behind main window

[Jon Agirre]

 Thanks for the heads-up.  Bernhard and I have fixed several of these
 window-order problems, but this one slipped by us (neither of us use a Mac
 :-).

 Fixed in 0.7.1


That's great news, Paul. Thank you for fixing it and others for pointing it
out. I've been always quite convinced that it was an XQuartz.app (aka X11
for OS X) related bug and therefore never reported it.

Jon

-- 
Jon Agirre, PhD
Unit of Biophysics (CSIC-UPV/EHU)
http://www.ehu.es/jon.agirre
http://sourceforge.net/projects/projectrecon/
+34656756888

Re: [ccp4bb] Off Topic: help locating CNS data

[Jon Agirre]

Add another extension to your search: *.mtf

If your structure was refined with CNS, chances are you'll find its
Molecular Topology File somewhere.

Best of luck,

Jon

2012/9/21 vellieux frederic.velli...@ibs.fr

  As was mentioned, the diffraction data files can be named according to
 the user's wish. But I'd try to locate files with extensions .hkl, .xpl,
 .cv (and .cns? although I have never seen that extension used myself)

 Fred.


 On 21/09/12 12:10, Rex Palmer wrote:

  I have been presented with the problem of locating protein data for a
 structure which was refined here ten years ago with the CNS program.
 Unfortunately I have never used this program so do not know what type of
 files I am looking for (or how many files).
 Any suggestions please

 Rex Palmer
 http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
 http://rexpalmer2010.homestead.com



 --
 Fred. Vellieux (B.Sc., Ph.D., hdr)
 IBS / ELMA
 41 rue Jules Horowitz
 F-38027 Grenoble Cedex 01
 Tel: +33 438789605
 Fax: +33 438785494




-- 
Jon Agirre, PhD
Unit of Biophysics (CSIC-UPV/EHU)
http://www.ehu.es/jon.agirre
http://sourceforge.net/projects/projectrecon/
+34656756888

Re: [ccp4bb] Improving microcrystals

[Jon Agirre]

I've had some success in the past following Terese Bergfors' advice:
http://xray.bmc.uu.se/terese/tutorial3.html

However, the last time I dealt with spherulites I just tuned the pH and it
worked like a charm.

Good luck,

Jon

2012/8/25 RHYS GRINTER r.grinte...@research.gla.ac.uk

 Hi Samuel,

 I've has good success going from sphereulites to crystals using an
 additive screen (the 96 condition Hampton one is good) with the conditions
 giving the spherulites. Just watch for salt crystals as you'll be adding
 some compounds that might cause your Ca ions to form insoluble CaSO4.

 http://hamptonresearch.com/product_detail.aspx?cid=1sid=36pid=27

 Cheers,

 Rhys
 
 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Samuel
 Johnson [samueljohnson...@yahoo.in]
 Sent: 25 August 2012 02:11
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: [ccp4bb] Improving microcrystals

 Hi everyone,

   I have been working on a protein for the past year.
 After a number of trials at crystallizing the protein i have identified
 conditions for getting spherulites/micro-crystaline material under micro
 batch method. I have confirmed that the crystalline material is protein, by
 using Izit-dye test. The condition is 50mM CaCl2, Mes pH 6.5 and 40% PEG
 400. I will be happy to get suggestions on improving conditions to obtain
 single crystals. I have already tried varying a number of parameters like
 salt, precipitant concentration and buffer pH but that didn't help.

 Thanks.




-- 
Jon Agirre, PhD
Unit of Biophysics (CSIC-UPV/EHU)
http://www.ehu.es/jon.agirre
http://sourceforge.net/projects/projectrecon/
+34656756888

Re: [ccp4bb] Crystallization Robots

[Jon Agirre]

Dear Sam,

I spent quite some time trying to get up and running a HT LCP setup in the
past years, and all I can say is that TTP has successfully automated in its
Mosquito LCP all the homemade workarounds I employed back then. For
instance, they tackle the dehydration problem by covering the drop with
precipitant subsequently to LCP dispensing. They also use a chamber to
control RH (I believe the NT8 uses a similar device too). They create a
droplet of precipitant prior to dispensing in order to avoid touching the
viscous LCP with a dry tip, which might cause it to stick. They even
calibrate the position of the syringe before starting the procedure; this
is really critical, since you have to manually fix the syringe in position
after making the LCP.

I've only watched brief demonstrations of the NT8 and Gryphon, and
specially the Gryphon experienced severe calibration problems which
prevented the LCP drops to be hydrated. NT8 seemed to be a fine piece of
hardware though, and it even spares you of the pain of changing the tip
roll every once in a while.

Jon

2012/8/2 Sam Jimmeson samjimme...@gmail.com

 Hello ccp4BBers,
Our lab is thinking about trying to purchase a crystallization robot.
 We need to be able to do LCP in addition to sitting drop experiments.  Does
 anyone have experience with the NT8 robot from formulatrix?  The other two
 robots I am aware of are the LCP Mosquito from TTP and the LCP Gryphon from
 ARI.  Does anyone have any experiences they could share with me about these
 instruments?  Feel free to email off list if you want.
 Thanks!
 -Sam




-- 
Jon Agirre, PhD
Biophysics Unit (CSIC-UPV/EHU)
http://www.ehu.es/jon.agirre
+34656756888

Re: [ccp4bb] Crystallization with antibody

[Jon Agirre]

I would advise against using anti-His FaBs for that particular purpose.
Even if you get them to bind to your complex, the inherent flexibility of
the terminal regions were His-tags are placed might ruin the final result,
and they're not cheap to begin with.

You can further characterize your system to spot if there are certain
experimental conditions that dissociate the complex, in order to avoid
designing crystallization trials that include those. There are a lot of
things to be tested before jumping into the Antibody train, and 200
conditions don't seem enough test ground to me for discarding traditional
screening.

Good luck,

Jon

2012/6/28 Theresa Hsu theresah...@live.com

 Dear crystallographers

 Trying to crystallize a membrane protein complex of 100 kDa with a soluble
 protein of 20 kDa which is interact with the membrane protein. So far, no
 co-crystals in  200 conditions. Some conditions gave crystals but mass
 spec of crystals show only either one protein present. I am thinking of
 antibody but don't know where to start. Can I use the anti-His tag antibody?

 Thank you.




-- 
Dr. Jon Agirre
Biophysics Unit (CSIC-UPV/EHU)
http://www.ehu.es/jon.agirre
+0034946013357

Re: [ccp4bb] Covert Structure Factor to mtz

[Jon Agirre]

I completely agree with Paul. That information could even be enclosed by
two commentary sections (i.e. '# Added by wwPDB mm-dd- hh:mm' and
'') to highlight the changes.

Jon

2012/5/18 Paul Emsley paul.ems...@bioch.ox.ac.uk

 On 17/05/12 20:16, martyn.w...@stfc.ac.uk wrote:

 Reflection cif files from the PDB do not always have cell and symmetry
 information in them, particularly the older ones, and it sounds like this
 is your case.


 My understanding is that these days they should have - and if you find
 such examples, they should be reported to the wwPDB authorities.

 Paul.




-- 
Dr. Jon Agirre
Postdoctoral Scientist - Protein and
Virus X-ray Crystallography Group
Biophysics Unit (CSIC-UPV/EHU)
+0034946013357

Re: [ccp4bb] Differentiate salt and protein crystals

[Jon Agirre]

The best reproduction I can suggest would be to setup one or two LCP
experiments exchanging the protein for its buffer. If you get crystals, you
know for sure they're not protein.

Cheers,

Jon

2012/3/15 Theresa H. Hsu theresah...@live.com

 Hi all.

 I set up some trays of membrane protein remotely in cubic phase. I don't
 have ready access to them so I can't shoot/pick the crystals. Under
 polarising lights, some crystals appears coloured across many conditions,
 making me think these are salt. Is there some knowledge of inorganic
 chemistry that be relied to prioritise some for reproductions at my lab?
 Can detergents crystallise and produce colours under polarising light?

 Thank you.

 Theresa




-- 
Dr. Jon Agirre
Postdoctoral Scientist - Protein and
Virus X-ray Crystallography Group
Biophysics Unit (CSIC-UPV/EHU)
+0034946013357

Re: [ccp4bb] Crystal Structures as Snapshots

[Jon Agirre]

Hi Nat,

there are a number of viruses in which a domain swap occurs inside the
capsid, with the hinge sequence being highly conserved among their
respective families. Perhaps I'm missing your point, but I won't attribute
that kind of domain swap to any sort of crystal packing artifact.

Jon

2012/2/10 Nat Echols nathaniel.ech...@gmail.com

 Just to clarify - I actually think the original assumption that Jacob
 posted is generally reasonable.  But it needn't necessarily follow
 that the conformation we see in crystal structures is always
 representative of the solution state; given the extreme range of
 conditions in which crystals grow, I would be surprised if there
 weren't counter-examples.  I'm not familiar enough with the literature
 on domain swapping (e.g. diptheria toxin) to know if any of those
 structures are crystal packing artifacts.

 On Fri, Feb 10, 2012 at 1:04 PM, George gkontopi...@vet.uth.gr wrote:
 Packing billions of copies into a compact lattice
  Not so compact there is 40-80% water
 freezing it to 100K
  We have frozen many times protein solutions in liquid nitrogen and then
 thaw
  and were working OK
  non-physiological amounts of salt and various organics
  What is the amount of salt and osmotic pressure in the cell??
 non-physiological pH too
  What is the non-physiological pH too? I am sure that some enzymes they
 are
  not working in pH 7. Also most of the proteins they have crystallized in
 pH
  close to 7 so I would not say non-physiological.
 
  George
 
  PS There are lots of solution NMR structures as well supporting the
  physiological crystal structures
 
 
  -Original Message-
  From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
 Nat
  Echols
  Sent: Friday, February 10, 2012 10:35 PM
  To: CCP4BB@JISCMAIL.AC.UK
  Subject: Re: [ccp4bb] Crystal Structures as Snapshots
 
  On Fri, Feb 10, 2012 at 12:29 PM, James Stroud xtald...@gmail.com
 wrote:
  How could they not be snapshots of conformations adopted in solution?
 
  Packing billions of copies of an irregularly-shaped protein into a
  compact lattice and freezing it to 100K isn't necessarily
  representative of solution, especially when your solution contains
  non-physiological amounts of salt and various organics (and possibly
  non-physiological pH too).
 
  -Nat
 




-- 
Dr. Jon Agirre
Postdoctoral Scientist - Protein and
Virus X-ray Crystallography Group
Biophysics Unit (CSIC-UPV/EHU)
+0034946013357