[ccp4bb] Postdoctoral Position in the Liang laboratory at Emory University

[Liang, Bo]

Dear colleagues,

Applications are invited for a postdoctoral fellow position at the Liang lab @ 
Department of Biochemistry, Emory University School of Medicine.

The principal goal of the Liang laboratory is to understand the molecular 
mechanisms and scrutinize high-resolution structural details of traditionally 
challenging and interesting biological systems using integrated approaches of 
cryo-EM and x-ray crystallography. We are seeking a talented and motivated 
scientist with a strong background in biochemistry and structural biology to 
analyze the viral RNA synthesis machinery.

For this search, we prioritize candidates with solid backgrounds in 
biochemistry, cryo-EM and/or x-ray crystallography. Experience in structural 
biology is desired but not required. A qualified applicant should hold a Ph.D. 
or expect to have a Ph.D. in the area of biochemistry, biophysics, structural 
and molecular biology. We offer a unique training environment for research and 
career development.

The position is available immediately until the position is filled. For 
detailed information and to apply, please see:
https://faculty-emory.icims.com/jobs/76853/job

Please contact me directly for further information or questions at 
bo.li...@emory.edu. If you know a suitable candidate, would you please help to 
distribute this position information? Thank you!

Sincerely,
Bo Liang

---
Bo Liang, Ph.D.
Assistant Professor
Department of Biochemistry
Emory University School of Medicine
www.biochem.emory.edu/liang



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Re: [ccp4bb] Antwort: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Eleanor Dodson]

I dont think you expect much better R factors with twinning or without -
the fact is the "crystal"  is not perfect . Sometimes it is worth screening
other crystals from the batch - smaller ones may not be twinned at all..
Have you looked back atthe images? Gerard suggested there might be lattice
translocation..
Eleanor

On Tue, 31 Aug 2021 at 16:46, Peer Mittl  wrote:

> Dear Herman, Kay, Eleanor and CCp4C
>
> At the beginning I was very enthusiastic about the twinning option, but
> meanwhile the enthusiasm has vanished. I basically get the same Rfactors
> after refining the structure in P32 with 5 chains in Refmac (test
> reflections selected in resolution shells with sftools straight from the
> beginning).
>
> Refinement with tight NCS restrains on 4 chains and twinning results in
> Rf/Rfree 24.2/30.0, without twinning I get 27.0/32.5. With slightly relaxed
> NCS restrains for the side chains and no twinning its 24.3/31.8. A Rfree
> difference of 2% is that sufficient to confirm twinning?
>
> What bothers me even more is the difference ED for the "extra" chain (the
> on on the special position in P3221). After refienement with twinning the
> difference density is slightly reduced but it is still present.
> Furthermore, I can replace the "extra" chain by a 180° rotated copy and the
> refinemnt ends up in basically the same Rfactors. I attached two screen
> shots from the superposition of the initial structure (all atoms in wheat)
> on the rotated structure (blue Ca-trace) with the corresponding ED maps.
>
> All the best,
> Peer
>
> -"CCP4 bulletin board"  schrieb: -
> An: CCP4BB@JISCMAIL.AC.UK
> Von: "Schreuder, Herman /DE"
> Gesendet von: "CCP4 bulletin board"
> Datum: 27.08.2021 16:37
> Betreff: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on
> 2-fold axis?
>
>
>  Dear Lijun and others,
>
>  As Kay rightly pointed out, twinning is fundamentally different from e.g.
> disorder or alternative conformations. However, it does not depend on a
> chain or side chain rapidly jumping  between two states, but whether they
> are within coherent length of each other. Since most data are collected
> from frozen crystals, no side chain will be rapidly jumping between two
> states. They will be frozen either conformation A or conformation B and
> since  these conformations are randomly distributed throughout the crystal,
> they are in general within coherent length of each other and causing
> interference of their diffracted X-ray’s, so their complex structure
> factors are added.
>
>  However, for twinned crystals, the twin domains (twin pieces as you call
> it), behave as independent crystals and their intensities are added and not
> their (complex) structure factors.
>
>  I did not realize it when I first looked at the thread but the correct
> treatment of these crystals will depend on whether there are twin domains
> present in the crystals, or whether the  two orientations of the disordered
> chain are randomly distributed throughout the crystal. Given that the two
> orientations have different twin fractions, my bet is that the twin
> supporters are right.
>
>  Best,
>  Herman
>
>
>
>
>
>  Von: Lijun Liu 
>  Gesendet: Freitag, 27. August 2021 15:57
>  An: Schreuder, Herman /DE 
>  Cc: ccp4bb@jiscmail.ac.uk
>  Betreff: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold
> axis?
>
>  Dear Herman:
>
>
>
>  if you say “twinned” chains, then it already means same thing of the two
> and the side chain interactions could not be different (as you can see only
> one copy in the output coordinates), unless you talking about borders
> between twin pieces.
>
>
>
>  In this situation, the only I could imagine to be if P3221, it would have
> to make that chain very very rapidly jump between two states in the same
> asu, which can be easily proven wrong.
>
>
>
>  I do agree if refined under P3221 without restraining the two strictly,
> side chain interactions may show differences —— data always not perfect!
>
>
>
>  Lijun
>
>  Sent from my iPhone
>
>
>
>
>   On Aug 27, 2021, at 8:12 AM, Schreuder, Herman /DE <
> herman.schreu...@sanofi.com> wrote:
>
>  
>  Dear Lijun,
>  with this argument I agree: the interactions between the two orientations
> of the “twinned” chain and the neighboring molecules will be different and
> the interacting side chains will  almost certainly have different
> orientations, which necessitates a twinning of the whole structure.
>  Best,
>  Herman
>
>
>
>  Von: CCP4 bulletin board  Im Auftrag von Lijun Liu
>  Gesendet: Freitag, 27. August 2021 14:22
>  An: CCP4BB@JISCMAIL.AC.UK
>  Betreff: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold
> axis?
>
>
>  I believe it is a twin from P32.
>
>
>
>
>
>
>
> Not like the assignment of double conformations with partial occupancies
> to small part of asu, for examples, a side chain of lysin or a small
> fragment of a protein, which have both conformations stayed in the same
> specific asu at the same time.  

[ccp4bb] Postdoctoral Position in Structural Biology in Montpellier, France

[Jakub Gruszczyk]

Dear Colleagues,

A Postdoctoral position in Structural Biology is available at the Centre 
for Structural Biology in Montpellier, France. Details of the offer and 
how to apply can be found here:


https://euraxess.ec.europa.eu/jobs/677950

With kind regards,

Jakub Gruszczyk

--
Jakub Gruszczyk (PhD)
Nuclear receptors as integrators of endogenous and environmental signals
Centre for Structural Biology
CNRS UMR5048 / INSERM U1054
29 rue de Navacelles
34090 Montpellier, France
Phone: 33 4 67 41 77 19
Fax: 33 4 67 41 79 13
http://www.cbs.cnrs.fr
http://www.cbs.cnrs.fr/index.php/en/research-equipea5/theme-4-structure-and-function-of-the-aryl-hydrocarbon-receptor-atip-avenir


--
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dangerous content by MailScanner, and is
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[ccp4bb] Postdoctoral Researcher for cryo-EM studies of large protein complexes involved in cellular immunity

[Harma Brondijk]

Dear All

 

I would like to draw your attention to a vacancy for a postdoctoral
researcher in the lab of Piet Gros at Utrecht University, The Netherlands.
To read the full text of the vacancy and to apply please follow this link
  to the Utrecht University vacancy pages. Applications
can be made until September 19th.

 

Postdoctoral Researcher for cryo-EM studies of large protein complexes
involved in cellular immunity.

 

 

The Structural Biochemistry group of Professor Piet Gros has a long-standing
track record at the frontiers of structural biology focusing on elucidating
the molecular mechanisms that underlie biological processes with a major
emphasis on human plasma-proteins and cell-surface receptors. The lab has an
internationally strong reputation in uncovering the molecular mechanisms
that underpin the complement system. We combine protein crystallography,
cryo-electron microscopy, light microscopy, biochemical and biophysical
assays to get a detailed picture of the molecular interactions that enable
the complement system to discriminate between healthy self-cells and
pathogens or dying/malignant cells.

We currently offer the opportunity for a postdoctoral Researcher to join
forces with us on an ERC funded project that investigates the correlation
between levels of organisation within the membrane and complement efficacy.
Most of the interactions we are looking into for this project are in the
high nM to mM range and involve large flexible multi-domain proteins. So,
the challenge for you will be to find conditions/tricks that capture the
complex of interest in a state that enables detailed structural analyses.

Prinicipal tasks and responsibilities:

*   deliver high quality protein samples for structural analyses;
*   collect and analyse cryo-EM data;
*   structure determination, atomic model building and validation;
*   function as a go-to for PhDs and Postdocs in the group for expert
advice on all aspects of cryo-EM sample preparation, data collection and
analyses;
*   communicate you research findings within the group and to the larger
scientific community.

Profile

We seek a highly motivated individual with the ability to run their project
independently, but who also likes to collaborate with and advice other
members of our team.

Required knowledge/skills/abilities:

*   a PhD in structural biology or a closely related field;
*   proven experience in cryo-EM;
*   purification and analysis of protein complexes;
*   excellent oral and written skills in English.


Optional skills/abilities that are considered an advantage:

*   protein crystallography;
*   Cryo-ET;
*   molecular biology;
*   handling of membrane proteins.

 

Harma Brondijk

 

 

Dr. T.H.C. Brondijk | Research Coordinator | Structural Biochemistry |
Faculty of Science | Utrecht University | David de Wied building, Room 2.35
| Universiteitsweg 99, 3584 CG Utrecht | |  
t.h.c.brond...@uu.nl | Aanwezig: ma-vrij

 

 

 

 

 




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[ccp4bb] PostDoctoral researcher in Protein Interaction Engineering, Birkbeck College, London UK

[Nikos Pinotsis]

Dear all,

apologies for the slightly off-topic advertisement.

We have an opening for a post-doctoral position at Birkbeck College 
focusing on Protein interaction engineering. This is part of the EU 
funded project MOSRBI (European Molecular-Scale Biophysics Research 
Infrastructure https://www.mosbri.eu/ ) which 
involves several structural biology and biophysics Laboratories across 
Europe.


Description of the job and further details about the post can be found 
here:


https://cis7.bbk.ac.uk/vacancy/postdoctoral-researcher-in-protein-interaction-engineering-456021.html

Application deadline is on the 3rd of October

--
Dr. Nikos Pinotsis
Protein Crystallography and Biophysics Centre
Institute of Structural and Molecular Biology
Department of Biological Sciences, Room B16b
Birkbeck College
Malet Street
London WC1E 7HX
Direct: +44 (0)20 3926 3507
Office: +44 (0)207 631 6458
Mobile: +44 (0)792 384 3593



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Re: [ccp4bb] Some questions on tools for CCP4i2cloud: pdbset, pdbcur, coordconv, sftools

[Eleanor Dodson]

ATTACHED SOME CORRESPONDENCE WITH David Lawson re these issues/.
Eleanor

On Tue, 31 Aug 2021 at 10:29, Robbie Joosten 
wrote:

> Hi everyone,
>
> Thank you for the replies so far on and off list, they are really helpful.
> Feel free to keep them coming.
>
> Cheers,
> Robbie
>
> > -Original Message-
> > From: CCP4 bulletin board  On Behalf Of Dirk
> > Kostrewa
> > Sent: Tuesday, August 31, 2021 10:24
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] Some questions on tools for CCP4i2cloud: pdbset,
> > pdbcur, coordconv, sftools
> >
> > Dear Robbie,
> >
> > I use pdbset in scripts from time to time, mainly to generate symmetry
> > equivalent copies. I use sftools on the command line more frequently,
> > because it allows a lot of mathematical operations on data in mtz files.
> > I also use sftools to produce lists of average data values against
> > resolution (that I plot then with gnuplot). I can't recall having used
> > coordconv at all.
> >
> > Best regards,
> >
> > Dirk.
> >
> > On 8/26/21 12:29 PM, Robbie Joosten wrote:
> > > Dear CCP4 users,
> > >
> > > We (as in, the CCP4 developers) are investigating some (potentially)
> > missing functionality in CCP4i2 and/or Cloud with respect to the programs
> > pdbset, pdbcur, coordconv, and sftools. Some of these tools are quite old
> > and may need to be replaced by other tools with similar functionality.
> Could
> > you answer a few questions:
> > >
> > > - Do you use any of these tools?
> > > - If so, how often? (Few times a week, month, year, or less than once a
> > year).
> > > - Which functionality of program X do you use?
> > > - Would you like a graphical interface to that functionality or are
> you happy
> > to use the command line?
> > >
> > > Personal example:
> > > I use pdbset a few times a month, but only the "noise" function. I
> don't
> > need a graphical interface for it (because it is used in the context of
> pdb-
> > redo). I also use sftools, "reduce -> merge average" a few times a year.
> Again,
> > only from the command line.
> > >
> > >
> > > Feel free to send your answers directly to me or to the bulletin board
> if
> > you want to start a discussion. Tips on alternative CCP4 tools to achieve
> > similar effects are probably also interesting for other BB users.
> > >
> > > Cheers,
> > > Robbie
> > >
> > >
> > >
> > >
> > >
> > ###
> > #
> > >
> > > 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/
> >
> > --
> >
> > ***
> > Dirk Kostrewa
> > Gene Center Munich
> > Department of Biochemistry, AG Hopfner
> > Ludwig-Maximilians-Universität München
> > Feodor-Lynen-Str. 25
> > D-81377 Munich
> > Germany
> > Phone:  +49-89-2180-76845
> > Fax:+49-89-2180-76998
> > E-mail: dirk.kostr...@lmu.de
> >  kostr...@genzentrum.lmu.de
> > WWW:www.genzentrum.lmu.de
> > ***
> >
> > ###
> > #
> >
> > 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/
>
> 
>
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>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
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DaveLawson.docx
Description: MS-Word 2007 document

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Eleanor Dodson]

Espec. Jan & Kay,

I had better check this out - ville wrote the code I believe, and I have
never actually checked the distribution!
Cheers Eleanor

On Tue, 31 Aug 2021 at 08:01, Jan Dohnalek  wrote:

> This is good to know indeed.
> Will improve my teaching now, I also did not know this is now done
> automatically. Thanks for pointing it out.
>
> Jan
>
>
> On Mon, Aug 30, 2021 at 9:44 PM Kay Diederichs <
> kay.diederi...@uni-konstanz.de> wrote:
>
>> Dear Eleanor,
>>
>> Thanks for pointing out that CCP4 FreeRflag selects the test set in the
>> highest possible symmetry for the crystal class! I didn't know that.
>>
>> The following sentences (which are somewhat difficult to understand for
>> me) in https://www.ccp4.ac.uk/html/freerflag.html appear to document
>> that:
>> "The FreeR_flag is randomly and uniformly distributed
>> reflexion-by-reflexion, but, additionally, if the keyword NOSYM is not set,
>> all reflections that are equivalent by the symmetry of the point group of
>> the twin lattice (assuming the data is twinned), obtain the same flag. This
>> includes both the possibility of merohedral and pseudomerohedral twinning.
>> In the latter case, the obliquity parameter can be set using the keyword
>> OBL."
>>
>> I wonder since which CCP4 version (or date) this is the default behaviour.
>>
>> best wishes,
>> Kay
>>
>> On Mon, 30 Aug 2021 18:28:23 +0100, Eleanor Dodson <
>> eleanor.dod...@york.ac.uk> wrote:
>>
>> >Back to FreeR factors - Phenix, and I believe FreeRflag now select FreeRs
>> >in the highest possible symmetry for the crystal class - eh P6/mmm for a
>> >trigonal crystal, and expand the set to fill the actual space group. This
>> >means the Free R assignment is suitable if later the crystal symmetry is
>> >reassigned. But this was not always done in the past so if you are trying
>> >to reuse free/work assignments from an old project there are
>> possibilities
>> >of not getting this. Maybe the best solution is to just generate a new
>> Free
>> >R set ?
>> >Eleanor
>> >
>> ...
>>
>> 
>>
>> 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/
>>
>
>
> --
> Jan Dohnalek, Ph.D
> Institute of Biotechnology
> Academy of Sciences of the Czech Republic
> Biocev
> Prumyslova 595
> 252 50 Vestec near Prague
> Czech Republic
>
> Tel. +420 325 873 758
>
> --
>
> 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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Re: [ccp4bb] Some questions on tools for CCP4i2cloud: pdbset, pdbcur, coordconv, sftools

[Robbie Joosten]

Hi everyone,

Thank you for the replies so far on and off list, they are really helpful. Feel 
free to keep them coming. 

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Dirk
> Kostrewa
> Sent: Tuesday, August 31, 2021 10:24
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Some questions on tools for CCP4i2cloud: pdbset,
> pdbcur, coordconv, sftools
> 
> Dear Robbie,
> 
> I use pdbset in scripts from time to time, mainly to generate symmetry
> equivalent copies. I use sftools on the command line more frequently,
> because it allows a lot of mathematical operations on data in mtz files.
> I also use sftools to produce lists of average data values against
> resolution (that I plot then with gnuplot). I can't recall having used
> coordconv at all.
> 
> Best regards,
> 
> Dirk.
> 
> On 8/26/21 12:29 PM, Robbie Joosten wrote:
> > Dear CCP4 users,
> >
> > We (as in, the CCP4 developers) are investigating some (potentially)
> missing functionality in CCP4i2 and/or Cloud with respect to the programs
> pdbset, pdbcur, coordconv, and sftools. Some of these tools are quite old
> and may need to be replaced by other tools with similar functionality. Could
> you answer a few questions:
> >
> > - Do you use any of these tools?
> > - If so, how often? (Few times a week, month, year, or less than once a
> year).
> > - Which functionality of program X do you use?
> > - Would you like a graphical interface to that functionality or are you 
> > happy
> to use the command line?
> >
> > Personal example:
> > I use pdbset a few times a month, but only the "noise" function. I don't
> need a graphical interface for it (because it is used in the context of pdb-
> redo). I also use sftools, "reduce -> merge average" a few times a year. 
> Again,
> only from the command line.
> >
> >
> > Feel free to send your answers directly to me or to the bulletin board if
> you want to start a discussion. Tips on alternative CCP4 tools to achieve
> similar effects are probably also interesting for other BB users.
> >
> > Cheers,
> > Robbie
> >
> >
> >
> >
> >
> ###
> #
> >
> > 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/
> 
> --
> 
> ***
> Dirk Kostrewa
> Gene Center Munich
> Department of Biochemistry, AG Hopfner
> Ludwig-Maximilians-Universität München
> Feodor-Lynen-Str. 25
> D-81377 Munich
> Germany
> Phone:  +49-89-2180-76845
> Fax:+49-89-2180-76998
> E-mail: dirk.kostr...@lmu.de
>  kostr...@genzentrum.lmu.de
> WWW:www.genzentrum.lmu.de
> ***
> 
> ###
> #
> 
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[ccp4bb] Call open for beamtime at XALOC (ALBA synchrotron) in 2022, deadline 6th September

[Roeland Boer]

Dear fellow crystallographers,

I would like to draw your attention to the call  for proposals for the 
XALOC beamline at the ALBA synchrotron, open until the 6th of September 
2021. The call is for experiments to be performed during the whole year 
of 2022.


Some features of XALOC:

 * Remote data collection supported, dewar shipment reimbursed for EU
   member countries
 * Supports SPINE (8 xtals/h) and Unipuck (12 xtals/h)
 * Tunable from 5-20 keV, SAD and MAD capabilities
 * Flux at 12.662 keV is 2E12 ph/s, and 3E11 ph/s at 6 keV
 * Software: MxCube and ISpyB (default data processing with AutoPROC
   and EDNAProc)
 o Continuous raster scans
 o Helical data collection
 o Global Phasing workflow
 * Plate diffraction experiments supported

Please also note that SSX is now a reality at XALOC. If you are 
interested in more details, please contact XALOC Staff.


Please visit https://www.cells.es/en/users/call-information

To submit a proposal, visit https://useroffice.cells.es/ 



Best regards,

Roeland Boer.



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Re: [ccp4bb] Some questions on tools for CCP4i2cloud: pdbset, pdbcur, coordconv, sftools

[Dirk Kostrewa]

Dear Robbie,

I use pdbset in scripts from time to time, mainly to generate symmetry 
equivalent copies. I use sftools on the command line more frequently, 
because it allows a lot of mathematical operations on data in mtz files. 
I also use sftools to produce lists of average data values against 
resolution (that I plot then with gnuplot). I can't recall having used 
coordconv at all.


Best regards,

Dirk.

On 8/26/21 12:29 PM, Robbie Joosten wrote:

Dear CCP4 users,

We (as in, the CCP4 developers) are investigating some (potentially) missing 
functionality in CCP4i2 and/or Cloud with respect to the programs pdbset, 
pdbcur, coordconv, and sftools. Some of these tools are quite old and may need 
to be replaced by other tools with similar functionality. Could you answer a 
few questions:

- Do you use any of these tools?
- If so, how often? (Few times a week, month, year, or less than once a year).
- Which functionality of program X do you use?
- Would you like a graphical interface to that functionality or are you happy 
to use the command line?

Personal example:
I use pdbset a few times a month, but only the "noise" function. I don't need a graphical 
interface for it (because it is used in the context of pdb-redo). I also use sftools, "reduce 
-> merge average" a few times a year. Again, only from the command line.


Feel free to send your answers directly to me or to the bulletin board if you 
want to start a discussion. Tips on alternative CCP4 tools to achieve similar 
effects are probably also interesting for other BB users.

Cheers,
Robbie


  




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--

***
Dirk Kostrewa
Gene Center Munich
Department of Biochemistry, AG Hopfner
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76998
E-mail: dirk.kostr...@lmu.de
kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***



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Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Jan Dohnalek]

This is good to know indeed.
Will improve my teaching now, I also did not know this is now done
automatically. Thanks for pointing it out.

Jan


On Mon, Aug 30, 2021 at 9:44 PM Kay Diederichs <
kay.diederi...@uni-konstanz.de> wrote:

> Dear Eleanor,
>
> Thanks for pointing out that CCP4 FreeRflag selects the test set in the
> highest possible symmetry for the crystal class! I didn't know that.
>
> The following sentences (which are somewhat difficult to understand for
> me) in https://www.ccp4.ac.uk/html/freerflag.html appear to document that:
> "The FreeR_flag is randomly and uniformly distributed
> reflexion-by-reflexion, but, additionally, if the keyword NOSYM is not set,
> all reflections that are equivalent by the symmetry of the point group of
> the twin lattice (assuming the data is twinned), obtain the same flag. This
> includes both the possibility of merohedral and pseudomerohedral twinning.
> In the latter case, the obliquity parameter can be set using the keyword
> OBL."
>
> I wonder since which CCP4 version (or date) this is the default behaviour.
>
> best wishes,
> Kay
>
> On Mon, 30 Aug 2021 18:28:23 +0100, Eleanor Dodson <
> eleanor.dod...@york.ac.uk> wrote:
>
> >Back to FreeR factors - Phenix, and I believe FreeRflag now select FreeRs
> >in the highest possible symmetry for the crystal class - eh P6/mmm for a
> >trigonal crystal, and expand the set to fill the actual space group. This
> >means the Free R assignment is suitable if later the crystal symmetry is
> >reassigned. But this was not always done in the past so if you are trying
> >to reuse free/work assignments from an old project there are possibilities
> >of not getting this. Maybe the best solution is to just generate a new
> Free
> >R set ?
> >Eleanor
> >
> ...
>
> 
>
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-- 
Jan Dohnalek, Ph.D
Institute of Biotechnology
Academy of Sciences of the Czech Republic
Biocev
Prumyslova 595
252 50 Vestec near Prague
Czech Republic

Tel. +420 325 873 758



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