Re: [ccp4bb] [3dem] [ccpem] Which resolution?

[Tim Gruene]

Hi Marin,

crystallography has long moved away from the term 'resolution', see e.g. 
https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2. It is merely a 
ballpark number, and it is good to know whether crystallographic data were cut 
at 1, 2, or 3 Angstrom, but not very important.

What counts is the interpretation of the model and conclusion that can be 
drawn on the system under study. It requires a broader understanding of 
crystallography in order to understand whether the conclusions are justified. 
Resolution plays only a minor role in this. It is more useful to take a look 
at the crystallographic map itself in order to understand.

EM is totally different from crystallography, and why would one mix concepts 
between the fields?

Best,
Tim

On Thursday, February 13, 2020 12:07:15 AM CET Marin van Heel wrote:
> Hi Tim,
> Good to hear from you!  No longer at PSI??
> See... You are already touching upon one of the logical breaking points in
> the resolutiton story...!  X-ray crystallography resolution criteria like
> R-factors make absolutely no sense outside the field of crystallography and
> of structural biology.  It is the result of a hybrid iterative optimisation
> process between the phases of a model structure and the measured amplitudes
> of a diffraction experiment!  The FRC/FSC resolution criteria, in contrast,
> are universal quality metrics not at all coupled to Cryo-EM or structural
> biology.  Using structural biology arguments like how well I see an alpha
> helix or how well I see the hole in an aromatic ring as an assessment
> criterion of whether a metric is good or not is a waste of time!  (Moreover
> filtering a map can completley change its appearance without changing its
> information contents). Even some my own (ex-)students and (ex-)postdocs
> sometimes completely miss this fundamental point. The FRC and FSC criteria
> are now used as quality metrics in all walks of image science like X-ray
> tomography and super-resolution light microscopy, fields of science where
> atomic coordinates of proteins are not an issue. The FRC / FSC functions
> are universal and very direct metrics that compare both the amplitudes and
> the phases of two independent measurements of images or 3D-densities of the
> same object. For more details, see the 2017 bioRxiv paper and references
> therein (https://www.biorxiv.org/content/10.1101/224402v1) and check my
> #WhyOWhy tweets (@marin_van_heel). See also: van Heel - Unveiling ribosomal
> structures: the final phases - Current opinion in structural biology 10
> (2000) 259-264.
> 
> Cheers,
> Marin
> 
> On Wed, Feb 12, 2020 at 11:22 AM Tim Gruene  wrote:
> > Dear Marin,
> > 
> > I did not read the enire thread, nor the manuscript you point at -
> > apologize
> > in case this has been discussed before.
> > 
> > What about a practical approach to determine the resolution of a cryoEM
> > map:
> > one could take a feature with scales of interest, e.g. an alpha-helix, and
> > shift and/or rotate it in steps of, say, 0.3A in several directions to
> > see, at
> > which magnitude (degree / distance) refinement does not take the helix
> > back to
> > its original position (within error margins).
> > 
> > One could also take a Monte-Carlo approach and do an arbitrary number of
> > random re-orientations of such a helix, refine, and calculate the
> > variation in
> > position and rotation.
> > 
> > This would reflect my understanding of resolution, much more than any
> > statistical descriptor.
> > 
> > Best regards,
> > Tim
> > 
> > On Wednesday, February 12, 2020 1:46:48 PM CET Marin van Heel wrote:
> > > Hi Laurence,
> > > 
> > > One thing is certain: the 0.143 threshold is RUBBISH and all CC50 etc
> > > are
> > > also based on the same SLOPPY STATISTICS  as are all  fixed-valued  FSC
> > > thresholds. This controversy has been ragings for a long long time and
> > 
> > the
> > 
> > > errors made were extensively described (again) in our most recent paper
> > > (Van Heel & Schatz 2017 BioRxiv:
> > > https://www.biorxiv.org/content/10.1101/224402v1) which has been
> > 
> > downloaded
> > 
> > > more than 3000 times. Further papers on the issue are in the pipeline.
> > 
> > The
> > 
> > > math BLUNDER behind this controversy is simple:  the inner product
> > 
> > between
> > 
> > > a signal vector and a noise vector is NOT zero (but rather proportional
> > 
> > to
> > 
> > > SQRT(N) where N is the length of the vectors) and cannot be left out of
> > 
> > the
> > 
> > > equations. This error goes back to a paper published in Nature in 1975
> > 
> > and
> > 
> > > has since been repeated frequently, including in the first paper
> > 
> > promoting
> > 
> > > the erroneous 0.143 FSC threshold. The consequences of this blunder in
> > > current processing are serious especially when these erroneous metrics
> > 
> > are
> > 
> > > used as an optimisation criterion in iterative refinements at
> > > resolutions
> > > close to Nyquist.  I get tired of facing this 

Re: [ccp4bb] [3dem] [ccpem] Which resolution?

[Marin van Heel]

Dear Pavel,
Your paper is one of the more elaborate ones on the issue with an
exhaustive list of references! No wonder, since some 20 years ago, Bruno
Klaholtz was a very successful post-doc in my group at Imperial in London.
However, I have discussed this paper with Bruno at our Brazil School in
2018 and I pointed out to him that your use of fixed-valued FSC thresholds
makes that your paper, like 95% of the papers on resolution in our field,
implicitly is based on the "sloppy statistics" of others, namely that the
inner product between signal and noise vectors cannot be neglected. As long
as those "sloppy statistics" papers are not taken from the literature,
years or decades after they have been refuted, and the criticism against
them is simply ignored or belittled, incorrect follow-up research along the
same sloppy pathways is the consequence, and that is so sad...
Sorry,
Marin

On Wed, Feb 12, 2020 at 8:34 PM Pavel Afonine  wrote:

> Interesting conversation! I see the 2017 paper is on bioRxiv. I wonder if
> it ever made into a peer reviewed journal (couldn't find quickly)?
> @Tim Gruene  : have a look at d_model in
> https://www.ncbi.nlm.nih.gov/pubmed/30198894 which is sort of along
> similar lines of what you are hinting here.
> Pavel
>
> On Wed, Feb 12, 2020 at 3:07 PM Marin van Heel <
> 057a89ab08a1-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Hi Tim,
>> Good to hear from you!  No longer at PSI??
>> See... You are already touching upon one of the logical breaking points
>> in the resolutiton story...!  X-ray crystallography resolution criteria
>> like R-factors make absolutely no sense outside the field of
>> crystallography and of structural biology.  It is the result of a hybrid
>> iterative optimisation process between the phases of a model structure and
>> the measured amplitudes of a diffraction experiment!  The FRC/FSC
>> resolution criteria, in contrast, are universal quality metrics not at all
>> coupled to Cryo-EM or structural biology.  Using structural biology
>> arguments like how well I see an alpha helix or how well I see the hole in
>> an aromatic ring as an assessment criterion of whether a metric is good or
>> not is a waste of time!  (Moreover filtering a map can completley change
>> its appearance without changing its information contents). Even some my own
>> (ex-)students and (ex-)postdocs sometimes completely miss this fundamental
>> point. The FRC and FSC criteria are now used as quality metrics in all
>> walks of image science like X-ray tomography and super-resolution light
>> microscopy, fields of science where atomic coordinates of proteins are not
>> an issue. The FRC / FSC functions are universal and very direct metrics
>> that compare both the amplitudes and the phases of two independent
>> measurements of images or 3D-densities of the same object. For more
>> details, see the 2017 bioRxiv paper and references therein (
>> https://www.biorxiv.org/content/10.1101/224402v1) and check my #WhyOWhy
>> tweets (@marin_van_heel). See also: van Heel - Unveiling ribosomal
>> structures: the final phases - Current opinion in structural biology 10
>> (2000) 259-264.
>>
>> Cheers,
>> Marin
>>
>>
>> On Wed, Feb 12, 2020 at 11:22 AM Tim Gruene 
>> wrote:
>>
>>> Dear Marin,
>>>
>>> I did not read the enire thread, nor the manuscript you point at -
>>> apologize
>>> in case this has been discussed before.
>>>
>>> What about a practical approach to determine the resolution of a cryoEM
>>> map:
>>> one could take a feature with scales of interest, e.g. an alpha-helix,
>>> and
>>> shift and/or rotate it in steps of, say, 0.3A in several directions to
>>> see, at
>>> which magnitude (degree / distance) refinement does not take the helix
>>> back to
>>> its original position (within error margins).
>>>
>>> One could also take a Monte-Carlo approach and do an arbitrary number of
>>> random re-orientations of such a helix, refine, and calculate the
>>> variation in
>>> position and rotation.
>>>
>>> This would reflect my understanding of resolution, much more than any
>>> statistical descriptor.
>>>
>>> Best regards,
>>> Tim
>>>
>>> On Wednesday, February 12, 2020 1:46:48 PM CET Marin van Heel wrote:
>>> > Hi Laurence,
>>> >
>>> > One thing is certain: the 0.143 threshold is RUBBISH and all CC50 etc
>>> are
>>> > also based on the same SLOPPY STATISTICS  as are all  fixed-valued  FSC
>>> > thresholds. This controversy has been ragings for a long long time and
>>> the
>>> > errors made were extensively described (again) in our most recent paper
>>> > (Van Heel & Schatz 2017 BioRxiv:
>>> > https://www.biorxiv.org/content/10.1101/224402v1) which has been
>>> downloaded
>>> > more than 3000 times. Further papers on the issue are in the pipeline.
>>> The
>>> > math BLUNDER behind this controversy is simple:  the inner product
>>> between
>>> > a signal vector and a noise vector is NOT zero (but rather
>>> proportional to
>>> > SQRT(N) where N is the length of the vectors) and cannot be left out

Re: [ccp4bb] [3dem] [ccpem] Which resolution?

[Pavel Afonine]

Interesting conversation! I see the 2017 paper is on bioRxiv. I wonder if
it ever made into a peer reviewed journal (couldn't find quickly)?
@Tim Gruene  : have a look at d_model in
https://www.ncbi.nlm.nih.gov/pubmed/30198894 which is sort of along similar
lines of what you are hinting here.
Pavel

On Wed, Feb 12, 2020 at 3:07 PM Marin van Heel <
057a89ab08a1-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi Tim,
> Good to hear from you!  No longer at PSI??
> See... You are already touching upon one of the logical breaking points in
> the resolutiton story...!  X-ray crystallography resolution criteria like
> R-factors make absolutely no sense outside the field of crystallography and
> of structural biology.  It is the result of a hybrid iterative optimisation
> process between the phases of a model structure and the measured amplitudes
> of a diffraction experiment!  The FRC/FSC resolution criteria, in contrast,
> are universal quality metrics not at all coupled to Cryo-EM or structural
> biology.  Using structural biology arguments like how well I see an alpha
> helix or how well I see the hole in an aromatic ring as an assessment
> criterion of whether a metric is good or not is a waste of time!  (Moreover
> filtering a map can completley change its appearance without changing its
> information contents). Even some my own (ex-)students and (ex-)postdocs
> sometimes completely miss this fundamental point. The FRC and FSC criteria
> are now used as quality metrics in all walks of image science like X-ray
> tomography and super-resolution light microscopy, fields of science where
> atomic coordinates of proteins are not an issue. The FRC / FSC functions
> are universal and very direct metrics that compare both the amplitudes and
> the phases of two independent measurements of images or 3D-densities of the
> same object. For more details, see the 2017 bioRxiv paper and references
> therein (https://www.biorxiv.org/content/10.1101/224402v1) and check my
> #WhyOWhy tweets (@marin_van_heel). See also: van Heel - Unveiling
> ribosomal structures: the final phases - Current opinion in structural
> biology 10 (2000) 259-264.
>
> Cheers,
> Marin
>
>
> On Wed, Feb 12, 2020 at 11:22 AM Tim Gruene 
> wrote:
>
>> Dear Marin,
>>
>> I did not read the enire thread, nor the manuscript you point at -
>> apologize
>> in case this has been discussed before.
>>
>> What about a practical approach to determine the resolution of a cryoEM
>> map:
>> one could take a feature with scales of interest, e.g. an alpha-helix,
>> and
>> shift and/or rotate it in steps of, say, 0.3A in several directions to
>> see, at
>> which magnitude (degree / distance) refinement does not take the helix
>> back to
>> its original position (within error margins).
>>
>> One could also take a Monte-Carlo approach and do an arbitrary number of
>> random re-orientations of such a helix, refine, and calculate the
>> variation in
>> position and rotation.
>>
>> This would reflect my understanding of resolution, much more than any
>> statistical descriptor.
>>
>> Best regards,
>> Tim
>>
>> On Wednesday, February 12, 2020 1:46:48 PM CET Marin van Heel wrote:
>> > Hi Laurence,
>> >
>> > One thing is certain: the 0.143 threshold is RUBBISH and all CC50 etc
>> are
>> > also based on the same SLOPPY STATISTICS  as are all  fixed-valued  FSC
>> > thresholds. This controversy has been ragings for a long long time and
>> the
>> > errors made were extensively described (again) in our most recent paper
>> > (Van Heel & Schatz 2017 BioRxiv:
>> > https://www.biorxiv.org/content/10.1101/224402v1) which has been
>> downloaded
>> > more than 3000 times. Further papers on the issue are in the pipeline.
>> The
>> > math BLUNDER behind this controversy is simple:  the inner product
>> between
>> > a signal vector and a noise vector is NOT zero (but rather proportional
>> to
>> > SQRT(N) where N is the length of the vectors) and cannot be left out of
>> the
>> > equations. This error goes back to a paper published in Nature in 1975
>> and
>> > has since been repeated frequently, including in the first paper
>> promoting
>> > the erroneous 0.143 FSC threshold. The consequences of this blunder in
>> > current processing are serious especially when these erroneous metrics
>> are
>> > used as an optimisation criterion in iterative refinements at
>> resolutions
>> > close to Nyquist.  I get tired of facing this systematic misuse of the
>> FSC
>> > function, which I myself have introduced into the literature in
>> 1982/1986,
>> > and people nevertheless feel they know better (with no scientific
>> arguments
>> > to support!) and they feel justified to use it beyond its definition
>> range,
>> > and to continue to ignore the correct math. To counter this systematic
>> > abuse of my brain child - over decades - I feel the need to use CLEAR
>> > LANGUAGE!
>> > Have fun!
>> > Marin
>>
>> --
>> --
>> Tim Gruene
>> Head of the Centre for X-ray Structure Analysis
>> Faculty of Chemistry
>> 

Re: [ccp4bb] [3dem] [ccpem] Which resolution?

[Marin van Heel]

Hi Tim,
Good to hear from you!  No longer at PSI??
See... You are already touching upon one of the logical breaking points in
the resolutiton story...!  X-ray crystallography resolution criteria like
R-factors make absolutely no sense outside the field of crystallography and
of structural biology.  It is the result of a hybrid iterative optimisation
process between the phases of a model structure and the measured amplitudes
of a diffraction experiment!  The FRC/FSC resolution criteria, in contrast,
are universal quality metrics not at all coupled to Cryo-EM or structural
biology.  Using structural biology arguments like how well I see an alpha
helix or how well I see the hole in an aromatic ring as an assessment
criterion of whether a metric is good or not is a waste of time!  (Moreover
filtering a map can completley change its appearance without changing its
information contents). Even some my own (ex-)students and (ex-)postdocs
sometimes completely miss this fundamental point. The FRC and FSC criteria
are now used as quality metrics in all walks of image science like X-ray
tomography and super-resolution light microscopy, fields of science where
atomic coordinates of proteins are not an issue. The FRC / FSC functions
are universal and very direct metrics that compare both the amplitudes and
the phases of two independent measurements of images or 3D-densities of the
same object. For more details, see the 2017 bioRxiv paper and references
therein (https://www.biorxiv.org/content/10.1101/224402v1) and check my
#WhyOWhy tweets (@marin_van_heel). See also: van Heel - Unveiling ribosomal
structures: the final phases - Current opinion in structural biology 10
(2000) 259-264.

Cheers,
Marin


On Wed, Feb 12, 2020 at 11:22 AM Tim Gruene  wrote:

> Dear Marin,
>
> I did not read the enire thread, nor the manuscript you point at -
> apologize
> in case this has been discussed before.
>
> What about a practical approach to determine the resolution of a cryoEM
> map:
> one could take a feature with scales of interest, e.g. an alpha-helix, and
> shift and/or rotate it in steps of, say, 0.3A in several directions to
> see, at
> which magnitude (degree / distance) refinement does not take the helix
> back to
> its original position (within error margins).
>
> One could also take a Monte-Carlo approach and do an arbitrary number of
> random re-orientations of such a helix, refine, and calculate the
> variation in
> position and rotation.
>
> This would reflect my understanding of resolution, much more than any
> statistical descriptor.
>
> Best regards,
> Tim
>
> On Wednesday, February 12, 2020 1:46:48 PM CET Marin van Heel wrote:
> > Hi Laurence,
> >
> > One thing is certain: the 0.143 threshold is RUBBISH and all CC50 etc are
> > also based on the same SLOPPY STATISTICS  as are all  fixed-valued  FSC
> > thresholds. This controversy has been ragings for a long long time and
> the
> > errors made were extensively described (again) in our most recent paper
> > (Van Heel & Schatz 2017 BioRxiv:
> > https://www.biorxiv.org/content/10.1101/224402v1) which has been
> downloaded
> > more than 3000 times. Further papers on the issue are in the pipeline.
> The
> > math BLUNDER behind this controversy is simple:  the inner product
> between
> > a signal vector and a noise vector is NOT zero (but rather proportional
> to
> > SQRT(N) where N is the length of the vectors) and cannot be left out of
> the
> > equations. This error goes back to a paper published in Nature in 1975
> and
> > has since been repeated frequently, including in the first paper
> promoting
> > the erroneous 0.143 FSC threshold. The consequences of this blunder in
> > current processing are serious especially when these erroneous metrics
> are
> > used as an optimisation criterion in iterative refinements at resolutions
> > close to Nyquist.  I get tired of facing this systematic misuse of the
> FSC
> > function, which I myself have introduced into the literature in
> 1982/1986,
> > and people nevertheless feel they know better (with no scientific
> arguments
> > to support!) and they feel justified to use it beyond its definition
> range,
> > and to continue to ignore the correct math. To counter this systematic
> > abuse of my brain child - over decades - I feel the need to use CLEAR
> > LANGUAGE!
> > Have fun!
> > Marin
>
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
>
> Phone: +43-1-4277-70202
>
> GPG Key ID = A46BEE1A
>



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[ccp4bb] Postdoc opportunity in San Francisco

[Oren R]

Dear ccp4bb Subscribers,



Would you like to use your expertise to combat important problems affecting
public health?  Are you interested in combining your skills in structural
biology with quantitative genetic approaches?   Do you enjoy working in a
collaborative, intellectually stimulating environment, situated in one of
the most exciting (and beautiful) cities in the world?


The Rosenberg lab, located at University of California - San Francisco
(UCSF) and affiliated with the Chan-Zuckerberg Biohub, has an NIH funded
position for a postdoctoral scholar to continue our work characterizing the
structural biology of host-pathogen interactions.  You will have exciting
opportunities to combine your structural findings with functional
characterization using microbial genetics.  In recent work, we have used a
variety of structural techniques to characterize bacterial virulence
systems (see for example, PMID: 31886769, PMID: 28252385, or PMID:
25865481).  We have also developed novel genetic tools that can be used to
study how pathogens interact with their hosts (PMID: 30617347, PMID:
31481541, or PMID: 31073154).


We are looking for a Ph.D. candidate or recipient trained in electron
microscopy or x-ray crystallography and with an interest in expanding their
structural tool kit.  Our facilities at UCSF include access to a Talos
Arctica Cryo-TEM for screening and a Krios with a K3 bioquantum for data
collection, as well as several other instruments for negative stain and
additional data collection.  We also have new funding for the installation
of a Cryo-FIB and a cryo-fluorescence microscope to facilitate CryoCLEM.
Additionally, there is a state-of-the-art, automated facility for protein
crystal growth, and essentially unlimited access to synchrotron time at
ALS. Many shared instruments are available for biophysical characterization
of proteins.


If you are interested, please contact Laura Wise (laura.w...@ucsf.edu) with
a cover letter and a CV describing your work and we will be in touch!
Please submit your application before April 1'st for full consideration,
though the start date is negotiable.


The University of California is an *Equal Opportunity*/Affirmative Action
*Employer*. All qualified applicants will receive consideration for
*employment* without regard to race, color, religion, sex, sexual
orientation, gender identity, national origin, disability, age or protected
veteran status.


Looking forward to hearing from you soon,


Oren

---

Oren Rosenberg
Associate Professor of Medicine

University of California, San Francisco



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[ccp4bb] Job posting: Scientist level positions at DFCI, Boston

[Hyuk-Soo Seo]

Structural Biology Core at Dana-Farber Cancer Institute has multiple
openings at Scientist levels. Please see the details and apply online using
the links below.

https://careers-dfci.icims.com/jobs/18426/research-fellow-dhe-paganon-lab/job


https://careers-dfci.icims.com/jobs/18424/research-technician-dhe-paganon-lab/job


Best,
Hyuk-Soo

Hyuk-Soo Seo, Ph.D.
Senior Scientist
Dana-Farber Cancer Institute
Harvard Medical School
360 Longwood Avenue
Boston, MA 02215



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[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline March 01, 2020

[Manfred S. Weiss]

Dear all,

the next MX-proposal application deadline: March 01, 2020 is approaching
https://www.helmholtz-berlin.de/user/beamtime/proposals/index_en.html

As usual, all proposals will be handled by our electronic user portal GATE,
https://www.helmholtz-berlin.de/pubbin/hzbgate

Hereby we would like to invite the submission of new proposals for
MX-beamtime at the HZB-MX beamlines for the next beam time period
(01/2021-07/2021).

In order to apply for beamtime, please register in GATE and submit
a new beam time application proposal.

Please note that we now expect from each research group only ONE proposal,
which can contain up to 20 individual projects.


IMPORTANT: If you have a running 2019-2 proposal, you may ask for extension.
For this, an interim report is necessary. You will also be able to edit
and modify your proposal by adding and deleting projects.


HZB provides MX-beamtime at the three MX-beamlines BL14.1, BL14.2
and BL14.3. The three beamlines are equipped with state-of-the-art
instrumentation and are currently the most productive MX-stations in
Germany with more than 3000 PDB depositions in total. Beamtime is granted
based on the reviewed proposals and on reports from previous research
activities. Please make sure to include them if available.

Experimental setup:

BL14.1:
- Photon energy range: 5.5-16 keV (wavelength: 0.775-2.25 A)
- Photon flux: 1.8x10¹¹ Phot/sec x 100 mA at sample position
 (0.04-1 sec exposure time per frame)
- PILATUS3 S 6M detector with 1000 µm Si sensor thickness, 141 mm-680 mm max. 
distance from the sample
- Microdiffractometer (MD2) with Mini-kappa goniometer
- Automatic sample changer (CATS), 90 sample storage capacity
 (SPINE-Pin & EMBL sample magazine compatibility)
- User defined beam shaping from 50 µm-100 µm diameter possible
- In situ crystal-screening using 96-well plates
- 32-core XEON-CPU server, with 10GB uplink to Pilatus 6M
- Data collection control via MXCuBE2
- Common MX-software installed including EDNA, XDS, iMOSFLM, CCP4,
 Phenix, SHELXC-D-E, etc.
- Automated data processing using XDSAPP
- Remotely controlled cryo-shutter for crystal annealing
- AMPTEK-XRF detector and XFEPLOT software available

We are also offering the hard- and software environment for
carrying out UV-RIP experiments at BL14.1. For further information,
please visit:
https://www.helmholtz-berlin.de/forschung/oe/np/gmx/ancillary-facilities/uvrip_en.html

BL14.2:
- Photon energy range: 5.5-16 keV (wavelength: 0.775-2.25 A)
- Photon flux: 1.6x10¹¹ Phot/sec x 100 mA at sample position
 (0.05-1 sec exposure time per frame)
- PILATUS3 S 2M detector with 1000 µm Si sensor thickness,
 85 mm - 800 mm distance from the sample (a special mode with
 56 mm distance is also available upon request)
- Nanodiffractometer with fast air-bearing axis and on-axis sample
 microscope
- User defined beam shaping from 30 µm-150 µm diameter possible
- Data collection control via MXCuBE2
- G-ROB sample changer for SPINE and UNIPUCK support
- 60-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- Common MX-software installed including EDNA, XDS, iMOSFLM, CCP4,
 Phenix, SHELXC-D-E, etc.
- Automated data processing using XDSAPP
- AMPTEK-XRF detector and XFEPLOT software available
- UV-Microsprectrophotometer offline setup available

If you need atomic resolution or better, BL14.2 is the beamline
of choice for you!!

BL14.3:
- Fixed photon energy: 13.8 keV (wavelength: 0.89 A)
- Photon flux: 1.6x10exp10 Phot/sec x 100mA at sample position
 (3-20 sec exposure time per frame)
- Rayonix MX-225 X-ray detector, 54 mm-450 mm distance from the
 sample (soon this detector will be replaced by a PILATUS 6M)
- MD2S microdiffractometer with mini-kappa goniometer
- In situ crystal-screening using 96-well plates
- RT data collection
- 60-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- Data collection control via MXCuBE2
- Common MX software installed including EDNA, XDS, iMOSFLM, CCP4,
 Phenix, SHELXC-D-E, etc.
- Automated data processing using XDSAPP
- Remotely controlled cryo-shutter for crystal annealing
- REX rapid nozzle exchanger
- HC-Lab dehydration device installed (please specify HC-Lab-beamtime
 in your proposal if needed)
- AMPTEK-XRF detector and XFEPLOT software available

Other facilities:
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom,
 8 Mpix CCD-camera
- Pressure chamber for noble gas derivatization (Xe, Kr available
 upon request)

S1-biolab facilities (separate registration required):
- Protein production and purification (AEKTA)
- nL 96-well crystallization plate formulation and storage at
 5°C and 20°C
- Biophysical characterization with real time PCR (thermofluor assay)
- Contactless compound pipetting using ATS

The HZB-MX group is also providing expert assistance as well as
access to a library of fragments for carrying out crystallographic
fragment-screening experiments. For more information please see

[ccp4bb] CCP-EM Icknield Model Building Workshop

[Tom Burnley - UKRI STFC]

Dear all,

We are pleased to announce our annual 'Icknield Model Building Workshop' will 
take place 16-20 March at RAL/Diamond Light Source, Oxfordshire, UK

This is a comprehensive course for EM model building covering advanced use of 
ARP/wARP, Buccaneer, CCP-EM, Coot, FlexEM, ISOLDE, LocScale, MolProbity, Refmac 
and new validation tools.  The course is designed such that applicants bring 
their own 'live' high resolution datasets to work on with the developers during 
the workshop.

Full details and registration:

http://www.cvent.com/d/fnqm5n

Confirmed tutors include:

Grzegorz Chojnowski (EMBL)
Tristan Croll (Cambridge)
Kevin Cowtan (York)
Judit Debreczeni (AstraZeneca)
Sony Malhotra (Birkbeck)
Garib Murshudov (MRC-LMB)
Rob Nicholls (MRC-LMB)
Maya Topf (Birkbeck)
Rangana Warshamanage (MRC-LMB)
Arjen Jakobi (TU Delft)
Tom Burnley (CCP-EM)
Agnel Joseph (CCP-EM)

The course will be held at the RAL / Diamond campus, Harwell, UK, site of the 
eBIC national facility.  Registration is £300 and we will provide food and 
accommodation at the Bear Hotel in nearby Wantage for nights of 16th (if 
required), 17th, 18th and 19th March.

The course is best suited for ‘high’ resolution datasets (<4Å) and details of 
the datasets will be asked for during registration (any details provided will 
be treated with absolute confidence).

There is a maximum of 50 places to register interest.  We will select the most 
suitable 20 applicants for each course and the course fees will be requested 
once the application is accepted.

Registration for the workshop will close either when all registration places 
are taken or by 21th Feb.  Successful applications will be informed shortly 
afterwards.

All the best,

Tom




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[ccp4bb] Phenix workshop at ACA 2020 (San Diego)

[Pavel Afonine]

Dear Colleagues,

please make a note of upcoming Phenix workshop focusing on crystallography
and Cryo-EM tools for structure solution, August 2nd 2020 in San Diego,
California. This is a day-long satellite workshop prior to ACA meeting. For
schedule and registration see ACA 2020 web site: www.acameeting.com
  (Program -> Workshops).

Looking forward to see you there!
Pavel



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[ccp4bb] Diacylglycerol

[JUAN LUIS BENAVENTE FERNANDEZ]

Dear all,

I am working with a protein that is supposed to bind diacylglycerol  
and I would like to know if you know any methods or protocol to handle  
DAG during purification and/or for crystallization experiments. Thanks  
in advance.


Juanlu



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Re: [ccp4bb] problem in structure solution of multidomain protein

[John R Helliwell]

Dear Rajnesh,
I wonder about your chosen space group?
I commend that you expand your diffraction data into P1, then run molecular 
replacement with Phaser in P1 and if a solution is determined by Phaser run the 
coordinates through Zanuda to determine the space group.
Best wishes,
John 
Emeritus Professor John R Helliwell DSc




> On 12 Feb 2020, at 07:23, Rajnesh Kumari Yadav  wrote:
> 
> Hello everyone,
> 
> I am working on a protein which have 5 domain in it, we have its 4 domain 
> structure and 3.0 Angstrom data of 5 domain protein crystal. While doing the 
> Molecular replacement we got solution with four domain with good electron 
> density and space for last domain without any density. When we tried 
> Molecular replacement with the missing domain (modelled) only we got solution 
> shows density for this missing domain but not able see electron density for 
> rest four domain even though room for 4 domain was visible in the solution. I 
> need help or suggestion for this issue.
> 
> 
> 
> 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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[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] problem in structure solution of multidomain protein

[Schreuder, Herman /DE]

Dear Rajnesh,

My experience with molecular replacement is that when you don’t have a model, 
you don’t get density. Only in exceptional cases (crystals with a very high 
solvent content) I see density for missing loops or domains, so missing density 
is very inconvenient, but no reason to be worried.

You say that with the 4 molecule search model you get a MR solution and 
density, but no density for the 5th molecule.
With the model for the 5th molecule, you also get a MR solution, but no density 
for molecules 1-4.

What happens if you load in coot both the solution for the 4 molecules and the 
solution for the 5th molecule? Does that produce a sensible crystal packing 
(e.g. no serious overlaps)? The solutions may be in different asymmetric units, 
so you may have to apply some crystallographic symmetry transformations to 
bring them together. If the crystal packing makes sense, you could merge the 
pdb files and see if you can refine the combined solutions.

Best,
Herman



Von: CCP4 bulletin board  Im Auftrag von Eleanor Dodson
Gesendet: Mittwoch, 12. Februar 2020 14:04
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] problem in structure solution of multidomain 
protein


EXTERNAL : Real sender is 
owner-ccp...@jiscmail.ac.uk

At 3A  finding missing domains is tricky.. Can you increase that resolution at 
all? Much easier at 2.5A!
But I would refine and rebuild the 4 domains   to the best possible maps, then 
see if there is any density unaccounted for.
(You will have to lower the COOT default contour level I guess..)

If there is you could use buccaneer to try and build it, keeping the fitted 
domains fixed ..
That can work IF there is density to build into..
Presumably you know the sequence?
MR from a modelling model is often tricky anyway.
Eleanor


On Wed, 12 Feb 2020 at 12:42, Boaz Shaanan 
mailto:bshaa...@bgu.ac.il>> wrote:
Hi,
One other option is to run MR in Phaser in one run with the tetramer made of 
the 4 monomers as model 1 and the single monomer as model 2. The gui offers 
this option and there is also an example in the documentaion.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Department of Life Sciences
Ben Gurion University of the Negev
Beer Sheva
Israel

On Feb 12, 2020 09:23, Rajnesh Kumari Yadav 
mailto:rajn...@rcb.res.in>> wrote:
Hello everyone,

I am working on a protein which have 5 domain in it, we have its 4 domain 
structure and 3.0 Angstrom data of 5 domain protein crystal. While doing the 
Molecular replacement we got solution with four domain with good electron 
density and space for last domain without any density. When we tried Molecular 
replacement with the missing domain (modelled) only we got solution shows 
density for this missing domain but not able see electron density for rest four 
domain even though room for 4 domain was visible in the solution. I need help 
or suggestion for this issue.



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Re: [ccp4bb] problem in structure solution of multidomain protein

[Eleanor Dodson]

At 3A  finding missing domains is tricky.. Can you increase that resolution
at all? Much easier at 2.5A!
But I would refine and rebuild the 4 domains   to the best possible maps,
then see if there is any density unaccounted for.
(You will have to lower the COOT default contour level I guess..)

If there is you could use buccaneer to try and build it, keeping the fitted
domains fixed ..
That can work IF there is density to build into..
Presumably you know the sequence?
MR from a modelling model is often tricky anyway.
Eleanor


On Wed, 12 Feb 2020 at 12:42, Boaz Shaanan  wrote:

> Hi,
> One other option is to run MR in Phaser in one run with the tetramer made
> of the 4 monomers as model 1 and the single monomer as model 2. The gui
> offers this option and there is also an example in the documentaion.
> Cheers,
> Boaz
>
> Boaz Shaanan, Ph.D.
> Department of Life Sciences
> Ben Gurion University of the Negev
> Beer Sheva
> Israel
>
> On Feb 12, 2020 09:23, Rajnesh Kumari Yadav  wrote:
> Hello everyone,
>
> I am working on a protein which have 5 domain in it, we have its 4 domain
> structure and 3.0 Angstrom data of 5 domain protein crystal. While doing
> the Molecular replacement we got solution with four domain with good
> electron density and space for last domain without any density. When we
> tried Molecular replacement with the missing domain (modelled) only we got
> solution shows density for this missing domain but not able see electron
> density for rest four domain even though room for 4 domain was visible in
> the solution. I need help or suggestion for this issue.
>
> 
>
> 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
>



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Re: [ccp4bb] problem in structure solution of multidomain protein

[Boaz Shaanan]

Hi,
One other option is to run MR in Phaser in one run with the tetramer made of the 4 monomers as model 1 and the single monomer as model 2. The gui offers this option and there is also an example in the documentaion. 
Cheers,

Boaz

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



On Feb 12, 2020 09:23, Rajnesh Kumari Yadav  wrote:




Hello everyone,

I am working on a protein which have 5 domain in it, we have its 4 domain structure and 3.0 Angstrom data of 5 domain protein crystal. While doing the Molecular replacement we got solution with four domain with good electron density and space for last domain
 without any density. When we tried Molecular replacement with the missing domain (modelled) only we got solution shows density for this missing domain but not able see electron density for rest four domain even though room for 4 domain was visible in the solution.
 I need help or suggestion for this issue.



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Re: [ccp4bb] problem in structure solution of multidomain protein

[Christian Roth]

Hi,
you mentioned that there is no electron density for your 5th domain. If
there is nothing coming up even after refinement of the four domains, than
maybe your 5th domain is not there, or so disordered that it doesn't show
up.

Christian

On Wed, Feb 12, 2020 at 9:47 AM RAJNESH KUMARI YADAV 
wrote:

> Thanks Clemens and Lumbini for your help.
> I had tried both the things but none of them worked for this problem.
>
> On Wed, Feb 12, 2020 at 1:56 PM Clemens Vonrhein <
> vonrh...@globalphasing.com> wrote:
>
>> Hi,
>>
>> MOLREP [1] has a nice feature of searching for structures in electron
>> density - with the known parts of your model fixed. Basically follow
>> the recipe in [1] (search for "refmac.mtz" - but you can use any other
>> set of amplitudes/phases as well). In your case the 4-domain model
>> would be given to the -mx flag and the 5th domain search model to -m.
>>
>> This worked for me a few times in the past ...
>>
>> Cheers
>>
>> Clemens
>>
>> [1] http://www.ccp4.ac.uk/html/molrep.html
>>
>> On Wed, Feb 12, 2020 at 07:12:48AM +, Rajnesh Kumari Yadav wrote:
>> > Hello everyone,
>> >
>> > I am working on a protein which have 5 domain in it, we have its 4
>> domain structure and 3.0 Angstrom data of 5 domain protein crystal. While
>> doing the Molecular replacement we got solution with four domain with good
>> electron density and space for last domain without any density. When we
>> tried Molecular replacement with the missing domain (modelled) only we got
>> solution shows density for this missing domain but not able see electron
>> density for rest four domain even though room for 4 domain was visible in
>> the solution. I need help or suggestion for this issue.
>> >
>> > 
>> >
>> > To unsubscribe from the CCP4BB list, click the following link:
>> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>> --
>>
>> *--
>> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
>> * Global Phasing Ltd., Sheraton House, Castle Park
>> * Cambridge CB3 0AX, UK   www.globalphasing.com
>> *--
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Lattice-translocation defect (LTD)

[Eleanor Dodson]

I am no expert, but a) a very strong peak 7A from the origin means two
molecules 7A apart?? Most unlikely ..

The first thing to look at is the actual images - Lattice translation
defects usually generate very streaky patterns.
Integration programs can cleverly select a lattice and ignore the
unpredicted pixels - (by the way - why don't the data integration programs
scream when this occurs? )
LTDs usually produce some strange intensity statistics too - what do the
moments/twin tests etc look like?


Otherwise your spacegroup must be wrong, although providing you have got
the right crystalclass, I cant think how that can generate such a Patterson
peak..

Good luck Eleanor
PS - maybe search out another crystal!

On Wed, 12 Feb 2020 at 10:25, Harry Powell - CCP4BB <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi
>
> Something else I should have mentioned - in iMosflm you can sum your
> images for viewing only if you have them as  HDF5 or Pilatus CBF (as well
> as summing them for processing if you have HDF5).
>
> Harry
>
> On 12 Feb 2020, at 10:18, Schreuder, Herman /DE <
> herman.schreu...@sanofi.com> wrote:
>
> Hi Daniele,
>
> I agree with Wim that the first thing you should check is your space group
> and especially whether a ncs symmetry element has been mistakenly
> identified as being crystallographic. Since your Patterson peak is along w
> (c-axis), you have to change the space group for processing such, that
> there are no rotation axes or other symmetry elements perpendicular to the
> c-axis any more. If you have a low-symmetry space group, you could also
> process in P1 to be absolutely on the safe side. Than you should run MR in
> this lower symmetry space group.
>
> Concerning lattice translocation defects, almost every case is unique and
> I am not aware of any software able to handle this. Here you will have to
> work out the maths for your particular case yourself and apply the
> correction with e.g. sftools. I am a little puzzled by your 7Å vector in
> your (native?) Patterson maps. I guess, if you translate your protein by 7Å
> it will strongly overlap with itself and I guess the same will be true for
> your ghost map. You should also have a look at your diffraction images,
> perhaps after summing them to 1° slices so become human-interpretable. In
> many cases, LTD is associated with a mix of sharp and fuzzy diffraction
> spots. Seeing those would be a strong indicator that you have the problem,
> but there are cases of LTD where all the spots are sharp. You may also want
> to check for statistical disorder.
>
> Good luck!
> Herman
>
> *Von:* CCP4 bulletin board  *Im Auftrag von *Wim
> Burmeister
> *Gesendet:* Mittwoch, 12. Februar 2020 08:57
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [EXTERNAL] Re: [ccp4bb] Lattice-translocation defect (LTD)
>
>
> *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk
>
>
>
> Hello,
>
> do you have some details about the space group ? Did the integration not
> miss any sports ? I would rather think of an ncs close to crystallographic
> symmetry, or maybe some twinning problem.
>
> I guess these are Pilatus data, can you combine the frames into 1 degree
> oscillations and try Mosflm processing to see how the patterns integrate ?
>
> Greetings
>
> Wim
> Le 11/02/2020 à 22:31, Daniele de Sanctis a écrit :
>
> Hi all,
>
> I'm currently dealing with what I think it is a case of LTD (off-origin
> Patterson peak, with vector along w of ~ 7A and electron density map
> showing a "ghost" map shifted by 7 A). I saw there are quite a few cases
> reported in literature  (for example Hare et al, 2006), but what I could
> not find is how I can demodulate the data. Is there any software that can
> be used for this?
>
> Thank you
>
> Daniele
>
> --
> ἀρετή
> ---
> Daniele de Sanctis, PhD
>
> Structural Biology Group
> ESRF, Grenoble, France
> Tel 33 (0)4 76 88 2869
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
>
> --
> Wim Burmeister
>
> Professeur
> Institut de Biologie Structurale (IBS) CIBB
> 71 avenue des Martyrs / CS 20192
> 38044 Grenoble Cedex 9, FRANCE
> E-mail: wim.burmeis...@ibs.fr
> Tel:+33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94 00
> website
> 

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Lattice-translocation defect (LTD)

[Harry Powell - CCP4BB]

Hi

Something else I should have mentioned - in iMosflm you can sum your images for 
viewing only if you have them as  HDF5 or Pilatus CBF (as well as summing them 
for processing if you have HDF5).

Harry

> On 12 Feb 2020, at 10:18, Schreuder, Herman /DE  
> wrote:
> 
> Hi Daniele,
>  
> I agree with Wim that the first thing you should check is your space group 
> and especially whether a ncs symmetry element has been mistakenly identified 
> as being crystallographic. Since your Patterson peak is along w (c-axis), you 
> have to change the space group for processing such, that there are no 
> rotation axes or other symmetry elements perpendicular to the c-axis any 
> more. If you have a low-symmetry space group, you could also process in P1 to 
> be absolutely on the safe side. Than you should run MR in this lower symmetry 
> space group.
>  
> Concerning lattice translocation defects, almost every case is unique and I 
> am not aware of any software able to handle this. Here you will have to work 
> out the maths for your particular case yourself and apply the correction with 
> e.g. sftools. I am a little puzzled by your 7Å vector in your (native?) 
> Patterson maps. I guess, if you translate your protein by 7Å it will strongly 
> overlap with itself and I guess the same will be true for your ghost map. You 
> should also have a look at your diffraction images, perhaps after summing 
> them to 1° slices so become human-interpretable. In many cases, LTD is 
> associated with a mix of sharp and fuzzy diffraction spots. Seeing those 
> would be a strong indicator that you have the problem, but there are cases of 
> LTD where all the spots are sharp. You may also want to check for statistical 
> disorder.
>  
> Good luck!
> Herman
>  
> Von: CCP4 bulletin board  > Im Auftrag von Wim Burmeister
> Gesendet: Mittwoch, 12. Februar 2020 08:57
> An: CCP4BB@JISCMAIL.AC.UK 
> Betreff: [EXTERNAL] Re: [ccp4bb] Lattice-translocation defect (LTD)
>  
> EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk 
> 
>  
> 
> Hello,
> 
> do you have some details about the space group ? Did the integration not miss 
> any sports ? I would rather think of an ncs close to crystallographic 
> symmetry, or maybe some twinning problem.
> 
> I guess these are Pilatus data, can you combine the frames into 1 degree 
> oscillations and try Mosflm processing to see how the patterns integrate ?
> 
> Greetings
> 
> Wim
> 
> Le 11/02/2020 à 22:31, Daniele de Sanctis a écrit :
> Hi all,
>  
> I'm currently dealing with what I think it is a case of LTD (off-origin 
> Patterson peak, with vector along w of ~ 7A and electron density map showing 
> a "ghost" map shifted by 7 A). I saw there are quite a few cases reported in 
> literature  (for example Hare et al, 2006), but what I could not find is how 
> I can demodulate the data. Is there any software that can be used for this?
>  
> Thank you
>  
> Daniele
> 
> -- 
> ἀρετή
> ---
> Daniele de Sanctis, PhD
> 
> Structural Biology Group
> ESRF, Grenoble, France
> Tel 33 (0)4 76 88 2869
>  
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
> 
> -- 
> Wim Burmeister
> Professeur
> Institut de Biologie Structurale (IBS) CIBB
> 71 avenue des Martyrs / CS 20192
> 38044 Grenoble Cedex 9, FRANCE
> E-mail: wim.burmeis...@ibs.fr 
> Tel:+33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94 00
> website 
> 
> map 
> 
> 
> Changement climatique : «Les autres combats n’ont aucun sens si celui-là est 
> perdu» (Aurélien Barrau)   
>  
> 
>  
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
> 

[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Lattice-translocation defect (LTD)

[Schreuder, Herman /DE]

Hi Daniele,

I agree with Wim that the first thing you should check is your space group and 
especially whether a ncs symmetry element has been mistakenly identified as 
being crystallographic. Since your Patterson peak is along w (c-axis), you have 
to change the space group for processing such, that there are no rotation axes 
or other symmetry elements perpendicular to the c-axis any more. If you have a 
low-symmetry space group, you could also process in P1 to be absolutely on the 
safe side. Than you should run MR in this lower symmetry space group.

Concerning lattice translocation defects, almost every case is unique and I am 
not aware of any software able to handle this. Here you will have to work out 
the maths for your particular case yourself and apply the correction with e.g. 
sftools. I am a little puzzled by your 7Å vector in your (native?) Patterson 
maps. I guess, if you translate your protein by 7Å it will strongly overlap 
with itself and I guess the same will be true for your ghost map. You should 
also have a look at your diffraction images, perhaps after summing them to 1° 
slices so become human-interpretable. In many cases, LTD is associated with a 
mix of sharp and fuzzy diffraction spots. Seeing those would be a strong 
indicator that you have the problem, but there are cases of LTD where all the 
spots are sharp. You may also want to check for statistical disorder.

Good luck!
Herman

Von: CCP4 bulletin board  Im Auftrag von Wim Burmeister
Gesendet: Mittwoch, 12. Februar 2020 08:57
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] Lattice-translocation defect (LTD)


EXTERNAL : Real sender is 
owner-ccp...@jiscmail.ac.uk


Hello,

do you have some details about the space group ? Did the integration not miss 
any sports ? I would rather think of an ncs close to crystallographic symmetry, 
or maybe some twinning problem.

I guess these are Pilatus data, can you combine the frames into 1 degree 
oscillations and try Mosflm processing to see how the patterns integrate ?

Greetings

Wim
Le 11/02/2020 à 22:31, Daniele de Sanctis a écrit :
Hi all,

I'm currently dealing with what I think it is a case of LTD (off-origin 
Patterson peak, with vector along w of ~ 7A and electron density map showing a 
"ghost" map shifted by 7 A). I saw there are quite a few cases reported in 
literature  (for example Hare et al, 2006), but what I could not find is how I 
can demodulate the data. Is there any software that can be used for this?

Thank you

Daniele

--
ἀρετή
---
Daniele de Sanctis, PhD

Structural Biology Group
ESRF, Grenoble, France
Tel 33 (0)4 76 88 2869



To unsubscribe from the CCP4BB list, click the following link:
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--
Wim Burmeister

Professeur
Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs / CS 20192
38044 Grenoble Cedex 9, FRANCE
E-mail: wim.burmeis...@ibs.fr
Tel:+33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94 00
website

map

Changement climatique : «Les autres combats n’ont aucun sens si celui-là est 
perdu» (Aurélien Barrau)





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Re: [ccp4bb] Lattice-translocation defect (LTD)

[Harry Powell - CCP4BB]

Hi

Apropos Mosflm - if you have HDF5 files from ESRF (or Diamond, probably 
elsewhere) you can sum the images internally to whatever rotation range per 
pseudo image you want (so if you have, say, 0.05º physical images you could 
process 0.1, 0.15, 0.20º, etc), provided you have installed Mosflm 7.3.* (not 
yet distributed as part of CCP4, as far as I can work out [apologies to CCP4 
core group if they’ve done this and I haven’t noticed], although it’s been 
available for quite some time…). 

I wouldn’t recommend summing to 1.0º unless the mosaicity is really quite large 
- iMosflm itself will suggest an appropriate value, and in my limited 
experience of processing reasonable quality datasets (during testing) the 
optimum often turns out to be ~0.2 - 0.5º (based on metrics like CC-1/2, Rmeas, 
I/sig(I) etc).

Just my two ha’porth

Harry

> On 12 Feb 2020, at 07:57, Wim Burmeister  wrote:
> 
> Hello,
> 
> do you have some details about the space group ? Did the integration not miss 
> any sports ? I would rather think of an ncs close to crystallographic 
> symmetry, or maybe some twinning problem. 
> I guess these are Pilatus data, can you combine the frames into 1 degree 
> oscillations and try Mosflm processing to see how the patterns integrate ?
> 
> Greetings
> 
> Wim
> Le 11/02/2020 à 22:31, Daniele de Sanctis a écrit :
>> Hi all,
>> 
>> I'm currently dealing with what I think it is a case of LTD (off-origin 
>> Patterson peak, with vector along w of ~ 7A and electron density map showing 
>> a "ghost" map shifted by 7 A). I saw there are quite a few cases reported in 
>> literature  (for example Hare et al, 2006), but what I could not find is how 
>> I can demodulate the data. Is there any software that can be used for this?
>> 
>> Thank you
>> 
>> Daniele
>> 
>> -- 
>> ἀρετή
>> ---
>> Daniele de Sanctis, PhD
>> 
>> Structural Biology Group
>> ESRF, Grenoble, France
>> Tel 33 (0)4 76 88 2869
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
>> -- 
> Wim Burmeister
> Professeur
> Institut de Biologie Structurale (IBS) CIBB
> 71 avenue des Martyrs / CS 20192
> 38044 Grenoble Cedex 9, FRANCE
> E-mail: wim.burmeis...@ibs.fr 
> Tel:+33 (0) 457 42 87 41   Fax: +33 (0) 476 20 94 00
> website 
> 
> map 
> 
> 
> Changement climatique : «Les autres combats n’ont aucun sens si celui-là est 
> perdu» (Aurélien Barrau) 
> 
> 
> 
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Re: [ccp4bb] problem in structure solution of multidomain protein

[RAJNESH KUMARI YADAV]

Thanks Clemens and Lumbini for your help.
I had tried both the things but none of them worked for this problem.

On Wed, Feb 12, 2020 at 1:56 PM Clemens Vonrhein 
wrote:

> Hi,
>
> MOLREP [1] has a nice feature of searching for structures in electron
> density - with the known parts of your model fixed. Basically follow
> the recipe in [1] (search for "refmac.mtz" - but you can use any other
> set of amplitudes/phases as well). In your case the 4-domain model
> would be given to the -mx flag and the 5th domain search model to -m.
>
> This worked for me a few times in the past ...
>
> Cheers
>
> Clemens
>
> [1] http://www.ccp4.ac.uk/html/molrep.html
>
> On Wed, Feb 12, 2020 at 07:12:48AM +, Rajnesh Kumari Yadav wrote:
> > Hello everyone,
> >
> > I am working on a protein which have 5 domain in it, we have its 4
> domain structure and 3.0 Angstrom data of 5 domain protein crystal. While
> doing the Molecular replacement we got solution with four domain with good
> electron density and space for last domain without any density. When we
> tried Molecular replacement with the missing domain (modelled) only we got
> solution shows density for this missing domain but not able see electron
> density for rest four domain even though room for 4 domain was visible in
> the solution. I need help or suggestion for this issue.
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
> --
>
> *--
> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
> * Global Phasing Ltd., Sheraton House, Castle Park
> * Cambridge CB3 0AX, UK   www.globalphasing.com
> *--
>



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Re: [ccp4bb] problems loading images in iMosflm under CCP4

[Andrew Leslie]

Dear Annette,

  Which version of iMosflm are you using? Version 7.2.2, 
that is currently distributed with the CCP4 suite, will not read Rigaku style 
Pilatus images (RIPI) correctly, you need version 7.3.0 that can be downloaded 
from the imosflm website:

https://www.mrc-lmb.cam.ac.uk/mosflm/imosflm/ver730/introduction.html 


Best wishes,

Andrew

> On 12 Feb 2020, at 00:50, Annette Herta Erbse  
> wrote:
> 
> Hi Everyone,
>  
> I apologize in advance I am probably doing something stupidly wrong, but I 
> have problems adding images taken with a Dectris Pilatus  200K detector  into 
> iMosflm. The files are .img files. I get the message “Error reading image 
> header. Message from Mosflm is Incorrect size of image for detector type 
> MAR”. But if I look at experiment settings detector it has recognized it as 
> RIPI Model 200K and under Experiment it has the beam position, the distance 
> and the wavelength right. So it is be able to read the header? I am confused 
> why it thinks it is a MAR detector image. 
>  
> Again I apologize if I am missing something obvious here.
> Best - Annette
>  
> Voice: ++1-303-492-0528 (office)
> Fax: ++1-303-492-8425
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>  
> 
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Re: [ccp4bb] problem in structure solution of multidomain protein

[Clemens Vonrhein]

Hi,

MOLREP [1] has a nice feature of searching for structures in electron
density - with the known parts of your model fixed. Basically follow
the recipe in [1] (search for "refmac.mtz" - but you can use any other
set of amplitudes/phases as well). In your case the 4-domain model
would be given to the -mx flag and the 5th domain search model to -m.

This worked for me a few times in the past ...

Cheers

Clemens

[1] http://www.ccp4.ac.uk/html/molrep.html

On Wed, Feb 12, 2020 at 07:12:48AM +, Rajnesh Kumari Yadav wrote:
> Hello everyone,
> 
> I am working on a protein which have 5 domain in it, we have its 4 domain 
> structure and 3.0 Angstrom data of 5 domain protein crystal. While doing the 
> Molecular replacement we got solution with four domain with good electron 
> density and space for last domain without any density. When we tried 
> Molecular replacement with the missing domain (modelled) only we got solution 
> shows density for this missing domain but not able see electron density for 
> rest four domain even though room for 4 domain was visible in the solution. I 
> need help or suggestion for this issue.
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

-- 

*--
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., Sheraton House, Castle Park 
* Cambridge CB3 0AX, UK   www.globalphasing.com
*--



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Re: [ccp4bb] problem in structure solution of multidomain protein

[Lumbini Yadav]

Dear Rajnesh,
Why don't you try refining the 4 domain structure initially. Once the R
factor and R free value is sufficiently low then try to see if there is any
density build up for domain 5.
This has atleast worked for me.

On Wed, 12 Feb 2020, 12:53 Rajnesh Kumari Yadav,  wrote:

> Hello everyone,
>
> I am working on a protein which have 5 domain in it, we have its 4 domain
> structure and 3.0 Angstrom data of 5 domain protein crystal. While doing
> the Molecular replacement we got solution with four domain with good
> electron density and space for last domain without any density. When we
> tried Molecular replacement with the missing domain (modelled) only we got
> solution shows density for this missing domain but not able see electron
> density for rest four domain even though room for 4 domain was visible in
> the solution. I need help or suggestion for this issue.
>
> 
>
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>



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