Re: [ccp4bb] 8/ 2263 spots indexed XDS

[Kay Diederichs]

Hi Almu,

I have yet to see a data set with clear reflections that cannot be indexed with 
XDS. The most often reason for failure is some wrong input, most often 
ORGX/ORGY and ROTATION_AXIS, but of course OSCILLATION_RANGE, X-RAY_WAVELENGTH, 
DETECTOR_DISTANCE must also be correct.
If you cannot solve the problem, then I offer my help - make the raw data 
available to me, using some cloud service, and I'll take a look. I'll keep your 
data confidential of course.

best,
Kay

On Fri, 29 Nov 2019 16:06:53 +0100, Almudena Ponce Salvatierra 
 wrote:

>Thank you Tim,
>
>I will try and let you know how it goes.
>
>All the best,
>
>Almudena
>
>El vie., 29 nov. 2019 a las 14:43, Tim Gruene ()
>escribió:
>
>> Dear Almudena,
>>
>> SPOT_MAXIMUM-CENTROID is probably the keyword in XDS.INP that you want to
>> increase in your situation. The default is 3. Try e.g. 5, and increase
>> slowly
>> to make sure that the suggested solution makes sense
>>
>> Best regards,
>> Tim
>>
>> On Friday, November 29, 2019 12:48:11 PM CET Almudena Ponce Salvatierra
>> wrote:
>> > Dear all,
>> >
>> > I have some data sets that don't want to be processed :p
>> >
>> > In one of them, when I look at IDXREF.LP I see virtually none of the
>> found
>> > spots were indexed and the reason is that they are "too far from the
>> > expected position". The spots are smeary and elongated, so not the
>> > prettiest.
>> >
>> > I have managed to process so far only one data set with decent statistics
>> > from another crystal harvested from the same drop, where the diffraction
>> > spots look better.
>> >
>> > I am trying to find in the xds wiki the keyword I should fine tune in
>> order
>> > to make those spots indexable.
>> >
>> > Could you help me please?
>> >
>> > Thank you very much in advance.
>> >
>> > Best wishes,
>> >
>> > Almu
>> >
>> > 
>> >
>> > To unsubscribe from the CCP4BB list, click the following link:
>> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>> --
>> --
>> 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
>>
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
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>



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Re: [ccp4bb] microscope camera

[Zhijie Li]

There are CCD modules (often come with lenses, which can be taken off) sold on 
Amazon, eBay or aliexpress (or even better, Taobao) costing USD 20-40. These 
modules should be capable of taking full HD movies (MPEG or YUV2 compressed) at 
30fps these days. Some may allow 120fps@640x480 or promise higher sensitivities.

A better alternative is old DSLR bodies, which have larger, better sensors. 
There should be plenty of them, cheaply, on 2nd-hand market. The aforementioned 
CCD modules all use the smallest, lowest-end (but OK for what we do) sensors, 
in constrast.


Then with a 3D printer and some black PLA filament it is fairly easy to make a 
custom mounting tube that directly puts the CCD or the camera sensor on the 
image plane of the microscope. Metal adaptors are also available for DSLR 
bodies.

To control the CCD modules through USB, one can use amcap or VLC player. For 
DSLR bodies, digiCamControl. If one has a Raspberrypi, on-line streaming can 
also be setup using mjpg-streamer (or simply use the streaming function of 
octoprint).

Zhijie


From: CCP4 bulletin board  on behalf of Dean Derbyshire 

Sent: Wednesday, November 27, 2019 11:35
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] microscope camera

Forgive the off topic subject:

Has anyone got any experience with moticam microscope cameras?
We are looking into cheap cameras for record keeping etc and this supplier 
looks good but…

Cheers in advance

Sent from Mail for Windows 10




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Re: [ccp4bb] microscope camera

[Peat, Tom (Manufacturing, Parkville)]

There are fairly cheap adapter eye-pieces that can be purchased that will hold 
most of the standard phones (iPhones 5, 6, 7, etc).
They work very well and we have replaced our old microscope camera with these 
and the pictures are great (for one offs, not for taking time courses over many 
drops/plates).
cheers, tom

Tom Peat
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au


From: CCP4 bulletin board  on behalf of Phoebe A. Rice 

Sent: Saturday, November 30, 2019 8:54 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] microscope camera


With a little fiddling and patience, one can just point a cell phone camera 
down the eyepiece.  It doesn’t produce the best pics, but works fine if you 
just want to stick a few in a notebook (or a grant …).



From: CCP4 bulletin board  on behalf of Sergei Strelkov 

Reply-To: Sergei Strelkov 
Date: Thursday, November 28, 2019 at 7:47 AM
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: [ccp4bb] microscope camera



Moticam 5 has been working well for us for a few years now (installed on a 
Leica binocular)



Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of 
Pharmaceutical Sciences, KU Leuven O, Campus Gasthuisberg, Herestraat 49 bus 
822, 3000 Leuven, Belgium Phone: +32 16 33 08 45, mobile: +32 486 29 41 32 Lab 
pages: 
http://pharm.kuleuven.be/Biocrystallography



From: CCP4 bulletin board  on behalf of Dean Derbyshire 

Sent: Wednesday, November 27, 2019 11:35
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] microscope camera



Forgive the off topic subject:



Has anyone got any experience with moticam microscope cameras?

We are looking into cheap cameras for record keeping etc and this supplier 
looks good but…



Cheers in advance



Sent from Mail for Windows 10







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Re: [ccp4bb] microscope camera

[Phoebe A. Rice]

With a little fiddling and patience, one can just point a cell phone camera 
down the eyepiece.  It doesn’t produce the best pics, but works fine if you 
just want to stick a few in a notebook (or a grant …).

From: CCP4 bulletin board  on behalf of Sergei Strelkov 

Reply-To: Sergei Strelkov 
Date: Thursday, November 28, 2019 at 7:47 AM
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: [ccp4bb] microscope camera


Moticam 5 has been working well for us for a few years now (installed on a 
Leica binocular)



Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of 
Pharmaceutical Sciences, KU Leuven O, Campus Gasthuisberg, Herestraat 49 bus 
822, 3000 Leuven, Belgium Phone: +32 16 33 08 45, mobile: +32 486 29 41 32 Lab 
pages: 
http://pharm.kuleuven.be/Biocrystallography


From: CCP4 bulletin board  on behalf of Dean Derbyshire 

Sent: Wednesday, November 27, 2019 11:35
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] microscope camera

Forgive the off topic subject:

Has anyone got any experience with moticam microscope cameras?
We are looking into cheap cameras for record keeping etc and this supplier 
looks good but…

Cheers in advance

Sent from Mail for Windows 10




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Re: [ccp4bb] technical question

[Robbie Joosten]

Or use the residue name MHO if SME has the wrong hand around the sulfur.

Cheers,
Robbie

On 29 Nov 2019 21:47, Paul Emsley  wrote:

On 29/11/2019 18:06, amit gaur wrote:

> I want to replace a particular methionine in a pdbwith methionine sulfoxide( 
> an oxidized form of
> methionine). Can body please tell me how to do this? I am familiar with 
> pymol, chimera and coot software.

In Coot:

Extensions -> Modelling -> Replace Residue -> SME -> Mutate



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Re: [ccp4bb] technical question

[Paul Emsley]

On 29/11/2019 18:06, amit gaur wrote:

I want to replace a particular methionine in a pdbwith methionine sulfoxide( an oxidized form of 
methionine). Can body please tell me how to do this? I am familiar with pymol, chimera and coot software.


In Coot:

Extensions -> Modelling -> Replace Residue -> SME -> Mutate



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Re: [ccp4bb] space group "P 21 21 2 A"?

[Murpholino Peligro]

Thank you very much

El vie., 29 de nov. de 2019 a la(s) 12:40, Eleanor Dodson (
eleanor.dod...@york.ac.uk) escribió:

> That is a code for P21 21 2 symmetry where the origin is positioned at
> 1/4,0,0
> The sym ops in the PDB header presumably reflect that..
>
>
> On Fri, 29 Nov 2019 at 18:16, Murpholino Peligro 
> wrote:
>
>> Entry 1gzx has space group P 21 21 2 A (
>> https://www.rcsb.org/structure/1gzx)
>> I am lost!
>> This is the first time that I see a letter at the end of a (protein)
>> space group.
>> Can somebody explain this? Please.
>>
>>
>> Thanks
>>
>> --
>>
>> 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] space group "P 21 21 2 A"?

[Eleanor Dodson]

That is a code for P21 21 2 symmetry where the origin is positioned at
1/4,0,0
The sym ops in the PDB header presumably reflect that..


On Fri, 29 Nov 2019 at 18:16, Murpholino Peligro 
wrote:

> Entry 1gzx has space group P 21 21 2 A (
> https://www.rcsb.org/structure/1gzx)
> I am lost!
> This is the first time that I see a letter at the end of a (protein) space
> group.
> Can somebody explain this? Please.
>
>
> Thanks
>
> --
>
> 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] technical question

[amit gaur]

Hi everbody,
I want to replace a particular methionine in a pdb with methionine
sulfoxide( an oxidized form of methionine). Can body please tell me how to
do this? I am familiar with pymol, chimera and coot software.
-- 
*Amit Gaur*

*Post Doctoral ResearcherThomas Jefferson University*
*1020, Locust Street, Suite 418*
*Philadelphia, PA 19107*



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[ccp4bb] space group "P 21 21 2 A"?

[Murpholino Peligro]

Entry 1gzx has space group P 21 21 2 A (https://www.rcsb.org/structure/1gzx)
I am lost!
This is the first time that I see a letter at the end of a (protein) space
group.
Can somebody explain this? Please.


Thanks



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Re: [ccp4bb] 8/ 2263 spots indexed XDS

[Almudena Ponce Salvatierra]

Thank you Tim,

I will try and let you know how it goes.

All the best,

Almudena

El vie., 29 nov. 2019 a las 14:43, Tim Gruene ()
escribió:

> Dear Almudena,
>
> SPOT_MAXIMUM-CENTROID is probably the keyword in XDS.INP that you want to
> increase in your situation. The default is 3. Try e.g. 5, and increase
> slowly
> to make sure that the suggested solution makes sense
>
> Best regards,
> Tim
>
> On Friday, November 29, 2019 12:48:11 PM CET Almudena Ponce Salvatierra
> wrote:
> > Dear all,
> >
> > I have some data sets that don't want to be processed :p
> >
> > In one of them, when I look at IDXREF.LP I see virtually none of the
> found
> > spots were indexed and the reason is that they are "too far from the
> > expected position". The spots are smeary and elongated, so not the
> > prettiest.
> >
> > I have managed to process so far only one data set with decent statistics
> > from another crystal harvested from the same drop, where the diffraction
> > spots look better.
> >
> > I am trying to find in the xds wiki the keyword I should fine tune in
> order
> > to make those spots indexable.
> >
> > Could you help me please?
> >
> > Thank you very much in advance.
> >
> > Best wishes,
> >
> > Almu
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
> --
> --
> 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] RES: [ccp4bb] Xray-dataset usable despite low completeness ?

[Rafael Marques]

Lol

__

Rafael Marques da Silva
Mestrando em Física Biomolecular
Universidade de São Paulo

Bacharel em Ciências Biológicas
Universidade Federal de São Carlos

phone: +55 16 99766-0021

   "A sorte acompanha uma mente bem treinada"



De: CCP4 bulletin board  em nome de Bernhard Rupp 

Enviado: Friday, November 29, 2019 1:18:41 AM
Para: CCP4BB@JISCMAIL.AC.UK 
Assunto: Re: [ccp4bb] Xray-dataset usable despite low completeness ?

It has come to our attention that on this bulletin board insensitive and 
hurtful comments have
been made towards animals with disability. Particularly concerning is the 
display of white privilege
and racial bias towards a minority individual  given that the turkey is also 
referred to in German as 'Indian'.
In view of this non-inclusive and divisive display of unwokeness, the faculty 
Bias Response Team
will contact you shortly and allow you to present your self-critique.

We want this board to remain a safe zone inclusive of all animals, complete or 
not.

Stuffed, BR

-Original Message-
From: CCP4 bulletin board  On Behalf Of Jurgen Bosch
Sent: Thursday, November 28, 2019 13:51
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Xray-dataset usable despite low completeness ?

Think of completeness with an analogy to turkey.
Say you happen to find a one-legged turkey (incomplete by conventional 
standard) you could still stuff it and put it in the oven and enjoy 93% of the 
turkey. The 7% missing, who cares? Other than I like both legs of the turkey :-)

Happy Thanksgiving everyone

Jürgen

P.S. back to my wine & ducks to be roasted. @BR, mit Rotkraut & Kartoffelknödel

> On Nov 28, 2019, at 4:38 PM, Bernhard Rupp  wrote:
>
> Sorry for being late on this thread -
>
> but the completeness myth is one of these conventional wisdoms I am
> seriously questioning and completeness as a global statistic is almost
> uninformative, short of telling you 'fewer than all recordable reflections up 
> to the reported (likely isotropic) resolution limit given whatever (likely 
> isotropic) cutoff was applied'. Sounds not very clear to me.
>
> Kay mentioned already that any information is better than no
> information, with the caveat that you cannot expect map quality (being
> an upper limit for model quality - not going into precision vs
> accuracy issue here) corresponding to the highest resolution reported, which 
> is in reality frequently anisotropic (but not reported or reflected 
> adequately in the PDB reports).
> We posted some remarks to this effect recently, pointing out that
> highly incomplete and anisotropic data can still yield limited but
> useful information as long as your claim remains correspondingly
> modest. Section 3.4 in
> http://journals.iucr.org/d/issues/2019/12/00/di5032/index.html
>
> Having said that, while random incompleteness is not problematic,
> systematic reciprocal space incompleteness leads to corresponding
> systematic real space effects on the map, the simplest being
> anisotropic data reflecting anisotropic reciprocal map resolution.
> This is different for example when wedges are missing or absence of serial 
> extinctions makes space group determination more challenging (although we are 
> almost in the age where 'record 360 deg of data and try every SG' works). 
> James Holton has video examples for incompleteness effects and some images 
> are also in my book.
> https://bl831.als.lbl.gov/~jamesh/movies/
>
> Cheers & Happy Thanksgiving, BR
>
> PS: A systemic rant regarding data quality representation can be found
> here
> https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2
>
> --
> Bernhard Rupp
> http://www.hofkristallamt.org/
> b...@hofkristallamt.org
> --
> All models are wrong
> but some are useful.
> --
>
> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Kay
> Diederichs
> Sent: Monday, November 25, 2019 08:07
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Xray-dataset usable despite low completeness ?
>
> Dear Matthias,
>
> Of course, high completeness is better than low completeness.
> But as long as your low resolution is pretty much complete, there is no such 
> thing as "too low completeness" at high resolution. Each reflection adds 
> information to the map, and serves as a restraint in refinement.
>
> best,
> Kay
>
>
> On Mon, 25 Nov 2019 14:11:52 +0100, Matthias Oebbeke 
>  wrote:
>
>> Dear ccp4 Bulletin Board,
>>
>> I collected a dataset at a synchrotron beamline and got the
>> statistics
>> (CORRECT.LP) after processing (using xds) shown in the attached
>> pdf-file.
>>
>> Do you think this dataset is usable, due to its low completeness? As
>> you can see in the attached file the completeness is just 50% in 

Re: [ccp4bb] 8/ 2263 spots indexed XDS

[Tim Gruene]

Dear Almudena,

SPOT_MAXIMUM-CENTROID is probably the keyword in XDS.INP that you want to 
increase in your situation. The default is 3. Try e.g. 5, and increase slowly 
to make sure that the suggested solution makes sense

Best regards,
Tim

On Friday, November 29, 2019 12:48:11 PM CET Almudena Ponce Salvatierra wrote:
> Dear all,
> 
> I have some data sets that don't want to be processed :p
> 
> In one of them, when I look at IDXREF.LP I see virtually none of the found
> spots were indexed and the reason is that they are "too far from the
> expected position". The spots are smeary and elongated, so not the
> prettiest.
> 
> I have managed to process so far only one data set with decent statistics
> from another crystal harvested from the same drop, where the diffraction
> spots look better.
> 
> I am trying to find in the xds wiki the keyword I should fine tune in order
> to make those spots indexable.
> 
> Could you help me please?
> 
> Thank you very much in advance.
> 
> Best wishes,
> 
> Almu
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

-- 
--
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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Description: This is a digitally signed message part.

[ccp4bb] AW: [EXTERNAL] [ccp4bb] 8/ 2263 spots indexed XDS

[Schreuder, Herman /DE]

Dear Almu,

were your data collected at a synchrotron? Many synchrotrons run automatic 
processing of the data being collected and it is worth looking if there is some 
processing directory between the frames you collected. If so, these data may 
already be quite decent, and in any case, the XDS.INP file may tell you how to 
set the optimal processing parameters for this particular beamline.

You can also look at the refined parameters of your successful XDS run, 
especially the ORGX and ORGY. Try to rerun XDS, using the refined parameters of 
the successful run.

Good luck!
Herman

Von: CCP4 bulletin board  Im Auftrag von Almudena Ponce 
Salvatierra
Gesendet: Freitag, 29. November 2019 12:48
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] 8/ 2263 spots indexed XDS


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

Dear all,

I have some data sets that don't want to be processed :p

In one of them, when I look at IDXREF.LP I see virtually none of the found 
spots were indexed and the reason is that they are "too far from the expected 
position". The spots are smeary and elongated, so not the prettiest.

I have managed to process so far only one data set with decent statistics from 
another crystal harvested from the same drop, where the diffraction spots look 
better.

I am trying to find in the xds wiki the keyword I should fine tune in order to 
make those spots indexable.

Could you help me please?

Thank you very much in advance.

Best wishes,

Almu



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[ccp4bb] 15 PhD scholarships in Braunschweig, Germany

[Blankenfeldt, Wulf]

Dear colleagues & prospective Ph.D. students,

The Technische Universität Braunschweig in collaboration with Helmholtz Centre 
for Infection Research and Ostfalia University of Applied Sciences currently 
initiate the doctoral program "Drug Discovery and Cheminformatics for New 
Anti-Infectives (iCA)" which is granted by the Ministry of Science and Culture 
of Lower Saxony.  The program aims at studying fundamental principles of drug 
discovery by combining life sciences and digital sciences.

The iCA consortium is offering 15 Georg-Christoph-Lichtenberg scholarships 
(duration: 3 years).

The program of the iCA consortium offers an ambitious, structured and 
interdisciplinary training based on top-level fundamental research. This joint 
program provides an internationally competitive research environment with 
state-of-the-art facilities. The participating groups use a variety of 
different methods, including experimental, digital, and theoretical approaches.

More information about specific projects and participating groups can be found 
at:
https://www.tu-braunschweig.de/en/pharmchem/translate-to-english-promotionsprogramm-ica

The graduate program starts in the period from February to July 2020. For 
details and individual project descriptions please refer to the scholarship 
announcement attached. If you have any questions, please contact 
pvz-ap...@tu-braunschweig.de.

The program is open for applications now. Applications should include letter of 
motivation, curriculum vitae, certificates, etc. combined in a single PDF file 
(max. 15 MB). Please send your application to 
pvz-ap...@tu-braunschweig.de until 31 
December, 2019.

Please forward these information to interested colleagues.

Kind regards,


Wulf Blankenfeldt





Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 
Braunschweig | www.helmholtz-hzi.de

Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling
Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für 
Wissenschaft und Kultur
Geschäftsführung: Prof. Dr. Dirk Heinz; Silke Tannapfel
Gesellschaft mit beschränkter Haftung (GmbH)
Sitz der Gesellschaft: Braunschweig
Handelsregister: Amtsgericht Braunschweig, HRB 477



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Re: [ccp4bb] 8/ 2263 spots indexed XDS

[THOMPSON Andrew]

Hi Almudena
I wouldn't claim to be a great expert on XDS, but, based on the experience of 
analyzing a load of data on the beamline,  there are many things you can try -
The most important ones are to use lots (all?) your images for the spot search 
(SPOT_RANGE) , and not to hesitate cutting the resolution limit for the search 
to something very low where the spots are not streaky (3, 4, 5 Angstrom?). 
There may be "good regions" and "bad regions", so you can get the integration 
"going" from a good region. Once things are indexed and analyse OK you can add 
the other data back.
Other interesting keywords will be
STRONG_PIXEL (might need to be bigger or smaller!), 
MAXIMUM_NUMBER_OF_PIXELS_IN_A_SPOT (same) and DELPHI (once you have indexed)
Since you have processed one data set, you can give XDS the correct unit cell, 
that always helps.
Once you have got the integration going, *save* the processing directory as, 
with terrible looking spots, you can get "driven away" from the right indexing 
by the post refinement.
I always add data in "block by block".
I have successfully processed some pretty awful looking data with XDS, but it 
needs a bit of determination and quite a lot of time (hours, not minutes), so 
only invest if the data set is just unique
Good luck
Andy


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Almudena Ponce 
Salvatierra [maps.fa...@gmail.com]
Envoyé : vendredi 29 novembre 2019 12:48
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] 8/ 2263 spots indexed XDS

Dear all,

I have some data sets that don't want to be processed :p

In one of them, when I look at IDXREF.LP I see virtually none of the found 
spots were indexed and the reason is that they are "too far from the expected 
position". The spots are smeary and elongated, so not the prettiest.

I have managed to process so far only one data set with decent statistics from 
another crystal harvested from the same drop, where the diffraction spots look 
better.

I am trying to find in the xds wiki the keyword I should fine tune in order to 
make those spots indexable.

Could you help me please?

Thank you very much in advance.

Best wishes,

Almu



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[ccp4bb] 8/ 2263 spots indexed XDS

[Almudena Ponce Salvatierra]

Dear all,

I have some data sets that don't want to be processed :p

In one of them, when I look at IDXREF.LP I see virtually none of the found
spots were indexed and the reason is that they are "too far from the
expected position". The spots are smeary and elongated, so not the
prettiest.

I have managed to process so far only one data set with decent statistics
from another crystal harvested from the same drop, where the diffraction
spots look better.

I am trying to find in the xds wiki the keyword I should fine tune in order
to make those spots indexable.

Could you help me please?

Thank you very much in advance.

Best wishes,

Almu



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[ccp4bb] Position at Diamond: XChem Beamline Scientist

[Frank Von Delft]

Dear all,
We are recruiting as permanent position a Beamline Scientist on the XChem 
fragment screening facility at Diamond.

This role is to join the XChem team to support academic and industrial users 
with experiments and service work, co-manage the XChem lab, develop new 
fragment-related methodologies, and over next few years, work on expanding the 
XChem offering beyond hit identification.

If you are a technically-minded crystallographer that enjoys teaching or 
training people, like an organised life, thrive on collaboration and like to 
see how you're making others productive, you will enjoy this job.

Besides, Diamond is incredibly collegial and has a terrific user community.

The ad is here:

https://vacancies.diamond.ac.uk/vacancy/xchem-beamline-scientist-404499.html 
(for some reason you may need to click twice on the link to make it work).

The application deadline is the 15th Dec 2019, and we wil linterview on 17th 
Dec (i.e. before Xmas).
If you have questions, contact me or Alice Douangamath 
, who 
heads the facility.
Frank

--
Frank von Delft
Professor for Structural Chemical Biology

Principal Beamline Scientist: I04-1
Diamond Light Source
+44 1235 778997 (office: M,T,T)
+44 7471 026103 (mobile)

Principal Investigator: Protein Crystallography
Structural Genomics Consortium
Oxford University
+44 1865 617583 (office: W,F)



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[ccp4bb] ESRF User Meeting 2020 - UDM3 Call for abstracts - Deadline Sunday 1st December

[Daniele de Sanctis]

 Hi all,

there is a last chance to submit an abstract for the ESRF User-Dedicated
Microsymposia "UDM3. Multi-crystal and serial data collection in Structural
Biology "

which will take place on *5th February 2020* during the 2020 User Meeting
at the ESRF.

Participants of each UDM are invited to propose contributions to
*talks *through
the *submission of abstracts*. Invited talks from users will be selected
from the received abstracts. The deadline for UDM abstract submission
is *Sunday
1st December 2019*.

*More information on the Call for abstracts page
**.*

IMPORTANT DATES

*1 December 2019   *   Deadline for UDM abstracts submission
*10 December 2019*Notification of accepted authors after abstract
review
*19 January 2020  *   Deadline for registration to the User Meeting


* For further details, please visit:*

   - The UDM3 Call for abstracts webpage:
   http://www.esrf.fr/UM2020/UDM3/ABSTRACTS
   - The UDM3 webpage: http://www.esrf.fr/UM2020/UDM3
   - The User Meeting homepage: http://www.esrf.fr/UM2020


We look forward to meeting you at the 2020 User Meeting.

The UDM3 Organisers



-- 
ἀρετή
---
Daniele de Sanctis, PhD

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



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