Re: [ccp4bb] B-factors very high

[Jon Cooper]

Hello, it might be to do with the TLS group refinement which is mentioned in 
your log file. Maybe try without TLS and see if it makes a difference, to the 
B-factors at least.

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent with [ProtonMail](https://protonmail.com) Secure Email.

‐‐‐ Original Message ‐‐‐
On Monday, 4 January 2021 14:58, Napolitano Silvia 
 wrote:

> Dear Eleanor,
>
> Thank you for your answer. You are right, I totally forgot to provide this 
> information.
>
> The resolution is lower than 3 (2.19) Angstrom.
>
> Attached is the run log of the last refinement. I hope that now it will be 
> clearer!
>
> Best
>
> Silvia
>
> Silvia Napolitano
> ETH Zurich
> Institute of Molecular Biology and Biophysics
> Otto-Stern-Weg 5, HPK E14
> CH–8093 Zurich
> Phone: +41 44 6332482
> ---
>
> Da: Eleanor Dodson 
> Inviato: lunedì 4 gennaio 2021 15:43:03
> A: Napolitano Silvia
> Cc: CCP4BB@JISCMAIL.AC.UK
> Oggetto: Re: [ccp4bb] B-factors very high
>
> Well - you dont give the resolution of your data or the "wilson B" which will 
> be recorded in the data processing log.
> If the resolution is 3A or less a) it is hard to refine a B value, and b) it 
> certainly should be high..
>
> So more information is needed.
> Eleanor
>
> On Mon, 4 Jan 2021 at 14:39, Silvia Napolitano 
>  wrote:
>
>> Dear CCP4 Community,
>> I am currently working on the structure of a monomeric protein of 23KDa. The 
>> protein is generally quite "loopy" and I think I am mid-way refinement.
>> At the moment I am struggling, among other things, with an extremely high 
>> B-factor and I'm not sure how to lower it.
>> Do you have any suggestions on how I can proceed to obtain a lower average 
>> B-factor? (I am sorry if the question is rather naive, but I have worked 
>> very little on X-ray structures so far)
>> I attached a screenshot of the polygon obtained from the last refinement 
>> (the geometry now should be a bit improved, I am running a new job at the 
>> moment). I will be happy to provide further files if needed.
>> Many thanks in advance for your precious help!
>> I wish you a nice start to the new year.
>> Best
>> Silvia
>>
>> 
>>
>> 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 
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> ---
>
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[ccp4bb] Call for papers M 2021

[Giovanna Scapin]

Dear all

The Microscopy & Microanalysis 2021 meeting will be held in Pittsburgh, 
Pennsylvania, August 1-5. In addition to 4 days of the world's largest 
Microscopy products and services commercial expo hall, M 2021 will have over 
1200 platform and poster sessions, Pre-Meeting Congresses, Short Courses, and a 
variety of other workshops, sessions, tutorials, and networking events.  For a 
complete description of the symposium please see the following link: 
https://www.microscopy.org/MandM/2021/meetings/MM2021_CallforPapers.pdf.
 
We would like to invite you to submit an abstract for the Biological Sciences 
Symposium “CryoEM in Drug Discovery”, which will focus on the potential 
applications and uses of cryoEM at the R stages of drug discovery. Topics of 
interest are (and not limited to) the use of cryo-EM structures to drive 
structure-based drug discovery, integration of cryoEM and modeling in small 
molecule design and optimization, epitope mapping, methods aimed at optimizing 
(faster, cheaper, better) the process, microED and tomography.  We encourage 
both academic and industrial researchers to submit a paper.  Young researchers 
(students, post-doc and professional technical staff members) can also apply 
for M Meeting Awards and memorial awards, which consist of full meeting 
registration and up to $1,000 for travel-related expenses.
 
Among the submitted abstracts 10 will be selected for oral presentations (15 
minutes each with 5 minutes for discussion).  All abstracts can of course be 
part of the poster sessions.
 
Deadline for abstract submission is  February 18, 2021.  Information on how to 
submit the abstract can be found in the meeting homepage 
(https://www.microscopy.org/MandM/2021/) We sincerely hope that you will join 
us at M 2021
 
Sincerely
 
Giovanna Scapin
Christel Verboven
Leah Frye
 
B08 - Cryo-EM in Drug Discovery
ORGANIZERS:
Leah Frye, Schrodinger
Giovanna Scapin, NanoImaging Services
Christel Verboven, Thermo Fisher Scientific
 
Recent advances in cryo-EM technology have resulted in the ability to obtain 
structures of pharmaceutically relevant proteins with atomic level resolutions 
in a timely fashion. Importantly, cryo-EM greatly expands the availability of 
structures for large protein assemblies and membrane bound proteins which have 
been difficult to access via X-ray crystallography. This symposium will focus 
on the use of cryo-EM in drug discovery. Presentations will describe projects 
utilizing cryo-EM structures to drive structure-based drug discovery efforts 
for the optimization of potency and selectivity, including selectivity against 
ADMET targets, in projects from both industrial and academic groups.




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Re: [ccp4bb] B-factors very high

[Paul Emsley]

On 04/01/2021 14:38, Silvia Napolitano wrote:

Dear CCP4 Community,
I am currently working on the structure of a monomeric protein of 23KDa. The protein is 
generally quite "loopy" and I think I am mid-way refinement.
At the moment I am struggling, among other things, with an extremely high 
B-factor


I take it that you mean "extremely high average B-factor" - to which I 
ask "is it though?" - and then I would ask "what of it?"


The B-factor distribution is something that is more worthy of your 
attention. If you are using Coot then you can use


b_factor_distribution_graph(imol)

to see it. High (and low in the general case (but probably not for you)) 
outliers are of particular interest. Masmaliyeva, Babaib, Murshudov 
(2020) Acta Cryst D for more on that.




  and I'm not sure how to lower it.
Do you have any suggestions on how I can proceed to obtain a lower average 
B-factor?


Is the calculation of the average B-factor occupancy weighted? If not, 
you can use Coot to generate some waters that will bring down the 
average B-factor.


First, using scripting

set_default_temperature_factor_for_new_atoms(1.5)

Then use the difference map peaks dialog and set the threshold to 1.5, 
scroll to the bottom of the list. Now work your way up the list (using 
",") adding waters as you go. Make a note of the start and end residue 
numbers.


When you've added enough (you will probably need to add quite a few to 
bring the average B-factor to less than 74.3) then use


set_occupancy_residue_range() so that the occupancy of the new waters in 
the given residue range is 0.01.


(TFPIC, natch)


Paul.



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Re: [ccp4bb] B-factors very high

[Phoebe A. Rice]

Dear Silvia,
  While high Bs can be a sign that parts of your model are incorrect (and 
therefore some careful manual rebuilding may be required), for things like 
poorly-ordered surface loops, they can simply be truth.  
A point worth remembering for newbies: your goal is to produce the model that 
best reflects the data, which seems obvious, but that means don't try to model 
what you can't see (e.g. seriously disordered surface loops) and don't worry if 
bits where the density was marginal have high Bs.
 Best,
 Phoebe


On 1/4/21, 8:39 AM, "CCP4 bulletin board on behalf of Silvia Napolitano" 
 wrote:

Dear CCP4 Community,
I am currently working on the structure of a monomeric protein of 23KDa. 
The protein is generally quite "loopy" and I think I am mid-way refinement. 
At the moment I am struggling, among other things, with an extremely high 
B-factor and I'm not sure how to lower it.
Do you have any suggestions on how I can proceed to obtain a lower average 
B-factor? (I am sorry if the question is rather naive, but I have worked very 
little on X-ray structures so far)
I attached a screenshot of the polygon obtained from the last refinement 
(the geometry now should be a bit improved, I am running a new job at the 
moment). I will be happy to provide further files if needed.
Many thanks in advance for your precious help!
I wish you a nice start to the new year.
Best
Silvia




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Re: [ccp4bb] B-factors very high

[Barone, Matthias]

--Individual ADP refinement--


R-FACTORS   WEIGHT   TARGETS
 work  free  delta   data restr
28.36 32.91   4.55 14.984  101.982  0.0795.042
28.25 33.03   4.78 14.788  103.837  0.0795.023

minmax   meaniso aniso
   Overall:   47.49 211.88  96.79  10.75  2956  2930
   Protein:   47.49 211.88  96.79  10.75  2930  2930
   Water: 63.50 130.55  88.98N/A19 0
   Other:109.20 140.77 117.24N/A 7 0
   Chain  A:  74.14 153.67  99.01N/A  1474  1474
   Chain  C: 109.20 140.77 117.24N/A 7 0
   Chain  B:  47.49 211.88  94.54N/A  1456  1456
   Chain  S:  63.50 130.55  88.98N/A19 0

at this point I would def. look at the pointless and xtriage outputs...




Dr. Matthias Barone

AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin

Germany
Phone: +49 (0)30 94793-284


From: CCP4 bulletin board  on behalf of Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Sent: Monday, January 4, 2021 4:16:05 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] B-factors very high

Hmm - this is extracted from your log file: it looks more sensible..


2899:  b_iso_mean   = 66.62

2907:  b_iso_min= 63.50   (limit = 1.00)

2908:  b_iso_max= 68.13   (limit = 80.00)

2909:  b_iso_mean   = 66.62


The average B is 66??


I am  more familiar with REFMAC and the fact that the iso_min and iso_max are 
so close looks odd to me, but maybe that is a PHENIX quirk?


But you need to look at the data processing log if you have access to it.

The CCP4I2 gives a very useful analysis of your data..

Eleanor



On Mon, 4 Jan 2021 at 15:03, Barone, Matthias 
mailto:bar...@fmp-berlin.de>> wrote:

dear silvia,

apart from the resolution, it would be good to know your current refinement 
strategy and if you fed the structure to pdbredo yet. How did that turn out? 
the polygon values are picked from structures at similar resolution afaik. In 
any case, a better list of B-factors is the one you find in the refinement tab 
"Atomic properties", where phenix lists them for the macromolecules and ligands 
separately. In that tab you will also find a list of which atoms cause such 
high ADPs. I think Eleanor is talking about such a screenshot

best, matthias



Dr. Matthias Barone

AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin

Germany
Phone: +49 (0)30 94793-284


From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Sent: Monday, January 4, 2021 3:44:33 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] B-factors very high

That polygon is not very useful I dont think. The statistics need to be given 
separately for structures solved at given resolutions.
Eleanor

On Mon, 4 Jan 2021 at 14:43, Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>> wrote:
Well - you dont give the resolution of your data or the "wilson B" which will 
be recorded in the data processing log.
If the resolution is 3A or less a) it is hard to refine a B value, and b) it 
certainly should be high..

So more information is needed.
Eleanor

On Mon, 4 Jan 2021 at 14:39, Silvia Napolitano 
mailto:silvia.napolit...@mol.biol.ethz.ch>> 
wrote:
Dear CCP4 Community,
I am currently working on the structure of a monomeric protein of 23KDa. The 
protein is generally quite "loopy" and I think I am mid-way refinement.
At the moment I am struggling, among other things, with an extremely high 
B-factor and I'm not sure how to lower it.
Do you have any suggestions on how I can proceed to obtain a lower average 
B-factor? (I am sorry if the question is rather naive, but I have worked very 
little on X-ray structures so far)
I attached a screenshot of the polygon obtained from the last refinement (the 
geometry now should be a bit improved, I am running a new job at the moment). I 
will be happy to provide further files if needed.
Many thanks in advance for your precious help!
I wish you a nice start to the new year.
Best
Silvia




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Re: [ccp4bb] B-factors very high

[Eleanor Dodson]

Hmm - this is extracted from your log file: it looks more sensible..

2899:  b_iso_mean   = 66.62

2907:  b_iso_min= 63.50   (limit = 1.00)

2908:  b_iso_max= 68.13   (limit = 80.00)

2909:  b_iso_mean   = 66.62


The average B is 66??


I am  more familiar with REFMAC and the fact that the iso_min and iso_max
are so close looks odd to me, but maybe that is a PHENIX quirk?


But you need to look at the data processing log if you have access to it.

The CCP4I2 gives a very useful analysis of your data..

Eleanor



On Mon, 4 Jan 2021 at 15:03, Barone, Matthias  wrote:

> dear silvia,
>
> apart from the resolution, it would be good to know your current
> refinement strategy and if you fed the structure to pdbredo yet. How did
> that turn out? the polygon values are picked from structures at similar
> resolution afaik. In any case, a better list of B-factors is the one you
> find in the refinement tab "Atomic properties", where phenix lists them for
> the macromolecules and ligands separately. In that tab you will also find a
> list of which atoms cause such high ADPs. I think Eleanor is talking about
> such a screenshot
>
> best, matthias
>
>
>
> Dr. Matthias Barone
>
> AG Kuehne, Rational Drug Design
>
> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
> Robert-Rössle-Strasse 10
> 13125 Berlin
>
> Germany
> Phone: +49 (0)30 94793-284
> --
> *From:* CCP4 bulletin board  on behalf of Eleanor
> Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
> *Sent:* Monday, January 4, 2021 3:44:33 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] B-factors very high
>
> That polygon is not very useful I dont think. The statistics need to be
> given separately for structures solved at given resolutions.
> Eleanor
>
> On Mon, 4 Jan 2021 at 14:43, Eleanor Dodson 
> wrote:
>
>> Well - you dont give the resolution of your data or the "wilson B" which
>> will be recorded in the data processing log.
>> If the resolution is 3A or less a) it is hard to refine a B value, and b)
>> it certainly should be high..
>>
>> So more information is needed.
>> Eleanor
>>
>> On Mon, 4 Jan 2021 at 14:39, Silvia Napolitano <
>> silvia.napolit...@mol.biol.ethz.ch> wrote:
>>
>>> Dear CCP4 Community,
>>> I am currently working on the structure of a monomeric protein of 23KDa.
>>> The protein is generally quite "loopy" and I think I am mid-way refinement.
>>> At the moment I am struggling, among other things, with an extremely
>>> high B-factor and I'm not sure how to lower it.
>>> Do you have any suggestions on how I can proceed to obtain a lower
>>> average B-factor? (I am sorry if the question is rather naive, but I have
>>> worked very little on X-ray structures so far)
>>> I attached a screenshot of the polygon obtained from the last refinement
>>> (the geometry now should be a bit improved, I am running a new job at the
>>> moment). I will be happy to provide further files if needed.
>>> Many thanks in advance for your precious help!
>>> I wish you a nice start to the new year.
>>> Best
>>> Silvia
>>>
>>>
>>> 
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>>
>>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
>>> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
>>> available at https://www.jiscmail.ac.uk/policyandsecurity/
>>>
>>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
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Re: [ccp4bb] B-factors very high

[Alexandre Ourjoumtsev]

Dear Eleanor, 

You are absolutely right. 
However, in Polygon, you could compare the models selected by resolution, by 
size, etc. 

I use this occasion to wish you and others a happy New Year ! 

Sacha Urzhumtsev 

- Le 4 Jan 21, à 15:44, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> a écrit : 

> That polygon is not very useful I dont think. The statistics need to be given
> separately for structures solved at given resolutions.
> Eleanor



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Re: [ccp4bb] B-factors very high

[Pedro Matias]

Dear Silvia,


In addition to your high-B values I would also worry about your high 
R/R-free values - I suggest running your dataset through xtriage to 
check for twinning (or look carefully at the output of your data 
processing - it should also include some checks for twinning).



The B-value estimated from the Wilson Plot would also be useful.


Best regards,


Pedro


Às 14:58 de 04/01/2021, Napolitano Silvia escreveu:


Dear Eleanor,

Thank you for your answer. You are right, I totally forgot to provide 
this information.


The resolution is lower than 3 (2.19) Angstrom.

Attached is the run log of the last refinement. I hope that now it 
will be clearer!


Best

Silvia


Silvia Napolitano
ETH Zurich
Institute of Molecular Biology and Biophysics
Otto-Stern-Weg 5, HPK E14
CH–8093 Zurich
Phone: +41 44 6332482

*Da:* Eleanor Dodson 
*Inviato:* lunedì 4 gennaio 2021 15:43:03
*A:* Napolitano Silvia
*Cc:* CCP4BB@JISCMAIL.AC.UK
*Oggetto:* Re: [ccp4bb] B-factors very high
Well - you dont give the resolution of your data or the "wilson B" 
which will be recorded in the data processing log.
If the resolution is 3A or less a) it is hard to refine a B value, and 
b) it certainly should be high..


So more information is needed.
Eleanor

On Mon, 4 Jan 2021 at 14:39, Silvia Napolitano 
> wrote:


Dear CCP4 Community,
I am currently working on the structure of a monomeric protein of
23KDa. The protein is generally quite "loopy" and I think I am
mid-way refinement.
At the moment I am struggling, among other things, with an
extremely high B-factor and I'm not sure how to lower it.
Do you have any suggestions on how I can proceed to obtain a lower
average B-factor? (I am sorry if the question is rather naive, but
I have worked very little on X-ray structures so far)
I attached a screenshot of the polygon obtained from the last
refinement (the geometry now should be a bit improved, I am
running a new job at the moment). I will be happy to provide
further files if needed.
Many thanks in advance for your precious help!
I wish you a nice start to the new year.
Best
Silvia




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


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Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
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Re: [ccp4bb] B-factors very high

[Barone, Matthias]

dear silvia,

apart from the resolution, it would be good to know your current refinement 
strategy and if you fed the structure to pdbredo yet. How did that turn out? 
the polygon values are picked from structures at similar resolution afaik. In 
any case, a better list of B-factors is the one you find in the refinement tab 
"Atomic properties", where phenix lists them for the macromolecules and ligands 
separately. In that tab you will also find a list of which atoms cause such 
high ADPs. I think Eleanor is talking about such a screenshot

best, matthias



Dr. Matthias Barone

AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin

Germany
Phone: +49 (0)30 94793-284


From: CCP4 bulletin board  on behalf of Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Sent: Monday, January 4, 2021 3:44:33 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] B-factors very high

That polygon is not very useful I dont think. The statistics need to be given 
separately for structures solved at given resolutions.
Eleanor

On Mon, 4 Jan 2021 at 14:43, Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>> wrote:
Well - you dont give the resolution of your data or the "wilson B" which will 
be recorded in the data processing log.
If the resolution is 3A or less a) it is hard to refine a B value, and b) it 
certainly should be high..

So more information is needed.
Eleanor

On Mon, 4 Jan 2021 at 14:39, Silvia Napolitano 
mailto:silvia.napolit...@mol.biol.ethz.ch>> 
wrote:
Dear CCP4 Community,
I am currently working on the structure of a monomeric protein of 23KDa. The 
protein is generally quite "loopy" and I think I am mid-way refinement.
At the moment I am struggling, among other things, with an extremely high 
B-factor and I'm not sure how to lower it.
Do you have any suggestions on how I can proceed to obtain a lower average 
B-factor? (I am sorry if the question is rather naive, but I have worked very 
little on X-ray structures so far)
I attached a screenshot of the polygon obtained from the last refinement (the 
geometry now should be a bit improved, I am running a new job at the moment). I 
will be happy to provide further files if needed.
Many thanks in advance for your precious help!
I wish you a nice start to the new year.
Best
Silvia




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Re: [ccp4bb] B-factors very high

[Eleanor Dodson]

That polygon is not very useful I dont think. The statistics need to be
given separately for structures solved at given resolutions.
Eleanor

On Mon, 4 Jan 2021 at 14:43, Eleanor Dodson 
wrote:

> Well - you dont give the resolution of your data or the "wilson B" which
> will be recorded in the data processing log.
> If the resolution is 3A or less a) it is hard to refine a B value, and b)
> it certainly should be high..
>
> So more information is needed.
> Eleanor
>
> On Mon, 4 Jan 2021 at 14:39, Silvia Napolitano <
> silvia.napolit...@mol.biol.ethz.ch> wrote:
>
>> Dear CCP4 Community,
>> I am currently working on the structure of a monomeric protein of 23KDa.
>> The protein is generally quite "loopy" and I think I am mid-way refinement.
>> At the moment I am struggling, among other things, with an extremely high
>> B-factor and I'm not sure how to lower it.
>> Do you have any suggestions on how I can proceed to obtain a lower
>> average B-factor? (I am sorry if the question is rather naive, but I have
>> worked very little on X-ray structures so far)
>> I attached a screenshot of the polygon obtained from the last refinement
>> (the geometry now should be a bit improved, I am running a new job at the
>> moment). I will be happy to provide further files if needed.
>> Many thanks in advance for your precious help!
>> I wish you a nice start to the new year.
>> Best
>> Silvia
>>
>>
>> 
>>
>> 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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Re: [ccp4bb] B-factors very high

[Eleanor Dodson]

Well - you dont give the resolution of your data or the "wilson B" which
will be recorded in the data processing log.
If the resolution is 3A or less a) it is hard to refine a B value, and b)
it certainly should be high..

So more information is needed.
Eleanor

On Mon, 4 Jan 2021 at 14:39, Silvia Napolitano <
silvia.napolit...@mol.biol.ethz.ch> wrote:

> Dear CCP4 Community,
> I am currently working on the structure of a monomeric protein of 23KDa.
> The protein is generally quite "loopy" and I think I am mid-way refinement.
> At the moment I am struggling, among other things, with an extremely high
> B-factor and I'm not sure how to lower it.
> Do you have any suggestions on how I can proceed to obtain a lower average
> B-factor? (I am sorry if the question is rather naive, but I have worked
> very little on X-ray structures so far)
> I attached a screenshot of the polygon obtained from the last refinement
> (the geometry now should be a bit improved, I am running a new job at the
> moment). I will be happy to provide further files if needed.
> Many thanks in advance for your precious help!
> I wish you a nice start to the new year.
> Best
> Silvia
>
>
> 
>
> 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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Re: [ccp4bb] Reprocessing images collected on an Eiger2 detector using Xia2Dials on CCP4i2's GUI

[Tim Gruene]

Dear Andreas,

the eiger2cbf code also contains a plugin. I have been using it for
at least 2 years with the LIB= keywords in XDS.

The compilation is not automatically switched on with the Makefile, but
it takes very litte adjustment to create the binary plugin-worker and
the plugin plugin.so

It works greatly.

Best,
Tim

On Mon, 4 Jan 2021 11:10:34 +0100 Andreas Förster
 wrote:

> Dear Graeme, all,
> 
> to make it easier for Rigaku Oxford Diffraction's CrysAlisPro to
> process EIGER and EIGER2 data collected at the synchrotron, Herbert
> Bernstein created a Windows installer for Takanori Nakane's eiger2cbf
> converter.  You can find it here:
> https://github.com/nsls-ii-mx/eiger2cbf.  Documentation is at the
> very bottom.  It works for CAP.  I haven't tried to see how useful it
> is in other contexts.  It's a converter, not a plugin, but it lets
> you work with HDF5 data under Windows.
> 
> All best.
> 
> Andreas
> 
> 
> 
> On Mon, Jan 4, 2021 at 10:22 AM Winter, Graeme (DLSLtd,RAL,LSCI) <
> graeme.win...@diamond.ac.uk> wrote:  
> 
> > Hi All,
> >
> > Sorry for the slow response - holiday season & all (I am sure many
> > of us needed a break at the end of 2020)
> >
> > Windows is currently not super well supported for xia2 / DIALS work
> > and won’t work at all for xia2 / XDS for the simple reason that XDS
> > is not available for the platform (hence absence of durin plugin
> > for Windows mentioned elsewhere in this thread)
> >
> > Your data are from 2019 I would guess from the log text
> >
> > In this case I would honestly suggest that the best method to
> > process this data is to either -
> >  - work on a UNIX based system
> > or
> >  - restage the data to Diamond and process there
> >
> > I’m happy to help (off list) with the details of this if it would
> > help
> >
> > We probably should invest some effort in properly supporting
> > Windows for xia2 / DIALS - however there are a bunch of rather
> > nasty jobs to do in making this possible and it’s never “the most
> > important thing” sorry :-(
> >
> > Happy new year & best wishes Graeme
> >
> > On 22 Dec 2020, at 16:53, Irwin Selvam <  
> > irwin.sel...@postgrad.manchester.ac.uk> wrote:  
> >
> > Hi,
> >
> > I'd like to reprocess some data that were collected on an Eiger2
> > detector at Diamond with Xia2Dials using CCP4i2's GUI. I'm running
> > CCP4i2 on a 64-bit Windows 10 machine. The data were processed
> > successfully at Diamond with no obvious pathologies, the high
> > resolution limit was just a little generous. The folder in question
> > contains a Diamond specific file (.nsx extension), two image files
> > (.h5), a header (.cbf), a master (.h5) and meta file (.h5). I've
> > tried pointing Xia2 to the folder itself (which works when
> > processing data collected on PILATUS detectors) and each of the
> > files contained therein (except the Diamond specific file). Each
> > time this results in the error " -ERROR- None:56 Error in wrapper
> > xia2_dials 0.0:: External process exited with exit code != 0
> > Process: C:\CCP4-7\7.1\bin\xia2.bat -ERROR- None:47 Error in
> > wrapper xia2_dials 0.0:: Error in checking external process after
> > completion exit status and code: 0 1". I've attached the error,
> > debug etc files for a representative 'run' to this email. Which
> > files do I need to point xia2 towards to get it to run? Any help
> > would be appreciated.
> >
> > All the best,
> >
> > Irwin
> >
> > --
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> > 
> >
> >
> >
> >
> > --
> >
> > This e-mail and any attachments may contain confidential, copyright
> > and or privileged material, and are for the use of the intended
> > addressee only. If you are not the intended addressee or an
> > authorised recipient of the addressee please notify us of receipt
> > by returning the e-mail and do not use, copy, retain, distribute or
> > disclose the information in or attached to the e-mail.
> > Any opinions expressed within this e-mail are those of the
> > individual and not necessarily of Diamond Light Source Ltd.
> > Diamond Light Source Ltd. cannot guarantee that this e-mail or any
> > attachments are free from viruses and we cannot accept liability
> > for any damage which you may sustain as a result of software
> > viruses which may be transmitted in or with the message.
> > Diamond Light Source Limited (company no. 4375679). Registered in
> > England and Wales with its registered office at Diamond House,
> > Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11
> > 0DE, United Kingdom
> >
> >
> > --
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?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 

Re: [ccp4bb] Reprocessing images collected on an Eiger2 detector using Xia2Dials on CCP4i2's GUI

[Andreas Förster]

Dear Graeme, all,

to make it easier for Rigaku Oxford Diffraction's CrysAlisPro to process
EIGER and EIGER2 data collected at the synchrotron, Herbert Bernstein
created a Windows installer for Takanori Nakane's eiger2cbf converter.  You
can find it here:  https://github.com/nsls-ii-mx/eiger2cbf.  Documentation
is at the very bottom.  It works for CAP.  I haven't tried to see how
useful it is in other contexts.  It's a converter, not a plugin, but it
lets you work with HDF5 data under Windows.

All best.

Andreas



On Mon, Jan 4, 2021 at 10:22 AM Winter, Graeme (DLSLtd,RAL,LSCI) <
graeme.win...@diamond.ac.uk> wrote:

> Hi All,
>
> Sorry for the slow response - holiday season & all (I am sure many of us
> needed a break at the end of 2020)
>
> Windows is currently not super well supported for xia2 / DIALS work and
> won’t work at all for xia2 / XDS for the simple reason that XDS is not
> available for the platform (hence absence of durin plugin for Windows
> mentioned elsewhere in this thread)
>
> Your data are from 2019 I would guess from the log text
>
> In this case I would honestly suggest that the best method to process this
> data is to either -
>  - work on a UNIX based system
> or
>  - restage the data to Diamond and process there
>
> I’m happy to help (off list) with the details of this if it would help
>
> We probably should invest some effort in properly supporting Windows for
> xia2 / DIALS - however there are a bunch of rather nasty jobs to do in
> making this possible and it’s never “the most important thing” sorry :-(
>
> Happy new year & best wishes Graeme
>
> On 22 Dec 2020, at 16:53, Irwin Selvam <
> irwin.sel...@postgrad.manchester.ac.uk> wrote:
>
> Hi,
>
> I'd like to reprocess some data that were collected on an Eiger2 detector
> at Diamond with Xia2Dials using CCP4i2's GUI. I'm running CCP4i2 on a
> 64-bit Windows 10 machine. The data were processed successfully at Diamond
> with no obvious pathologies, the high resolution limit was just a little
> generous. The folder in question contains a Diamond specific file (.nsx
> extension), two image files (.h5), a header (.cbf), a master (.h5) and meta
> file (.h5). I've tried pointing Xia2 to the folder itself (which works
> when processing data collected on PILATUS detectors) and each of the files
> contained therein (except the Diamond specific file). Each time this
> results in the error " -ERROR- None:56 Error in wrapper xia2_dials 0.0::
> External process exited with exit code != 0 Process:
> C:\CCP4-7\7.1\bin\xia2.bat -ERROR- None:47 Error in wrapper xia2_dials
> 0.0:: Error in checking external process after completion exit status and
> code: 0 1". I've attached the error, debug etc files for a representative
> 'run' to this email. Which files do I need to point xia2 towards to get it
> to run? Any help would be appreciated.
>
> All the best,
>
> Irwin
>
> --
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
>
>
>
>
> --
>
> This e-mail and any attachments may contain confidential, copyright and or
> privileged material, and are for the use of the intended addressee only. If
> you are not the intended addressee or an authorised recipient of the
> addressee please notify us of receipt by returning the e-mail and do not
> use, copy, retain, distribute or disclose the information in or attached to
> the e-mail.
> Any opinions expressed within this e-mail are those of the individual and
> not necessarily of Diamond Light Source Ltd.
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any
> attachments are free from viruses and we cannot accept liability for any
> damage which you may sustain as a result of software viruses which may be
> transmitted in or with the message.
> Diamond Light Source Limited (company no. 4375679). Registered in England
> and Wales with its registered office at Diamond House, Harwell Science and
> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>


-- 

Andreas Förster, Ph.D.
Application Scientist Crystallography, Area Sales Manager Asia & Pacific
Phone: +41 56 500 21 00 | Direct: +41 56 500 21 76 | Email:
andreas.foers...@dectris.com
DECTRIS Ltd. | Taefernweg 1 | 5405 Baden-Daettwil | Switzerland |
www.dectris.com







[image: LinkedIn]

[ccp4bb] Post-doctoral position at the University of Oxford: deadline Jan 11

[Opher Gileadi]

We are seeking highly motivated postdoc to investigate new targets for 
treatment of Alzheimer's disease. You will be joining the Structural Biology 
Core of an international, NIH-funded consortium (TREAT-AD, 
https://treatad.org/emory-sage-sgc/), contributing to testing new therapeutic 
hypotheses through structural biology, structure-assisted mnedicinal chemistry, 
and finctional studies of new potential targets.
For a full-description see:
https://my.corehr.com/pls/uoxrecruit/erq_jobspec_version_4.display_form?p_company=10_internal_external=E_display_in_irish=N_process_type=_applicant_no=_form_profile_detail=_display_apply_ind=Y_refresh_search=Y_recruitment_id=148810
 



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Re: [ccp4bb] Reprocessing images collected on an Eiger2 detector using Xia2Dials on CCP4i2's GUI

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Hi All,

Sorry for the slow response - holiday season & all (I am sure many of us needed 
a break at the end of 2020)

Windows is currently not super well supported for xia2 / DIALS work and won’t 
work at all for xia2 / XDS for the simple reason that XDS is not available for 
the platform (hence absence of durin plugin for Windows mentioned elsewhere in 
this thread)

Your data are from 2019 I would guess from the log text

In this case I would honestly suggest that the best method to process this data 
is to either -
 - work on a UNIX based system
or
 - restage the data to Diamond and process there

I’m happy to help (off list) with the details of this if it would help

We probably should invest some effort in properly supporting Windows for xia2 / 
DIALS - however there are a bunch of rather nasty jobs to do in making this 
possible and it’s never “the most important thing” sorry :-(

Happy new year & best wishes Graeme

On 22 Dec 2020, at 16:53, Irwin Selvam 
mailto:irwin.sel...@postgrad.manchester.ac.uk>>
 wrote:

Hi,

I'd like to reprocess some data that were collected on an Eiger2 detector at 
Diamond with Xia2Dials using CCP4i2's GUI. I'm running CCP4i2 on a 64-bit 
Windows 10 machine. The data were processed successfully at Diamond with no 
obvious pathologies, the high resolution limit was just a little generous. The 
folder in question contains a Diamond specific file (.nsx extension), two image 
files (.h5), a header (.cbf), a master (.h5) and meta file (.h5). I've tried 
pointing Xia2 to the folder itself (which works when processing data collected 
on PILATUS detectors) and each of the files contained therein (except the 
Diamond specific file). Each time this results in the error " -ERROR- None:56 
Error in wrapper xia2_dials 0.0:: External process exited with exit code != 0 
Process: C:\CCP4-7\7.1\bin\xia2.bat -ERROR- None:47 Error in wrapper xia2_dials 
0.0:: Error in checking external process after completion exit status and code: 
0 1". I've attached the error, debug etc files for a representative 'run' to 
this email. Which files do I need to point xia2 towards to get it to run? Any 
help would be appreciated.

All the best,

Irwin


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



-- 
This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




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[ccp4bb] Research Technician at Imperial College London

[Thomas Meier]

Dear Colleagues

I am looking for a Research Technician in my membrane protein structural 
biology group at Imperial College London (South Kensington campus).


Job details are here: https://www.jobs.ac.uk/job/CDG232/research-technician

Happy New Year everyone!

Thomas


--
Prof. Dr. Thomas Meier
Director Centre for Structural Biology
Chair in Structural Biology
Wellcome Trust Investigator

Imperial College London
Department of Life Sciences
Sir Ernst Chain Building, rm 501
London SW7 2AZ, United Kingdom
phone: +44(0)2075943056



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