Re: [ccp4bb] number of frames to get a full dataset?

2020-06-23 Thread Peat, Tom (Manufacturing, Parkville) 
I have no disagreement that anomalous is helpful and very useful data to have. 
So I’m in agreement with you and Bernhard without any reservations whatsoever.
It just so happens that 360 degrees of data in the P1 spacegroup does not give 
you very good anomalous signal. In my limited experience, one needs at least 7 
fold multiplicity/ redundancy to get enough signal to solve structures with 
anomalous (at least with what I will call ‘standard’ anomalous scatterers, not 
things like lanthanides which give very large (beautiful!) signals). And you 
just don’t get that in P1.
In violent agreement again…
Cheers, tom

From: bogba...@yahoo.co.uk 
Sent: Wednesday, 24 June 2020 10:29 AM
To: Peat, Tom (Manufacturing, Parkville) 
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] number of frames to get a full dataset?

Well, it can still help. I used to be a great fan of inverse-beam expts! Oh, 
and some of us prefer the word 'multiplicity' ;-0
Jon Cooper

On 23 Jun 2020 22:04, "Peat, Tom (Manufacturing, Parkville)" 
 wrote:
I would just like to point out that for those of us who have worked too many 
times with P1 or P21 that even 360 degrees will not give you 'super' anomalous 
differences.
I'm not a minimalist when it comes to data- redundancy is a good thing to have.
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 
0c2488af9525-dmarc-requ...@jiscmail.ac.uk 
<0c2488af9525-dmarc-requ...@jiscmail.ac.uk>
Sent: Wednesday, June 24, 2020 1:10 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] number of frames to get a full dataset?

Someone told me there is a cubic space group where you can get away with 
something like 11 degrees of data. It would be interesting if that's correct. 
These minimum ranges for data collection rely on the crystal being 
pre-oriented, which is unheard-of these days, although they can help if someone 
is nagging you to get off the beam line or if your diffraction fades quickly. 
Going for 180 degrees always makes sense for a well-behaved crystal, or 360 
degrees if you want super anomalous differences. Hope this helps a bit.
Jon Cooper

On 23 Jun 2020 07:29, Andreas Förster  wrote:
Hi Murpholino,

in my opinion (*), the question is neither number of frames nor degrees.  The 
only thing that matters to your crystal is dose.  How many photons does your 
crystal take before it dies?  Consequently, the question to ask is How best to 
use photons.  Some people have done exactly that.
https://doi.org/10.1107/S2059798319003528

All best.


Andreas


(*) Disclaimer:  I benefit when you use PILATUS or EIGER - but I want you to 
use them to your advantage.



On Tue, Jun 23, 2020 at 12:04 AM Murpholino Peligro 
mailto:murpholi...@gmail.com>> wrote:
Hi.
Quick question...
I have seen *somewhere* that to get a 'full dataset we need to collect n 
frames':
at least 180 frames if symmetry is X
at least 90 frames if symmetry is Y
at least 45 frames if symmetry is Z
Can somebody point where is *somewhere*?

...also...
what other factors can change n... besides symmetry and radiation damage?

Thanks



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


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Re: [ccp4bb] number of frames to get a full dataset?

2020-06-23 Thread 00000c2488af9525-dmarc-request 
Well, it can still help. I used to be a great fan of inverse-beam expts! Oh, and some of us prefer the word 'multiplicity' ;-0Jon CooperOn 23 Jun 2020 22:04, "Peat, Tom (Manufacturing, Parkville)"  wrote:

I would just like to point out that for those of us who have worked too many times with P1 or P21 that even 360 degrees will not give you 'super' anomalous differences.



I'm not a minimalist when it comes to data- redundancy is a good thing to have. 


cheers, tom 










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












From: CCP4 bulletin board  on behalf of 0c2488af9525-dmarc-request@JISCMAIL.AC.UK <0c2488af9525-dmarc-request@JISCMAIL.AC.UK>
Sent: Wednesday, June 24, 2020 1:10 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] number of frames to get a full dataset?
 


Someone told me there is a cubic space group where you can get away with something like 11 degrees of data. It would be interesting if that's correct. These minimum ranges for data collection rely on the crystal being pre-oriented, which is
 unheard-of these days, although they can help if someone is nagging you to get off the beam line or if your diffraction fades quickly. Going for 180 degrees always makes sense for a well-behaved crystal, or 360 degrees if you want super anomalous differences.
 Hope this helps a bit. 

Jon Cooper


On 23 Jun 2020 07:29, Andreas Förster  wrote:

Hi Murpholino,


in my opinion (*), the question is neither number of frames nor degrees.  The only thing that matters to your crystal is dose.  How many photons does your crystal take before it dies?  Consequently, the question to ask is How best to use photons.  Some
 people have done exactly that.
https://doi.org/10.1107/S2059798319003528

All best.




Andreas




(*) Disclaimer:  I benefit when you use PILATUS or EIGER - but I want you to use them to your advantage.







On Tue, Jun 23, 2020 at 12:04 AM Murpholino Peligro  wrote:


Hi. 
Quick question...
I have seen *somewhere* that to get a 'full dataset we need to collect n frames':
at least 180 frames if symmetry is X

at least 90 frames if symmetry is Y

at least 45 frames if symmetry is Z

Can somebody point where is *somewhere*? 



...also...

what other factors can change n... besides symmetry and radiation damage?



Thanks





To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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.foerster@dectris.com

DECTRIS Ltd. | Taefernweg
 1 | 5405 Baden-Daettwil | Switzerland | www.dectris.com




    






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Re: [ccp4bb] number of frames to get a full dataset?

2020-06-23 Thread Bernhard Rupp 
Tom makes a good point. The minimum RS coverage necessary to obtain a unique
data set is just a simple calculation

that involves no experimental reality. 

 

To judge the expected usefulness of the data, you need to have some idea
about the possible errors, random and systematic.  

Random is easy. Just collect longer (Poisson) and the counting error
(precision) improves (sqrt(n)). Easy, would not

radiation damage throw a wrench in into this concept, cf. all the threads by
Holton, Elsbeth et al.

 

Systematic, error, in absence of knowing the true value, becomes more
interesting. One can average out some 

systematic errors by averaging multiple independent reflections (redundancy
is rarely a bad thing, except for additional systematic

error by overdoing exposure (as in hunt for highest resolution…) , but at
least the mean will become more precise (not

always, but often, more accurate too).

 

Without advertisement for Dectris, collecting as much as you can
(anomalously) as fast (lowest dose) as you can

and sort out the stats later is a reasonable default in absence of other
prior information. 

 

In his context, I’d like to make a push for routine anomalous data, I was
often surprised about the interpretative confirmation

you can gain from a few clear anomalous peaks (or their absence).   

 

Best, BR

 

From: CCP4 bulletin board  On Behalf Of Peat, Tom
(Manufacturing, Parkville)
Sent: Tuesday, June 23, 2020 14:04
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] number of frames to get a full dataset?

 

I would just like to point out that for those of us who have worked too many
times with P1 or P21 that even 360 degrees will not give you 'super'
anomalous differences. 

I'm not a minimalist when it comes to data- redundancy is a good thing to
have. 

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 mailto:CCP4BB@JISCMAIL.AC.UK> > on behalf of
0c2488af9525-dmarc-requ...@jiscmail.ac.uk

<0c2488af9525-dmarc-requ...@jiscmail.ac.uk
 >
Sent: Wednesday, June 24, 2020 1:10 AM
To: CCP4BB@JISCMAIL.AC.UK 
mailto:CCP4BB@JISCMAIL.AC.UK> >
Subject: Re: [ccp4bb] number of frames to get a full dataset? 

 

Someone told me there is a cubic space group where you can get away with
something like 11 degrees of data. It would be interesting if that's
correct. These minimum ranges for data collection rely on the crystal being
pre-oriented, which is unheard-of these days, although they can help if
someone is nagging you to get off the beam line or if your diffraction fades
quickly. Going for 180 degrees always makes sense for a well-behaved
crystal, or 360 degrees if you want super anomalous differences. Hope this
helps a bit. 

Jon Cooper

 

On 23 Jun 2020 07:29, Andreas Förster mailto:andreas.foers...@dectris.com> > wrote:

Hi Murpholino,

 

in my opinion (*), the question is neither number of frames nor degrees.
The only thing that matters to your crystal is dose.  How many photons does
your crystal take before it dies?  Consequently, the question to ask is How
best to use photons.  Some people have done exactly that.

https://doi.org/10.1107/S2059798319003528


All best.

 

 

Andreas

 

 

(*) Disclaimer:  I benefit when you use PILATUS or EIGER - but I want you to
use them to your advantage.

 

 

 

On Tue, Jun 23, 2020 at 12:04 AM Murpholino Peligro mailto:murpholi...@gmail.com> > wrote:

Hi. 
Quick question...

I have seen *somewhere* that to get a 'full dataset we need to collect n
frames':

at least 180 frames if symmetry is X

at least 90 frames if symmetry is Y

at least 45 frames if symmetry is Z

Can somebody point where is *somewhere*? 

 

...also...

what other factors can change n... besides symmetry and radiation damage?

 

Thanks

 

  _  

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

 

 

  


  

 
 

 

Confidentiality Note: This message is intended only for the use of the named
recipient(s)

and may contain confidential and/or privileged information. If you are not
the i

Re: [ccp4bb] number of frames to get a full dataset?

2020-06-23 Thread Peat, Tom (Manufacturing, Parkville) 
I would just like to point out that for those of us who have worked too many 
times with P1 or P21 that even 360 degrees will not give you 'super' anomalous 
differences.
I'm not a minimalist when it comes to data- redundancy is a good thing to have.
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 
0c2488af9525-dmarc-requ...@jiscmail.ac.uk 
<0c2488af9525-dmarc-requ...@jiscmail.ac.uk>
Sent: Wednesday, June 24, 2020 1:10 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] number of frames to get a full dataset?

Someone told me there is a cubic space group where you can get away with 
something like 11 degrees of data. It would be interesting if that's correct. 
These minimum ranges for data collection rely on the crystal being 
pre-oriented, which is unheard-of these days, although they can help if someone 
is nagging you to get off the beam line or if your diffraction fades quickly. 
Going for 180 degrees always makes sense for a well-behaved crystal, or 360 
degrees if you want super anomalous differences. Hope this helps a bit.

Jon Cooper

On 23 Jun 2020 07:29, Andreas Förster  wrote:
Hi Murpholino,

in my opinion (*), the question is neither number of frames nor degrees.  The 
only thing that matters to your crystal is dose.  How many photons does your 
crystal take before it dies?  Consequently, the question to ask is How best to 
use photons.  Some people have done exactly that.
https://doi.org/10.1107/S2059798319003528

All best.


Andreas


(*) Disclaimer:  I benefit when you use PILATUS or EIGER - but I want you to 
use them to your advantage.



On Tue, Jun 23, 2020 at 12:04 AM Murpholino Peligro 
mailto:murpholi...@gmail.com>> wrote:
Hi.
Quick question...
I have seen *somewhere* that to get a 'full dataset we need to collect n 
frames':
at least 180 frames if symmetry is X
at least 90 frames if symmetry is Y
at least 45 frames if symmetry is Z
Can somebody point where is *somewhere*?

...also...
what other factors can change n... besides symmetry and radiation damage?

Thanks



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


[https://www.dectris.com/files/content/images/signatur/logo_signatur.png]

[LinkedIn]
[facebook][https://www.dectris.com/files/content/images/signatur/twitter_20px.png]

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[ccp4bb] Reminder: Scientific Data Curation positions at PDBe and EMDB/EMPIAR

2020-06-23 Thread John Berrisford 
Dear Colleagues

 

There are two curator positions available in the PDBe and EMDB/EMPIAR teams
at the European Bioinformatics Institute (EBI) on the Wellcome Genome Campus
near Cambridge.

 

We are looking to recruit an expert structural biologist to join the PDBe
curation team. The work involves annotating preliminary PDB and EMDB
submissions and extracting relevant biological information.

 

We are also looking for an expert cryo-electron microscopist to join the
EMDB/EMPIAR team. The work will involve biocuration of EMDB and EMPIAR
depositions and the integration of this data with other bioinformatics
resources.

 

The closing date for applications for both posts is 30th June 2020. For more
information on the positions, please visit:

 

PDBe:  
https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01532

 

EMDB/EMPIAR:  
https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01622

 

Kind regards,

 

John

 

--

John Berrisford

PDBe

European Bioinformatics Institute (EMBL-EBI)

European Molecular Biology Laboratory

Wellcome Trust Genome Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

  http://www.pdbe.org

 
http://www.facebook.com/proteindatabank

  http://twitter.com/PDBeurope

 




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Re: [ccp4bb] Phenix: No reference model matches

2020-06-23 Thread Oleg Sobolev 
Dear Clemens,

If the working model and reference model are exactly identical, you may try
to use the same file in both the working and reference model to see if it
works. I don't see anything strange in the pdb lines you attached. I'm
happy to have a closer look if you are willing to share (off-list) the pdb
files and the full log (no data required).

FYI, there is a Phenix specific bulletin board:
http://www.phenix-online.org/mailman/listinfo/phenixbb

Best regards,
Oleg Sobolev.


On Tue, Jun 23, 2020 at 12:18 AM Clemens Grimm <
clemens.gr...@biozentrum.uni-wuerzburg.de> wrote:

> Dear All,
>
> I am not getting any reference model matches in Phenix:
>
> 
> Reference Model Matching Summary:
>
> reference file: reference.pdb
>
> Model:  Reference:
>
> Total # of matched residue pairs: 0
> Total # of reference model restraints: 0
> 
>
> working model and reference are exactly identical. I suspect that this
> has to do with some specificities of the PDB files (below). Has
> anybody else encountered such a problem?
>
> Thanks,
> Clemens
>
>
>
> 
>
> ATOM  1  N   ASP I   2 265.380 222.283 314.077  1.00121.12
>N
> ATOM  2  CA  ASP I   2 266.526 221.945 313.241  1.00121.12
>C
> ATOM  3  C   ASP I   2 266.172 222.082 311.764  1.00121.12
>C
> ATOM  4  O   ASP I   2 266.687 222.959 311.071  1.00121.12
>O
> ATOM  5  CB  ASP I   2 267.014 220.523 313.548  1.00121.12
>C
> ATOM  6  CG  ASP I   2 268.389 220.226 312.962  1.00121.12
>C
> ATOM  7  OD1 ASP I   2 268.514 220.091 311.725  1.00121.12
>O
> ATOM  8  OD2 ASP I   2 269.356 220.128 313.748  1.00121.12
>O
> ATOM  9  N   SER I   3 265.292 221.202 311.291  1.00116.78
>N
> ATOM 10  CA  SER I   3 264.929 221.164 309.884  1.00116.78
>C
> ATOM 11  C   SER I   3 264.010 222.332 309.531  1.00116.78
>C
> ATOM 12  O   SER I   3 263.497 223.041 310.397  1.00116.78
>O
> ATOM 13  CB  SER I   3 264.250 219.839 309.548  1.00116.78
>C
> ATOM 14  OG  SER I   3 265.045 218.745 309.967  1.00116.78
>O
>
>
> 
>
>
> ATOM   6438  N   ASN I 795 197.555 302.028 252.461  1.00 91.20
>N
> ATOM   6439  CA  ASN I 795 196.094 301.970 252.599  1.00 91.20
>C
> ATOM   6440  C   ASN I 795 195.641 301.634 254.015  1.00 91.20
>C
> ATOM   6441  O   ASN I 795 195.666 302.490 254.898  1.00 91.20
>O
> ATOM   6442  CB  ASN I 795 195.497 300.970 251.599  1.00 91.20
>C
> ATOM   6443  CG  ASN I 795 196.000 301.190 250.183  1.00 91.20
>C
> ATOM   6444  ND2 ASN I 795 195.297 302.023 249.427  1.00 91.20
>N
> ATOM   6445  OD1 ASN I 795 197.011 300.617 249.776  1.00 91.20
>O
> ATOM   6446  OXT ASN I 795 195.241 300.505 254.300  1.00 91.20
>O
> END
>
> --
> Dr. Clemens Grimm
> Institut für Biochemie
> Biozentrum der Universität Würzburg
> Am Hubland
> D-97074 Würzburg
> Germany
> e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de
> phone : +49 0931 31 84031
> -
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
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Re: [ccp4bb] number of frames to get a full dataset?

2020-06-23 Thread Bernhard Rupp 
1/48th of reciprocal space is the minimum in certain SGs..

 

Table 6.6 in BMC or

http://www.ruppweb.org/new_comp/spacegroup_decoder.htm

 

Best, BR

 

 

From: CCP4 bulletin board  On Behalf Of 
0c2488af9525-dmarc-requ...@jiscmail.ac.uk
Sent: Tuesday, June 23, 2020 08:11
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] number of frames to get a full dataset?

 

Someone told me there is a cubic space group where you can get away with 
something like 11 degrees of data. It would be interesting if that's correct. 
These minimum ranges for data collection rely on the crystal being 
pre-oriented, which is unheard-of these days, although they can help if someone 
is nagging you to get off the beam line or if your diffraction fades quickly. 
Going for 180 degrees always makes sense for a well-behaved crystal, or 360 
degrees if you want super anomalous differences. Hope this helps a bit. 

Jon Cooper

 

On 23 Jun 2020 07:29, Andreas Förster mailto:andreas.foers...@dectris.com> > wrote:

Hi Murpholino,

 

in my opinion (*), the question is neither number of frames nor degrees.  The 
only thing that matters to your crystal is dose.  How many photons does your 
crystal take before it dies?  Consequently, the question to ask is How best to 
use photons.  Some people have done exactly that.

https://doi.org/10.1107/S2059798319003528


All best.

 

 

Andreas

 

 

(*) Disclaimer:  I benefit when you use PILATUS or EIGER - but I want you to 
use them to your advantage.

 

 

 

On Tue, Jun 23, 2020 at 12:04 AM Murpholino Peligro mailto:murpholi...@gmail.com> > wrote:

Hi. 
Quick question...

I have seen *somewhere* that to get a 'full dataset we need to collect n 
frames':

at least 180 frames if symmetry is X

at least 90 frames if symmetry is Y

at least 45 frames if symmetry is Z

Can somebody point where is *somewhere*? 

 

...also...

what other factors can change n... besides symmetry and radiation damage?

 

Thanks

 

  _  

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB 
 &A=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 | 
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Re: [ccp4bb] number of frames to get a full dataset?

2020-06-23 Thread 00000c2488af9525-dmarc-request 
Someone told me there is a cubic space group where you can get away with something like 11 degrees of data. It would be interesting if that's correct. These minimum ranges for data collection rely on the crystal being pre-oriented, which is unheard-of these days, although they can help if someone is nagging you to get off the beam line or if your diffraction fades quickly. Going for 180 degrees always makes sense for a well-behaved crystal, or 360 degrees if you want super anomalous differences. Hope this helps a bit. Jon CooperOn 23 Jun 2020 07:29, Andreas Förster  wrote:Hi Murpholino,in my opinion (*), the question is neither number of frames nor degrees.  The only thing that matters to your crystal is dose.  How many photons does your crystal take before it dies?  Consequently, the question to ask is How best to use photons.  Some people have done exactly that.https://doi.org/10.1107/S2059798319003528All best.Andreas(*) Disclaimer:  I benefit when you use PILATUS or EIGER - but I want you to use them to your advantage.On Tue, Jun 23, 2020 at 12:04 AM Murpholino Peligro  wrote:Hi. Quick question... I have seen *somewhere* that to get a 'full dataset we need to collect n frames':at least 180 frames if symmetry is Xat least 90 frames if symmetry is Yat least 45 frames if symmetry is ZCan somebody point where is *somewhere*? ...also...what other factors can change n... besides symmetry and radiation damage?Thanks


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-- 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.foerster@dectris.comDECTRIS Ltd. | Taefernweg 1 | 5405 Baden-Daettwil | Switzerland | www.dectris.com    Confidentiality Note: This message is intended only for the use of the named recipient(s)and may contain confidential and/or privileged information. If you are not the intendedrecipient, please contact the sender and delete the message. Any unauthorized use ofthe information contained in this message is prohibited.


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[ccp4bb] PhD Position in serial crystallography and drug design, the European Synchrotron Radiation Facility, Grenoble, France

2020-06-23 Thread Max Nanao 

Hi All,
We have an exciting opportunity for a PhD project on drug design and 
serial crystallography at the ESRF. The project will be in collaboration 
with the Servier Institute. More details can be found on the ESRF 
website (https://esrf.gestmax.eu/1432/1/phd-student-id23-2/en_US), or 
below



CONTEXT & JOB DESCRIPTION
X-ray crystallography is a critical tool in modern drug design. Ligand 
and/or fragment screening campaigns for drug design are typically 
carried out by collecting diffraction data at 100 K from large (> 30 
mm), robust, well diffracting crystals. However, there is increasing 
evidence that crystal soaking protocols are more efficient when applied 
to smaller crystals and that the cryo-cooling of crystals may obscure 
biologically relevant information. Post ESRF-EBS X-ray beams will allow 
us to apply recently developed multi-crystal (MDX) data collection 
protocols to complexes of micro-crystals with small molecules. However, 
how best to combine the partial data sets obtained in MDX in order to 
obtain the best electron density for bound fragments or ligands and the 
best analysis of modes of binding to their target molecules is an area 
requiring optimisation.


The aims of this PhD work are:

1). To provide a systematic analysis of the effect of crystal size of 
the ligand/fragment occupancy obtained in soaking experiments;


2). To improve and optimize protocols for the combination of MDX data 
sets using enhanced protocols for hierarchical cluster analysis (HCA) 
and genetic algorithms (GAs), areas which are being actively developed 
at ESRF.


The project proposed here is based on a combination of methodology 
development at the ESRF and access to material, training expertise and 
insight from IDRS Servier, Suresnes, France. This opportunity will thus 
provide an unrivalled opportunity for a young scientist interested in 
optimising structure-based drug design processes, which exploit 
microcrystals. During the PhD work, the student will learn experimental 
methodology (protein production and purification, crystallisation, 
diffraction data collection, data analysis) and interpretation of 
real-world results in an area designed to overcome major bottlenecks in 
the drug design process.


Further information may be obtained from Max Nanao (tel.: +33 (0)4 76 88 
4087, email: na...@esrf.fr).


EXPECTED PROFILE
Degree allowing enrollment for a PhD (such as MSc, Master 2 de 
Recherche, Laurea or equivalent) in chemistry, physics, materials 
science or closely related science
A background in Statistics is desirable as is some knowledge of 
Structural Biology
The candidate should show a strong aptitude for team working and have 
excellent communications skills

Proficiency in English (working language at the ESRF)
WORKING CONDITIONS
Contract of two years renewable (subject to satisfactory progress) for 
one year.


The ESRF is an equal opportunity employer and encourages diversity.





--
Max Nanao
European Synchrotron Radiation Facility
Structural Biology Group
71,Avenue des Martyrs
F-38000 Grenoble
Tel: +33.(0)4.76.88.40.87
ORCID: -0002-6340-1376



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[ccp4bb] Phenix: No reference model matches

2020-06-23 Thread Clemens Grimm 

Dear All,

I am not getting any reference model matches in Phenix:


Reference Model Matching Summary:

reference file: reference.pdb

Model:  Reference:

Total # of matched residue pairs: 0
Total # of reference model restraints: 0


working model and reference are exactly identical. I suspect that this  
has to do with some specificities of the PDB files (below). Has  
anybody else encountered such a problem?


Thanks,
Clemens





ATOM  1  N   ASP I   2 265.380 222.283 314.077  1.00121.12   N
ATOM  2  CA  ASP I   2 266.526 221.945 313.241  1.00121.12   C
ATOM  3  C   ASP I   2 266.172 222.082 311.764  1.00121.12   C
ATOM  4  O   ASP I   2 266.687 222.959 311.071  1.00121.12   O
ATOM  5  CB  ASP I   2 267.014 220.523 313.548  1.00121.12   C
ATOM  6  CG  ASP I   2 268.389 220.226 312.962  1.00121.12   C
ATOM  7  OD1 ASP I   2 268.514 220.091 311.725  1.00121.12   O
ATOM  8  OD2 ASP I   2 269.356 220.128 313.748  1.00121.12   O
ATOM  9  N   SER I   3 265.292 221.202 311.291  1.00116.78   N
ATOM 10  CA  SER I   3 264.929 221.164 309.884  1.00116.78   C
ATOM 11  C   SER I   3 264.010 222.332 309.531  1.00116.78   C
ATOM 12  O   SER I   3 263.497 223.041 310.397  1.00116.78   O
ATOM 13  CB  SER I   3 264.250 219.839 309.548  1.00116.78   C
ATOM 14  OG  SER I   3 265.045 218.745 309.967  1.00116.78   O





ATOM   6438  N   ASN I 795 197.555 302.028 252.461  1.00 91.20   N
ATOM   6439  CA  ASN I 795 196.094 301.970 252.599  1.00 91.20   C
ATOM   6440  C   ASN I 795 195.641 301.634 254.015  1.00 91.20   C
ATOM   6441  O   ASN I 795 195.666 302.490 254.898  1.00 91.20   O
ATOM   6442  CB  ASN I 795 195.497 300.970 251.599  1.00 91.20   C
ATOM   6443  CG  ASN I 795 196.000 301.190 250.183  1.00 91.20   C
ATOM   6444  ND2 ASN I 795 195.297 302.023 249.427  1.00 91.20   N
ATOM   6445  OD1 ASN I 795 197.011 300.617 249.776  1.00 91.20   O
ATOM   6446  OXT ASN I 795 195.241 300.505 254.300  1.00 91.20   O
END

--
Dr. Clemens Grimm
Institut für Biochemie
Biozentrum der Universität Würzburg
Am Hubland
D-97074 Würzburg
Germany
e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de
phone : +49 0931 31 84031
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