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

[James Holton]

What could possibly go wrong?

-James Holton
MAD Scientist

On 6/29/2020 6:17 PM, Edward A. Berry wrote:
Now can we get rid of all the superfluous disks in our RAID? Or at 
least not replace them when they fail?


On 06/29/2020 06:24 PM, Andreas Förster wrote:
I like to think that the reflections I carefully measured at high 
multiplicity are not redundant, which the dictionary on my computer 
defines as "not or no longer needed or useful; superfluous" and the 
American Heritage Dictionary as "exceeding what is necessary or 
natural; superfluous" and "needlessly repetitive; verbose".


Please don't use the term Needless repetitivity in your Table 1.  It 
sends the wrong message.  Multiplicity is good.


All best.


Andreas



On Tue, Jun 30, 2020 at 12:03 AM James Holton > wrote:


    I have found that the use of "redundancy" vs "multiplicity" 
correlates very well with the speaker's favorite processing 
software.  The Denzo/HKL program scalepack outputs "redundancy", 
whereas scala/aimless and other more Europe-centric programs output 
"multiplicity".


    At least it is not as bad as "intensity", which is so ambiguous 
as to be almost useless as a word on its own.


    -James Holton
    MAD Scientist

    On 6/24/2020 10:27 AM, Bernhard Rupp wrote:


    > Oh, and some of us prefer the word 'multiplicity' ;-0

    Hmmm…maybe not. ‘Multiplicity’ in crystallography is context 
sensitive, and not uniquely defined. It can refer to 


 1. the position multiplicity (number of equivalent sites per 
unit cell, aka Wyckoff-Multiplicity), the only (!) cif use of 
multiplicity
 2. the multiplicity of the reflection, which means the 
superposition of reflections with the same /d/  (mostly powder 
diffraction) 

 3. the multiplicity of observations, aka redundancy.

    While (a) and (b) are clearly defined, (c) is an arbitrary 
experimental number.


    How from (a) real space symmetry follows (b) in reciprocal space 
(including the epsilon zones, another ‘multiplicity’) is explained 
here 


    https://scripts.iucr.org/cgi-bin/paper?a14080 
 



    and also on page 306 in BMC.

    Too much multiplicity might create duplicity… 

    Cheers, BR

    __ __

    Jon Cooper

    __ __

    On 23 Jun 2020 22:04, "Peat, Tom (Manufacturing, Parkville)" 
mailto:tom.p...@csiro.au>> 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  
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 

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

[Edward A. Berry]

Now can we get rid of all the superfluous disks in our RAID? Or at least not 
replace them when they fail?

On 06/29/2020 06:24 PM, Andreas Förster wrote:

I like to think that the reflections I carefully measured at high multiplicity are not redundant, which the 
dictionary on my computer defines as "not or no longer needed or useful; superfluous" and the 
American Heritage Dictionary as "exceeding what is necessary or natural; superfluous" and 
"needlessly repetitive; verbose".

Please don't use the term Needless repetitivity in your Table 1.  It sends the 
wrong message.  Multiplicity is good.

All best.


Andreas



On Tue, Jun 30, 2020 at 12:03 AM James Holton mailto:jmhol...@lbl.gov>> wrote:

I have found that the use of "redundancy" vs "multiplicity" correlates very well with the 
speaker's favorite processing software.  The Denzo/HKL program scalepack outputs "redundancy", whereas 
scala/aimless and other more Europe-centric programs output "multiplicity".

At least it is not as bad as "intensity", which is so ambiguous as to be 
almost useless as a word on its own.

-James Holton
MAD Scientist

On 6/24/2020 10:27 AM, Bernhard Rupp wrote:


> Oh, and some of us prefer the word 'multiplicity' ;-0

Hmmm…maybe not. ‘Multiplicity’ in crystallography is context sensitive, and 
not uniquely defined. It can refer to 

 1. the position multiplicity (number of equivalent sites per unit cell, 
aka Wyckoff-Multiplicity), the only (!) cif use of multiplicity
 2. the multiplicity of the reflection, which means the superposition of 
reflections with the same /d/  (mostly powder diffraction) 
 3. the multiplicity of observations, aka redundancy.

While (a) and (b) are clearly defined, (c) is an arbitrary experimental 
number.

How from (a) real space symmetry follows (b) in reciprocal space (including 
the epsilon zones, another ‘multiplicity’) is explained here 

https://scripts.iucr.org/cgi-bin/paper?a14080 

 

and also on page 306 in BMC.

Too much multiplicity might create duplicity… 

Cheers, BR

__ __

Jon Cooper

__ __

On 23 Jun 2020 22:04, "Peat, Tom (Manufacturing, Parkville)" mailto:tom.p...@csiro.au>> 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 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 

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

[Bernhard Rupp]

Ah…the rise of the replicants …

 

https://www.youtube.com/watch?v=yWPyRSURYFQ

 

…and don’t forget the and the Voight-Kampff Test results in Table 1.

 

Best, BR

 

From: Pierre Rizkallah  
Sent: Monday, June 29, 2020 15:46
To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK
Subject: RE: [ccp4bb] number of frames to get a full dataset?

 

You’re missing out on a grand opportunity for iconoclasm here. Try out ‘Degree 
of Replication’ or ‘Average Replication’ or ‘Replicate Frequency’. Any other 
offerings!

 

P.

***

Dr Pierre Rizkallah, Senior Lecturer Structural Biology 

Institute of Infection & Immunology, Sir Geraint Evans Building, 

School of Medicine, Heath Campus, Cardiff, CF14 4XN

email: rizkall...@cardiff.ac.uk  
phone: +44 29 2074 2248

http://www.cardiff.ac.uk/people/view/126690-rizkallah-pierre

 

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> On Behalf Of Bernhard Rupp
Sent: 29 June 2020 23:36
To: CCP4BB@JISCMAIL.AC.UK  
Subject: Re: [ccp4bb] number of frames to get a full dataset?

 

I think it is time to escalate that discussion to crystallographic definition 
purists like Massimo or to a logical consistency proponent like Ian who abhors 
definitional vacuum   

 

Cheers, BR

 

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> On Behalf Of Andreas Förster
Sent: Monday, June 29, 2020 15:24
To: CCP4BB@JISCMAIL.AC.UK  
Subject: Re: [ccp4bb] number of frames to get a full dataset?

 

I like to think that the reflections I carefully measured at high multiplicity 
are not redundant, which the dictionary on my computer defines as "not or no 
longer needed or useful; superfluous" and the American Heritage Dictionary as 
"exceeding what is necessary or natural; superfluous" and "needlessly 
repetitive; verbose".

 

Please don't use the term Needless repetitivity in your Table 1.  It sends the 
wrong message.  Multiplicity is good.

 

All best.

 

 

Andreas

 

 

 

On Tue, Jun 30, 2020 at 12:03 AM James Holton mailto:jmhol...@lbl.gov> > wrote:

I have found that the use of "redundancy" vs "multiplicity" correlates very 
well with the speaker's favorite processing software.  The Denzo/HKL program 
scalepack outputs "redundancy", whereas scala/aimless and other more 
Europe-centric programs output "multiplicity".

At least it is not as bad as "intensity", which is so ambiguous as to be almost 
useless as a word on its own.

-James Holton
MAD Scientist

On 6/24/2020 10:27 AM, Bernhard Rupp wrote:

> Oh, and some of us prefer the word 'multiplicity' ;-0

Hmmm…maybe not. ‘Multiplicity’ in crystallography is context sensitive, and not 
uniquely defined. It can refer to 

a.  the position multiplicity (number of equivalent sites per unit cell, 
aka Wyckoff-Multiplicity), the only (!) cif use of multiplicity
b.  the multiplicity of the reflection, which means the superposition of 
reflections with the same d  (mostly powder diffraction) 
c.  the multiplicity of observations, aka redundancy.

While (a) and (b) are clearly defined, (c) is an arbitrary experimental number.

How from (a) real space symmetry follows (b) in reciprocal space (including the 
epsilon zones, another ‘multiplicity’) is explained here 

https://scripts.iucr.org/cgi-bin/paper?a14080 

  

and also on page 306 in BMC.

Too much multiplicity might create duplicity…   

Cheers, BR

 

Jon Cooper

 

On 23 Jun 2020 22:04, "Peat, Tom (Manufacturing, Parkville)" mailto:tom.p...@csiro.au> > 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 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 

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

[Pierre Rizkallah]

You’re missing out on a grand opportunity for iconoclasm here. Try out ‘Degree 
of Replication’ or ‘Average Replication’ or ‘Replicate Frequency’. Any other 
offerings!

P.
***
Dr Pierre Rizkallah, Senior Lecturer Structural Biology
Institute of Infection & Immunology, Sir Geraint Evans Building,
School of Medicine, Heath Campus, Cardiff, CF14 4XN
email: rizkall...@cardiff.ac.ukphone: 
+44 29 2074 2248
http://www.cardiff.ac.uk/people/view/126690-rizkallah-pierre

From: CCP4 bulletin board  On Behalf Of Bernhard Rupp
Sent: 29 June 2020 23:36
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] number of frames to get a full dataset?

I think it is time to escalate that discussion to crystallographic definition 
purists like Massimo or to a logical consistency proponent like Ian who abhors 
definitional vacuum 

Cheers, BR

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Andreas Förster
Sent: Monday, June 29, 2020 15:24
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] number of frames to get a full dataset?

I like to think that the reflections I carefully measured at high multiplicity 
are not redundant, which the dictionary on my computer defines as "not or no 
longer needed or useful; superfluous" and the American Heritage Dictionary as 
"exceeding what is necessary or natural; superfluous" and "needlessly 
repetitive; verbose".

Please don't use the term Needless repetitivity in your Table 1.  It sends the 
wrong message.  Multiplicity is good.

All best.


Andreas



On Tue, Jun 30, 2020 at 12:03 AM James Holton 
mailto:jmhol...@lbl.gov>> wrote:
I have found that the use of "redundancy" vs "multiplicity" correlates very 
well with the speaker's favorite processing software.  The Denzo/HKL program 
scalepack outputs "redundancy", whereas scala/aimless and other more 
Europe-centric programs output "multiplicity".

At least it is not as bad as "intensity", which is so ambiguous as to be almost 
useless as a word on its own.

-James Holton
MAD Scientist
On 6/24/2020 10:27 AM, Bernhard Rupp wrote:
> Oh, and some of us prefer the word 'multiplicity' ;-0
Hmmm…maybe not. ‘Multiplicity’ in crystallography is context sensitive, and not 
uniquely defined. It can refer to

  1.  the position multiplicity (number of equivalent sites per unit cell, aka 
Wyckoff-Multiplicity), the only (!) cif use of multiplicity
  2.  the multiplicity of the reflection, which means the superposition of 
reflections with the same d  (mostly powder diffraction)
  3.  the multiplicity of observations, aka redundancy.
While (a) and (b) are clearly defined, (c) is an arbitrary experimental number.
How from (a) real space symmetry follows (b) in reciprocal space (including the 
epsilon zones, another ‘multiplicity’) is explained here
https://scripts.iucr.org/cgi-bin/paper?a14080
and also on page 306 in BMC.
Too much multiplicity might create duplicity…
Cheers, BR

Jon Cooper

On 23 Jun 2020 22:04, "Peat, Tom (Manufacturing, Parkville)" 
mailto:tom.p...@csiro.au>> 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 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,

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

[Bernhard Rupp]

I think it is time to escalate that discussion to crystallographic definition 
purists like Massimo or to a logical consistency proponent like Ian who abhors 
definitional vacuum   

 

Cheers, BR

 

From: CCP4 bulletin board  On Behalf Of Andreas Förster
Sent: Monday, June 29, 2020 15:24
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] number of frames to get a full dataset?

 

I like to think that the reflections I carefully measured at high multiplicity 
are not redundant, which the dictionary on my computer defines as "not or no 
longer needed or useful; superfluous" and the American Heritage Dictionary as 
"exceeding what is necessary or natural; superfluous" and "needlessly 
repetitive; verbose".

 

Please don't use the term Needless repetitivity in your Table 1.  It sends the 
wrong message.  Multiplicity is good.

 

All best.

 

 

Andreas

 

 

 

On Tue, Jun 30, 2020 at 12:03 AM James Holton mailto:jmhol...@lbl.gov> > wrote:

I have found that the use of "redundancy" vs "multiplicity" correlates very 
well with the speaker's favorite processing software.  The Denzo/HKL program 
scalepack outputs "redundancy", whereas scala/aimless and other more 
Europe-centric programs output "multiplicity".

At least it is not as bad as "intensity", which is so ambiguous as to be almost 
useless as a word on its own.

-James Holton
MAD Scientist

On 6/24/2020 10:27 AM, Bernhard Rupp wrote:

> Oh, and some of us prefer the word 'multiplicity' ;-0

Hmmm…maybe not. ‘Multiplicity’ in crystallography is context sensitive, and not 
uniquely defined. It can refer to 

a.  the position multiplicity (number of equivalent sites per unit cell, 
aka Wyckoff-Multiplicity), the only (!) cif use of multiplicity
b.  the multiplicity of the reflection, which means the superposition of 
reflections with the same d  (mostly powder diffraction) 
c.  the multiplicity of observations, aka redundancy.

While (a) and (b) are clearly defined, (c) is an arbitrary experimental number.

How from (a) real space symmetry follows (b) in reciprocal space (including the 
epsilon zones, another ‘multiplicity’) is explained here 

https://scripts.iucr.org/cgi-bin/paper?a14080 

and also on page 306 in BMC.

Too much multiplicity might create duplicity…   

Cheers, BR

 

Jon Cooper

 

On 23 Jun 2020 22:04, "Peat, Tom (Manufacturing, Parkville)" mailto:tom.p...@csiro.au> > 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 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:

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

[Andreas Förster]

I like to think that the reflections I carefully measured at high
multiplicity are not redundant, which the dictionary on my computer defines
as "not or no longer needed or useful; superfluous" and the American
Heritage Dictionary as "exceeding what is necessary or natural;
superfluous" and "needlessly repetitive; verbose".

Please don't use the term Needless repetitivity in your Table 1.  It sends
the wrong message.  Multiplicity is good.

All best.


Andreas



On Tue, Jun 30, 2020 at 12:03 AM James Holton  wrote:

> I have found that the use of "redundancy" vs "multiplicity" correlates
> very well with the speaker's favorite processing software.  The Denzo/HKL
> program scalepack outputs "redundancy", whereas scala/aimless and other
> more Europe-centric programs output "multiplicity".
>
> At least it is not as bad as "intensity", which is so ambiguous as to be
> almost useless as a word on its own.
>
> -James Holton
> MAD Scientist
>
> On 6/24/2020 10:27 AM, Bernhard Rupp wrote:
>
> > Oh, and some of us prefer the word 'multiplicity' ;-0
>
> Hmmm…maybe not. ‘Multiplicity’ in crystallography is context sensitive,
> and not uniquely defined. It can refer to
>
>1. the position multiplicity (number of equivalent sites per unit
>cell, aka Wyckoff-Multiplicity), the only (!) cif use of multiplicity
>2. the multiplicity of the reflection, which means the superposition
>of reflections with the same *d*  (mostly powder diffraction)
>3. the multiplicity of observations, aka redundancy.
>
> While (a) and (b) are clearly defined, (c) is an arbitrary experimental
> number.
>
> How from (a) real space symmetry follows (b) in reciprocal space
> (including the epsilon zones, another ‘multiplicity’) is explained here
>
> https://scripts.iucr.org/cgi-bin/paper?a14080
>
> and also on page 306 in BMC.
>
> Too much multiplicity might create duplicity…
>
> Cheers, BR
>
>
>
> Jon Cooper
>
>
>
> On 23 Jun 2020 22:04, "Peat, Tom (Manufacturing, Parkville)" <
> tom.p...@csiro.au> 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 
> 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=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] 
>
> [image: facebook]
> 

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

[James Holton]

I have found that the use of "redundancy" vs "multiplicity" correlates 
very well with the speaker's favorite processing software.  The 
Denzo/HKL program scalepack outputs "redundancy", whereas scala/aimless 
and other more Europe-centric programs output "multiplicity".


At least it is not as bad as "intensity", which is so ambiguous as to be 
almost useless as a word on its own.


-James Holton
MAD Scientist

On 6/24/2020 10:27 AM, Bernhard Rupp wrote:


> Oh, and some of us prefer the word 'multiplicity' ;-0

Hmmm…maybe not. ‘Multiplicity’ in crystallography is context 
sensitive, and not uniquely defined. It can refer to


 1. the position multiplicity (number of equivalent sites per unit
cell, aka Wyckoff-Multiplicity), the only (!) cif use of multiplicity
 2. the multiplicity of the reflection, which means the superposition
of reflections with the same /d/  (mostly powder diffraction)
 3. the multiplicity of observations, aka redundancy.

While (a) and (b) are clearly defined, (c) is an arbitrary 
experimental number.


How from (a) real space symmetry follows (b) in reciprocal space 
(including the epsilon zones, another ‘multiplicity’) is explained here


https://scripts.iucr.org/cgi-bin/paper?a14080

and also on page 306 in BMC.

Too much multiplicity might create duplicity…

Cheers, BR

Jon Cooper

On 23 Jun 2020 22:04, "Peat, Tom (Manufacturing, Parkville)" 
mailto:tom.p...@csiro.au>> 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 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




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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.foers...@dectris.com 

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


  

[ccp4bb] A Postdoctoral Position @Albert Einstein College of Medicine, New York

[Syun-Ru Yeh]

Dear all,

A NIH-funded postdoctoral position in structural biology is available 
immediately in the Syun-Ru Yeh Laboratory at Albert Einstein College of 
Medicine, New York. The postdoctoral fellow will take a lead in elucidating 
structure and function relationships in two classes of human immunosuppressive 
proteins, indoleamine 2,3-dioxygenase and tryptophan dioxygenase. The 
postdoctoral fellow will join an exciting program with a focus on biochemistry 
and spectroscopy-guided crystallography.

The successful applicant must have demonstrated experience in chemistry, 
biochemistry, biophysics or closely related fields. Expertise in spectroscopy, 
x-ray crystallography and/or computational modeling is a plus. Applicants 
should provide a CV and a cover letter justifying their suitability and 
interest in the position. Applicants should also arrange to have three letters 
of reference sent to Dr. Syun-Ru Yeh (syun-ru@einsteinmed.org).

Albert Einstein College of Medicine is located in New York in a scenic Bronx 
campus that includes comfortable, affordable housing in an area rich with 
recreation and entertainment. The scientific environment provides outstanding 
research training opportunities.

Best,

Syun-Ru

---
Syun-Ru Yeh, Professor
Department of Physiology and Biophysics
Albert Einstein Collage of Medicine
Bronx, NY 10461



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Re: [ccp4bb] COOT crash

[Denis Rousseau]

From: CCP4 bulletin board  on behalf of Denis Rousseau 

Sent: Monday, June 29, 2020 9:52 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] COOT crash

CAUTION: This email comes from an external source; the attachments and/or links 
may compromise our secure environment. Do not open or click on suspicious 
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Colleagues,

When I try to merge a ligand obtained from the library into my pdb file COOT 
shuts down. I am using COOT 0.8.9.2 downloaded with the latest CCP4. Is there 
an easy fix?

Thanks

Denis Rousseau









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Re: [ccp4bb] COOT crash

[Paul Emsley]

On 29/06/2020 14:52, Denis Rousseau wrote:



When I try to merge a ligand obtained from the library into my pdb 
file COOT shuts down. I am using COOT 0.8.9.2 downloaded with the 
latest CCP4. Is there an easy fix?





Coot 0.8.9.2 is not part of the latest CCP4 (unless you're running 
Windows). If you *are* running windows, a) why didn't you say so and b) 
try this:



https://bernhardcl.github.io/coot/wincoot-releases.html


Paul.






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Re: [ccp4bb] COOT crash

[Denis Rousseau]

Colleagues,

When I try to merge a ligand obtained from the library into my pdb file COOT 
shuts down. I am using COOT 0.8.9.2 downloaded with the latest CCP4. Is there 
an easy fix?

Thanks

Denis Rousseau




From: CCP4 bulletin board  on behalf of Matthew Miller 

Sent: Monday, June 29, 2020 9:06 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Crystallographer position at Eternity Bioscience

CAUTION: This email comes from an external source; the attachments and/or links 
may compromise our secure environment. Do not open or click on suspicious 
emails. Please click on the “Phish Alert” button on the top right of the 
Outlook dashboard to report any suspicious emails.
Structural Biologist Position:

Eternity Bioscience Inc. in Cranbury, New Jersey, USA, is a discovery research 
subsidiary of Jiangsu Hengrui Medicine Co., Ltd. of China. Our mission is to 
deliver high quality and translational preclinical drug candidates for critical 
medical needs. The company is seeking a well-qualified structural biologist to 
join its drug discovery team. The successful candidate will be proficient in 
working independently and collaboratively as part of multidisciplinary project 
teams and have the capacity to quickly adapt to project priority changes.

Job Description:

1.   Perform necessary duties including gene construct design, high throughput 
recombinant protein expression, purification and characterization, target/drug 
complex crystallization screening, remote-controlled (and occasional in-person) 
collection of X-ray diffraction data, and high-resolution atomic structure 
determination.

2.   Deliver high-quality and timely structure data to project teams to enable 
iterative structure-based drug design.

3.   Present the work clearly in internal project meetings.

Basic Requirements:

1.   PhD degree in structural biology, with drug discovery research experience 
desirable.

2.   Proficiency in the workflow from gene construct design to atomic structure 
determination.

3.   Knowledge in structure-based drug design using modern modeling and design 
tools.

4.   Ability to work in a diverse team setting and collaborate effectively on 
complex projects.

5.   Excellent communication, interpersonal, and organizational skills. 
Bilingual in English and Mandarin is a plus.

Prospective candidates are encouraged to visit the following link for more 
information: 
www.eternitybioscience.com.

As a well-funded biotech company, we pay highly competitive salaries and a 
comprehensive benefits package. Interested applicants are encouraged to submit 
their CV to the following email address: 
zhua...@eternitybioscience.com.





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[ccp4bb] Crystallographer position at Eternity Bioscience

[Matthew Miller]

Structural Biologist Position:

Eternity Bioscience Inc. in Cranbury, New Jersey, USA, is a discovery
research subsidiary of Jiangsu Hengrui Medicine Co., Ltd. of China. Our
mission is to deliver high quality and translational preclinical drug
candidates for critical medical needs. The company is seeking a
well-qualified structural biologist to join its drug discovery team. The
successful candidate will be proficient in working independently and
collaboratively as part of multidisciplinary project teams and have the
capacity to quickly adapt to project priority changes.

Job Description:

1.   Perform necessary duties including gene construct design, high
throughput recombinant protein expression, purification and
characterization, target/drug complex crystallization screening,
remote-controlled (and occasional in-person) collection of X-ray
diffraction data, and high-resolution atomic structure determination.

2.   Deliver high-quality and timely structure data to project teams to
enable iterative structure-based drug design.

3.   Present the work clearly in internal project meetings.

Basic Requirements:

1.   PhD degree in structural biology, with drug discovery research
experience desirable.

2.   Proficiency in the workflow from gene construct design to atomic
structure determination.

3.   Knowledge in structure-based drug design using modern modeling and
design tools.

4.   Ability to work in a diverse team setting and collaborate effectively
on complex projects.

5.   Excellent communication, interpersonal, and organizational skills.
Bilingual in English and Mandarin is a plus.

Prospective candidates are encouraged to visit the following link for more
information: www.eternitybioscience.com.

As a well-funded biotech company, we pay highly competitive salaries and a
comprehensive benefits package. Interested applicants are encouraged to
submit their CV to the following email address:
zhua...@eternitybioscience.com.



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Re: [ccp4bb] I cannot download xds

[Peter Naniima]

How about installing it from the terminal. The wiki installation page should 
have the commands that you just have to copy and paste in the terminal.

Sent from Outlook Mobile




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