Re: [ccp4bb] Question about P3, H3 and R3 space groups

[Eleanor Dodson]

Certainly to a mathematician by training P1 is ludicrous - any sensible
being wold set up an 3-D axial system with all axes of equal length and all
angles 90 degrees - I can still remember my disbelief at indexing any
lattice in any other way - E

On Wed, 22 Jul 2020 at 19:18, James Holton  wrote:

> It took me a long time to realize that the rhombohedral system is actually
> a form of centering.  Just like C, F, and I, the R lattice type has extra
> translation-related points.  What is unique about rhombohedral lattices is
> that there are two different kinds of "extra" centers.  In C, all you have
> is an extra point in the middle of one face, and for F it is all the
> faces.  For I it is an extra point at the exact center of the whole cell,
> but for R there are two extra points in the middle of the cell.
>
> The reason there are two is analogous to how an ellipse has two "foci" and
> a circle only has one.  Rhombohedral is just a distortion of a cubic cell:
> grab opposing corners and pull.  The relationship to hexagonal and trigonal
> is clear if you look at a cube down the corner-to-corner diagonal.  It
> looks like a hexagon.  And as it turns out if you re-define the lattice
> centering operations to be "symmetry operators", that are internal to the
> cell rather than relating different cells, you can map rhombohedral onto
> trigonal.  That's where "H" comes from.  Most any high-symmetry space group
> can be mapped onto another by turning centering into a translation-only
> symmetry operator.  However, if you want to follow the proper definition of
> a unit cell, anything that relates the whole lattice back onto itself via
> translation only is not a "symmetry operator", it is a whole-cell shift.
>
> For a lecture once, I made some movies showing how the different centering
> types relate. I make movies because 3D concepts are hard to show in 2D, and
> so why not provide some motion to give perspective? Some of you may find
> them useful in teaching.
> https://bl831.als.lbl.gov/~jamesh/powerpoint/CSHL_spacegroups_2019.pptx
>
> I find it can be more intuitive to students to go in "reverse": start with
> a cubic lattice, which has only one parameter to think about, then
> introduce centering.  After that rotations, and eventually arrive at P1,
> which has six degrees of freedom. Strange how we consider P1 to be the
> "simplest" unit cell, when to the unindoctrinated it certainly is not.
>
> -James Holton
> MAD Scientist
>
>
> On 7/22/2020 9:50 AM, Ian Tickle wrote:
>
>
> The original reference for the H cell is the very first edition of Int.
> Tab.:
>
> Hermann, C. (1935).  Internationale Tabellen zur Bestimmung von
> Kristallstrukturen.  Berlin: Gebrueder Borntraeger.
>
> Cheers
>
> -- Ian
>
>
> On Wed, 22 Jul 2020 at 17:34, Eleanor Dodson <
> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Well - yes . I am a true devotee of doctored cells to match something
>> already in existence in a higher symmetry which has become approximate in
>> some new manifestation! But I hadnt realised there were official versions
>> of doctoring..
>> Eleanor
>>
>> On Wed, 22 Jul 2020 at 16:29, Jeremy Karl Cockcroft 
>> wrote:
>>
>>> Dear Eleanor,
>>> What you say is absolutely spot-on! An H3 cell can be reduced down to
>>> the smaller P3 cell as you pointed out.
>>>
>>> However, sometimes it may be useful to use a larger unit cell. I can't
>>> give an example for trigonal space groups or from protein crystallography,
>>> but in a recent paper, I used a unit cell in C-1 (i.e. a doubled P-1
>>> triclinic cell) as this related to the C-centred monoclinic cell as
>>> exhibited in a higher temperature phase. I could have used P-1, but I knew
>>> that chemists would see the relationship between the phases more easily by
>>> using an enlarged cell. I have done this sort of thing many times, e.g. I
>>> used F2/d for the low temperature phase of DI (HI) many years ago instead
>>> of C2/c as this related to the face-centred cubic form. As I am interested
>>> in phase transitions, I  tabulated a range of space-group settings for
>>> enlarged unit cells on my site.
>>>
>>> I am not sure that this will make the CCP4 list as I am not subscribed
>>> to it - please feel free to echo it on there.
>>> Best regards,
>>> Jeremy Karl.
>>> ***
>>> Dr Jeremy Karl Cockcroft
>>> Department of Chemistry
>>> (University College London)
>>> Christopher Ingold Laboratories
>>> 20 Gordon Street
>>> London WC1H 0AJ
>>> +44 (0) 20 7679 1004 (laboratory)
>>> +44 (0) 7981 875 829 (cell/mobile)
>>> j.k.cockcr...@ucl.ac.uk or jeremyk...@gmail.com
>>> http://img.chem.ucl.ac.uk/www/cockcroft/homepage.htm
>>> ***
>>> 6 Wellington Road
>>> Horsham
>>> West Sussex
>>> RH12 1DD
>>> +44 (0) 1403 256946 (home)
>>> ***
>>>
>>>
>>> On Wed, 22 Jul 2020 at 14:51, Nicholas Keep 

Re: [ccp4bb] Question about P3, H3 and R3 space groups

[James Holton]

It took me a long time to realize that the rhombohedral system is 
actually a form of centering.  Just like C, F, and I, the R lattice type 
has extra translation-related points.  What is unique about rhombohedral 
lattices is that there are two different kinds of "extra" centers.  In 
C, all you have is an extra point in the middle of one face, and for F 
it is all the faces.  For I it is an extra point at the exact center of 
the whole cell, but for R there are two extra points in the middle of 
the cell.


The reason there are two is analogous to how an ellipse has two "foci" 
and a circle only has one.  Rhombohedral is just a distortion of a cubic 
cell: grab opposing corners and pull.  The relationship to hexagonal and 
trigonal is clear if you look at a cube down the corner-to-corner 
diagonal.  It looks like a hexagon.  And as it turns out if you 
re-define the lattice centering operations to be "symmetry operators", 
that are internal to the cell rather than relating different cells, you 
can map rhombohedral onto trigonal. That's where "H" comes from.  Most 
any high-symmetry space group can be mapped onto another by turning 
centering into a translation-only symmetry operator.  However, if you 
want to follow the proper definition of a unit cell, anything that 
relates the whole lattice back onto itself via translation only is not a 
"symmetry operator", it is a whole-cell shift.


For a lecture once, I made some movies showing how the different 
centering types relate. I make movies because 3D concepts are hard to 
show in 2D, and so why not provide some motion to give perspective? Some 
of you may find them useful in teaching.

https://bl831.als.lbl.gov/~jamesh/powerpoint/CSHL_spacegroups_2019.pptx

I find it can be more intuitive to students to go in "reverse": start 
with a cubic lattice, which has only one parameter to think about, then 
introduce centering.  After that rotations, and eventually arrive at P1, 
which has six degrees of freedom. Strange how we consider P1 to be the 
"simplest" unit cell, when to the unindoctrinated it certainly is not.


-James Holton
MAD Scientist


On 7/22/2020 9:50 AM, Ian Tickle wrote:


The original reference for the H cell is the very first edition of 
Int. Tab.:


Hermann, C. (1935).  Internationale Tabellen zur Bestimmung von 
Kristallstrukturen.  Berlin: Gebrueder Borntraeger.


Cheers

-- Ian


On Wed, 22 Jul 2020 at 17:34, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk 
> wrote:


Well - yes . I am a true devotee of doctored cells to match
something already in existence in a higher symmetry which has
become approximate in some new manifestation! But I hadnt realised
there were official versions of doctoring..
Eleanor

On Wed, 22 Jul 2020 at 16:29, Jeremy Karl Cockcroft
mailto:jeremyk...@gmail.com>> wrote:

Dear Eleanor,
What you say is absolutely spot-on! An H3 cell can be reduced
down to the smaller P3 cell as you pointed out.

However, sometimes it may be useful to use a larger unit cell.
I can't give an example for trigonal space groups or from
protein crystallography, but in a recent paper, I used a unit
cell in C-1 (i.e. a doubled P-1 triclinic cell) as this
related to the C-centred monoclinic cell as exhibited in a
higher temperature phase. I could have used P-1, but I knew
that chemists would see the relationship between the phases
more easily by using an enlarged cell. I have done this sort
of thing many times, e.g. I used F2/d for the low temperature
phase of DI (HI) many years ago instead of C2/c as this
related to the face-centred cubic form. As I am interested in
phase transitions, I  tabulated a range of space-group
settings for enlarged unit cells on my site.

I am not sure that this will make the CCP4 list as I am not
subscribed to it - please feel free to echo it on there.
Best regards,
Jeremy Karl.
***
Dr Jeremy Karl Cockcroft
Department of Chemistry
(University College London)
Christopher Ingold Laboratories
20 Gordon Street
London WC1H 0AJ
+44 (0) 20 7679 1004 (laboratory)
+44 (0) 7981 875 829 (cell/mobile)
j.k.cockcr...@ucl.ac.uk  or
jeremyk...@gmail.com 
http://img.chem.ucl.ac.uk/www/cockcroft/homepage.htm
***
6 Wellington Road
Horsham
West Sussex
RH12 1DD
+44 (0) 1403 256946 (home)
***


On Wed, 22 Jul 2020 at 14:51, Nicholas Keep
mailto:n.k...@mail.cryst.bbk.ac.uk>> 

Re: [ccp4bb] Question about P3, H3 and R3 space groups

[Ian Tickle]

The original reference for the H cell is the very first edition of Int.
Tab.:

Hermann, C. (1935).  Internationale Tabellen zur Bestimmung von
Kristallstrukturen.  Berlin: Gebrueder Borntraeger.

Cheers

-- Ian


On Wed, 22 Jul 2020 at 17:34, Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> Well - yes . I am a true devotee of doctored cells to match something
> already in existence in a higher symmetry which has become approximate in
> some new manifestation! But I hadnt realised there were official versions
> of doctoring..
> Eleanor
>
> On Wed, 22 Jul 2020 at 16:29, Jeremy Karl Cockcroft 
> wrote:
>
>> Dear Eleanor,
>> What you say is absolutely spot-on! An H3 cell can be reduced down to the
>> smaller P3 cell as you pointed out.
>>
>> However, sometimes it may be useful to use a larger unit cell. I can't
>> give an example for trigonal space groups or from protein crystallography,
>> but in a recent paper, I used a unit cell in C-1 (i.e. a doubled P-1
>> triclinic cell) as this related to the C-centred monoclinic cell as
>> exhibited in a higher temperature phase. I could have used P-1, but I knew
>> that chemists would see the relationship between the phases more easily by
>> using an enlarged cell. I have done this sort of thing many times, e.g. I
>> used F2/d for the low temperature phase of DI (HI) many years ago instead
>> of C2/c as this related to the face-centred cubic form. As I am interested
>> in phase transitions, I  tabulated a range of space-group settings for
>> enlarged unit cells on my site.
>>
>> I am not sure that this will make the CCP4 list as I am not subscribed to
>> it - please feel free to echo it on there.
>> Best regards,
>> Jeremy Karl.
>> ***
>> Dr Jeremy Karl Cockcroft
>> Department of Chemistry
>> (University College London)
>> Christopher Ingold Laboratories
>> 20 Gordon Street
>> London WC1H 0AJ
>> +44 (0) 20 7679 1004 (laboratory)
>> +44 (0) 7981 875 829 (cell/mobile)
>> j.k.cockcr...@ucl.ac.uk or jeremyk...@gmail.com
>> http://img.chem.ucl.ac.uk/www/cockcroft/homepage.htm
>> ***
>> 6 Wellington Road
>> Horsham
>> West Sussex
>> RH12 1DD
>> +44 (0) 1403 256946 (home)
>> ***
>>
>>
>> On Wed, 22 Jul 2020 at 14:51, Nicholas Keep 
>> wrote:
>>
>>>
>>>
>>>
>>>  Forwarded Message 
>>> Subject: Re: [ccp4bb] Question about P3, H3 and R3 space groups
>>> Date: Wed, 22 Jul 2020 14:41:27 +0100
>>> From: Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
>>> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
>>> Reply-To: Eleanor Dodson 
>>> 
>>> To: CCP4BB@JISCMAIL.AC.UK
>>>
>>> But surely P3 symmetry ' cell ( a,a,c 90 90 120) with origin shifts
>>> (⅓,⅔,0), +(⅔,⅓,0) can just be indexed as P3 with
>>> cell (a/sqrt(3), a/sqrt(3), c, 90 90 120) ??
>>> Eleanor
>>>
>>> On Wed, 22 Jul 2020 at 14:32, Nicholas Keep 
>>> wrote:
>>>
 I have an answer from Jeremy Cockcroft the author of the 'Birkbeck'
 Tables. Actually Jeremy has been at UCL for a decade or so and they are
 hosted from their

 Nick

 In answer to the question regarding the use of R and H for trigonal
 space groups, the letters refer to two distinct types of lattice centring
 symmetry operation, namely +(⅓,⅔,⅔), +(⅔,⅓,⅓) and +(⅓,⅔,0), +(⅔,⅓,0),
 respectively. For the subset of rhombohedral space groups, the symbol R
 should always be used.  When the alternative unit cell with a=b=c and
 α=β=γ is chosen, this cell corresponds to a primitive Bravais lattice, but
 the label P is not used as this would result in confusion with
 non-rhombohedral space groups.  (The choice of symmetry operators for
 rhombohedral space groups is wholly dependent of the choice of unit cell,
 i.e. hexagonal versus rhombohedral, so there is no ambiguity if the unit
 cell is specified.)

 For the non-rhombohedral space groups, it may occasionally be
 convenient to choose a larger H-centred unit cell that is not the usual
 primitive P one.  (The use of larger unit cells is quite common for
 systems that undergo phase transformations as it may enable the
 crystallographer to keep the contents of the unit cell the same in both
 phases.)  Note that the use of an H-centred lattice switches the order
 of the symmetry elements in these space group symbols, e.g. P312 becomes
 H321.

 I am not aware of any changes to this convention, which I believe has a
 long history.  However, it is possible that the letter H has been used
 unwittingly for other purposes.

 Jeremy Karl Cockcroft


 --

 NOTE NEW PHONE NUMBER JULY 2020

 Prof Nicholas H. Keep
 Executive Dean of School of Science
 Professor of Biomolecular Science
 Crystallography, Institute for Structural and 

Re: [ccp4bb] Question about P3, H3 and R3 space groups

[Eleanor Dodson]

Well - yes . I am a true devotee of doctored cells to match something
already in existence in a higher symmetry which has become approximate in
some new manifestation! But I hadnt realised there were official versions
of doctoring..
Eleanor

On Wed, 22 Jul 2020 at 16:29, Jeremy Karl Cockcroft 
wrote:

> Dear Eleanor,
> What you say is absolutely spot-on! An H3 cell can be reduced down to the
> smaller P3 cell as you pointed out.
>
> However, sometimes it may be useful to use a larger unit cell. I can't
> give an example for trigonal space groups or from protein crystallography,
> but in a recent paper, I used a unit cell in C-1 (i.e. a doubled P-1
> triclinic cell) as this related to the C-centred monoclinic cell as
> exhibited in a higher temperature phase. I could have used P-1, but I knew
> that chemists would see the relationship between the phases more easily by
> using an enlarged cell. I have done this sort of thing many times, e.g. I
> used F2/d for the low temperature phase of DI (HI) many years ago instead
> of C2/c as this related to the face-centred cubic form. As I am interested
> in phase transitions, I  tabulated a range of space-group settings for
> enlarged unit cells on my site.
>
> I am not sure that this will make the CCP4 list as I am not subscribed to
> it - please feel free to echo it on there.
> Best regards,
> Jeremy Karl.
> ***
> Dr Jeremy Karl Cockcroft
> Department of Chemistry
> (University College London)
> Christopher Ingold Laboratories
> 20 Gordon Street
> London WC1H 0AJ
> +44 (0) 20 7679 1004 (laboratory)
> +44 (0) 7981 875 829 (cell/mobile)
> j.k.cockcr...@ucl.ac.uk or jeremyk...@gmail.com
> http://img.chem.ucl.ac.uk/www/cockcroft/homepage.htm
> ***
> 6 Wellington Road
> Horsham
> West Sussex
> RH12 1DD
> +44 (0) 1403 256946 (home)
> ***
>
>
> On Wed, 22 Jul 2020 at 14:51, Nicholas Keep 
> wrote:
>
>>
>>
>>
>>  Forwarded Message 
>> Subject: Re: [ccp4bb] Question about P3, H3 and R3 space groups
>> Date: Wed, 22 Jul 2020 14:41:27 +0100
>> From: Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
>> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
>> Reply-To: Eleanor Dodson 
>> 
>> To: CCP4BB@JISCMAIL.AC.UK
>>
>> But surely P3 symmetry ' cell ( a,a,c 90 90 120) with origin shifts
>> (⅓,⅔,0), +(⅔,⅓,0) can just be indexed as P3 with
>> cell (a/sqrt(3), a/sqrt(3), c, 90 90 120) ??
>> Eleanor
>>
>> On Wed, 22 Jul 2020 at 14:32, Nicholas Keep 
>> wrote:
>>
>>> I have an answer from Jeremy Cockcroft the author of the 'Birkbeck'
>>> Tables. Actually Jeremy has been at UCL for a decade or so and they are
>>> hosted from their
>>>
>>> Nick
>>>
>>> In answer to the question regarding the use of R and H for trigonal
>>> space groups, the letters refer to two distinct types of lattice centring
>>> symmetry operation, namely +(⅓,⅔,⅔), +(⅔,⅓,⅓) and +(⅓,⅔,0), +(⅔,⅓,0),
>>> respectively. For the subset of rhombohedral space groups, the symbol R
>>> should always be used.  When the alternative unit cell with a=b=c and
>>> α=β=γ is chosen, this cell corresponds to a primitive Bravais lattice, but
>>> the label P is not used as this would result in confusion with
>>> non-rhombohedral space groups.  (The choice of symmetry operators for
>>> rhombohedral space groups is wholly dependent of the choice of unit cell,
>>> i.e. hexagonal versus rhombohedral, so there is no ambiguity if the unit
>>> cell is specified.)
>>>
>>> For the non-rhombohedral space groups, it may occasionally be convenient
>>> to choose a larger H-centred unit cell that is not the usual primitive P
>>> one.  (The use of larger unit cells is quite common for systems that
>>> undergo phase transformations as it may enable the crystallographer to keep
>>> the contents of the unit cell the same in both phases.)  Note that the
>>> use of an H-centred lattice switches the order of the symmetry elements in
>>> these space group symbols, e.g. P312 becomes H321.
>>>
>>> I am not aware of any changes to this convention, which I believe has a
>>> long history.  However, it is possible that the letter H has been used
>>> unwittingly for other purposes.
>>>
>>> Jeremy Karl Cockcroft
>>>
>>>
>>> --
>>>
>>> NOTE NEW PHONE NUMBER JULY 2020
>>>
>>> Prof Nicholas H. Keep
>>> Executive Dean of School of Science
>>> Professor of Biomolecular Science
>>> Crystallography, Institute for Structural and Molecular Biology,
>>> Department of Biological Sciences
>>> Birkbeck,  University of London,
>>> Malet Street,
>>> Bloomsbury
>>> LONDON
>>> WC1E 7HX
>>>
>>> Office G54a
>>>
>>> Dean Email; scid...@bbk.ac.uk
>>> Dept email n.k...@mail.cryst.bbk.ac.uk
>>> Telephone 020-3926-3475  (Will contact me at home if working as well as my 
>>> office)
>>>
>>> If you want to access me in person you have to come to the crystallography 
>>> entrance
>>> 

Re: [ccp4bb] Question about P3, H3 and R3 space groups

[Ian Tickle]

The important take-home message in this excellent article is surely the
conclusion:

"The significant amount of programming effort and user frustration caused
by the H3 and H32 space-group symbols is a good example of how time can be
lost by not adopting long-established standards.  This is not meant to
suggest revising the PDB as this would certainly only serve to increase the
confusion.  Rather, it is a salient reminder to the entire crystallographic
methods-developer community to avoid ad-hoc approaches whenever possible.
Ever more automated systems require highly reliable components and
unambiguous semantics.  The effort spent early in ensuring reliability and
clarity is usually rewarded many times over as time passes."

... and I would add adherence to established conventions.

Cheers

-- Ian


On Wed, 22 Jul 2020 at 14:42, Gildea, Richard (DLSLtd,RAL,LSCI) <
richard.gil...@diamond.ac.uk> wrote:

> There is a useful article in Computational Crystallography Newsletter
> 2011, 2, 12-14 that gives some background into the issues surrounding the
> H3 and H32 symbols:
>
>  "Fuzzy space group symbols: H3 and H32
>
> http://www.phenix-online.org/newsletter/CCN_2011_01.pdf
>
> Cheers,
>
> Richard
>
> Dr Richard Gildea
> Data Analysis Scientist
> Tel: +441235 77 8078
>
> Diamond Light Source Ltd.
> Diamond House
> Harwell Science & Innovation Campus
> Didcot
> Oxfordshire
> OX11 0DE
> --
> *From:* CCP4 bulletin board  on behalf of David
> Vizarraga Revuelto 
> *Sent:* 22 July 2020 12:20
> *To:* CCP4BB@JISCMAIL.AC.UK 
> *Subject:* [ccp4bb] Question about P3, H3 and R3 space groups
>
> Dear all,
>
> Let me ask a question about the P3,H3, R3 space group annotations.
> I had the idea that H3 was the recommended annotation for the hexagonal
> representation of R3 (space group number 146). However, in the Birbeck
> space groups web page (attached) H3 is associated with the space group
> number 143 corresponding to P3. Similarly for all the other H groups
> assigned in the page. Moreover in the web page none of the R space groups
> is assigned to an H annotation.
>
> H3 corresponds to 143 or  to 146?
> Is there a space group 154 annotated as H32 1 2?
>
> Many thanks.
>
>
>
> "Note that the figure showing the relationship between primitive and
> R-centred rhomohedral cells with hexagonal axes is clickable
>
> Rhombohedral with Hexagonal axes
> 146. *R* 3  148. *R* -3
>  155. *R* 3 2
>  160. *R* 3 *m*
>  161. *R* 3 *c*
>  166. *R* -3 *m*
> 
> 167. *R* -3 *c* 
> H-centred Trigonal
> 143. *H* 3  144. *H* 31
>  145. *H* 32
>  147. *H* -3
>  149. *H* 3 2 1
>  150. *H* 3 1 2
> 
> 151. *H* 31 2 1  152. *H*
>  31 1 2  153. *H* 32 2 1
>  154. *H* 32 1 2
>  156. *H* 3 1 *m*
>  157. *H* 3 *m* 1
> 
> 158. *H* 3 1 *c*  159. *H*
>  3 *c* 1  162. *H* -3 *m*
>  1  163. *H* -3 *c* 1
>  164. *H* -3 1 *m*
>  165. *H* -3 1 *c*
> 
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>
>
> --
>
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Re: [ccp4bb] Question about P3, H3 and R3 space groups

[LMB]

When I was writing Pointless I had to do all sorts of kludgy things to cope 
with the different “conventions” used by ccp4, clipper and cctbx libraries, 
scalepack etc.  The PDB should have stuck to established conventions to avoid 
confusion. And lots of people for some reason seem not to like space groups 
like I2 and P 2 21 21

Phil

Sent from my iPad

> On 22 Jul 2020, at 14:42, Gildea, Richard (DLSLtd,RAL,LSCI) 
>  wrote:
> 
> 
> There is a useful article in Computational Crystallography Newsletter 2011, 
> 2, 12-14 that gives some background into the issues surrounding the H3 and 
> H32 symbols:
> 
>  "Fuzzy space group symbols: H3 and H32
> 
> http://www.phenix-online.org/newsletter/CCN_2011_01.pdf
> 
> Cheers,
> 
> Richard
> 
> Dr Richard Gildea
> Data Analysis Scientist
> Tel: +441235 77 8078
>  
> Diamond Light Source Ltd.
> Diamond House
> Harwell Science & Innovation Campus
> Didcot
> Oxfordshire
> OX11 0DE
> From: CCP4 bulletin board  on behalf of David 
> Vizarraga Revuelto 
> Sent: 22 July 2020 12:20
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: [ccp4bb] Question about P3, H3 and R3 space groups
>  
> Dear all,
> 
> Let me ask a question about the P3,H3, R3 space group annotations. 
> I had the idea that H3 was the recommended annotation for the hexagonal 
> representation of R3 (space group number 146). However, in the Birbeck space 
> groups web page (attached) H3 is associated with the space group number 143 
> corresponding to P3. Similarly for all the other H groups assigned in the 
> page. Moreover in the web page none of the R space groups is assigned to an H 
> annotation.
> 
> H3 corresponds to 143 or  to 146?
> Is there a space group 154 annotated as H32 1 2?
> 
> Many thanks.
> 
>   
> 
> "Note that the figure showing the relationship between primitive and 
> R-centred rhomohedral cells with hexagonal axes is clickable
> Rhombohedral with Hexagonal axes
> 146. R 3  148. R -3   155. R 3 2  160. R 3 m  161. R 3 c  
> 166. R -3 m
> 167. R -3 c
> H-centred Trigonal
> 143. H 3  144. H 31   145. H 32   147. H -3   149. H 3 2 1
> 150. H 3 1 2
> 151. H 31 2 1 152. H 31 1 2   153. H 32 2 1   154. H 32 1 2   156. H 3 1 m
> 157. H 3 m 1
> 158. H 3 1 c  159. H 3 c 1162. H -3 m 1   163. H -3 c 1   164. H -3 1 m   
> 165. H -3 1 c
> 
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Re: [ccp4bb] Question about P3, H3 and R3 space groups

[Ian Tickle]

Hi Eleanor

H3 #143 is (and always has been) a triply-primitive cell setting of P3.

http://img.chem.ucl.ac.uk/sgp/large/143bz1.htm

Cheers

-- Ian


On Wed, 22 Jul 2020 at 14:42, Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> But surely P3 symmetry ' cell ( a,a,c 90 90 120) with origin shifts
> (⅓,⅔,0), +(⅔,⅓,0) can just be indexed as P3 with
> cell (a/sqrt(3), a/sqrt(3), c, 90 90 120) ??
> Eleanor
>
> On Wed, 22 Jul 2020 at 14:32, Nicholas Keep 
> wrote:
>
>> I have an answer from Jeremy Cockcroft the author of the 'Birkbeck'
>> Tables. Actually Jeremy has been at UCL for a decade or so and they are
>> hosted from their
>>
>> Nick
>>
>> In answer to the question regarding the use of R and H for trigonal space
>> groups, the letters refer to two distinct types of lattice centring
>> symmetry operation, namely +(⅓,⅔,⅔), +(⅔,⅓,⅓) and +(⅓,⅔,0), +(⅔,⅓,0),
>> respectively. For the subset of rhombohedral space groups, the symbol R
>> should always be used.  When the alternative unit cell with a=b=c and
>> α=β=γ is chosen, this cell corresponds to a primitive Bravais lattice, but
>> the label P is not used as this would result in confusion with
>> non-rhombohedral space groups.  (The choice of symmetry operators for
>> rhombohedral space groups is wholly dependent of the choice of unit cell,
>> i.e. hexagonal versus rhombohedral, so there is no ambiguity if the unit
>> cell is specified.)
>>
>> For the non-rhombohedral space groups, it may occasionally be convenient
>> to choose a larger H-centred unit cell that is not the usual primitive P
>> one.  (The use of larger unit cells is quite common for systems that
>> undergo phase transformations as it may enable the crystallographer to keep
>> the contents of the unit cell the same in both phases.)  Note that the
>> use of an H-centred lattice switches the order of the symmetry elements in
>> these space group symbols, e.g. P312 becomes H321.
>>
>> I am not aware of any changes to this convention, which I believe has a
>> long history.  However, it is possible that the letter H has been used
>> unwittingly for other purposes.
>>
>> Jeremy Karl Cockcroft
>>
>>
>> --
>>
>> NOTE NEW PHONE NUMBER JULY 2020
>>
>> Prof Nicholas H. Keep
>> Executive Dean of School of Science
>> Professor of Biomolecular Science
>> Crystallography, Institute for Structural and Molecular Biology,
>> Department of Biological Sciences
>> Birkbeck,  University of London,
>> Malet Street,
>> Bloomsbury
>> LONDON
>> WC1E 7HX
>>
>> Office G54a
>>
>> Dean Email;  scid...@bbk.ac.uk
>> Dept email n.k...@mail.cryst.bbk.ac.uk
>> Telephone 020-3926-3475  (Will contact me at home if working as well as my 
>> office)
>>
>> If you want to access me in person you have to come to the crystallography 
>> entrance
>> and ring me or the department office from the internal phone by the door
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Question about P3, H3 and R3 space groups

[Eleanor Dodson]

But surely P3 symmetry ' cell ( a,a,c 90 90 120) with origin shifts
(⅓,⅔,0), +(⅔,⅓,0) can just be indexed as P3 with
cell (a/sqrt(3), a/sqrt(3), c, 90 90 120) ??
Eleanor

On Wed, 22 Jul 2020 at 14:32, Nicholas Keep 
wrote:

> I have an answer from Jeremy Cockcroft the author of the 'Birkbeck'
> Tables. Actually Jeremy has been at UCL for a decade or so and they are
> hosted from their
>
> Nick
>
> In answer to the question regarding the use of R and H for trigonal space
> groups, the letters refer to two distinct types of lattice centring
> symmetry operation, namely +(⅓,⅔,⅔), +(⅔,⅓,⅓) and +(⅓,⅔,0), +(⅔,⅓,0),
> respectively. For the subset of rhombohedral space groups, the symbol R
> should always be used.  When the alternative unit cell with a=b=c and
> α=β=γ is chosen, this cell corresponds to a primitive Bravais lattice, but
> the label P is not used as this would result in confusion with
> non-rhombohedral space groups.  (The choice of symmetry operators for
> rhombohedral space groups is wholly dependent of the choice of unit cell,
> i.e. hexagonal versus rhombohedral, so there is no ambiguity if the unit
> cell is specified.)
>
> For the non-rhombohedral space groups, it may occasionally be convenient
> to choose a larger H-centred unit cell that is not the usual primitive P
> one.  (The use of larger unit cells is quite common for systems that
> undergo phase transformations as it may enable the crystallographer to keep
> the contents of the unit cell the same in both phases.)  Note that the
> use of an H-centred lattice switches the order of the symmetry elements in
> these space group symbols, e.g. P312 becomes H321.
>
> I am not aware of any changes to this convention, which I believe has a
> long history.  However, it is possible that the letter H has been used
> unwittingly for other purposes.
>
> Jeremy Karl Cockcroft
>
>
> --
>
> NOTE NEW PHONE NUMBER JULY 2020
>
> Prof Nicholas H. Keep
> Executive Dean of School of Science
> Professor of Biomolecular Science
> Crystallography, Institute for Structural and Molecular Biology,
> Department of Biological Sciences
> Birkbeck,  University of London,
> Malet Street,
> Bloomsbury
> LONDON
> WC1E 7HX
>
> Office G54a
>
> Dean Email;   scid...@bbk.ac.uk
> Dept email n.k...@mail.cryst.bbk.ac.uk
> Telephone 020-3926-3475  (Will contact me at home if working as well as my 
> office)
>
> If you want to access me in person you have to come to the crystallography 
> entrance
> and ring me or the department office from the internal phone by the door
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Question about P3, H3 and R3 space groups

[Gildea, Richard (DLSLtd,RAL,LSCI)]

There is a useful article in Computational Crystallography Newsletter 2011, 2, 
12-14 that gives some background into the issues surrounding the H3 and H32 
symbols:

 "Fuzzy space group symbols: H3 and H32

http://www.phenix-online.org/newsletter/CCN_2011_01.pdf

Cheers,

Richard

Dr Richard Gildea
Data Analysis Scientist
Tel: +441235 77 8078

Diamond Light Source Ltd.
Diamond House
Harwell Science & Innovation Campus
Didcot
Oxfordshire
OX11 0DE

From: CCP4 bulletin board  on behalf of David Vizarraga 
Revuelto 
Sent: 22 July 2020 12:20
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Question about P3, H3 and R3 space groups

Dear all,

Let me ask a question about the P3,H3, R3 space group annotations.
I had the idea that H3 was the recommended annotation for the hexagonal 
representation of R3 (space group number 146). However, in the Birbeck space 
groups web page (attached) H3 is associated with the space group number 143 
corresponding to P3. Similarly for all the other H groups assigned in the page. 
Moreover in the web page none of the R space groups is assigned to an H 
annotation.

H3 corresponds to 143 or  to 146?
Is there a space group 154 annotated as H32 1 2?

Many thanks.



"Note that the figure showing the relationship between primitive and R-centred 
rhomohedral cells with hexagonal axes is clickable

Rhombohedral with Hexagonal axes
146. R 3148. R 
-3   155. R 3 
2  160. R 3 
m  161. R 3 
c  166. R -3 
m
167. R -3 c
H-centred Trigonal
143. H 3144. H 
31   145. H 
32   147. H 
-3   149. H 3 2 
1150. H 3 1 
2
151. H 31 2 1   152. H 31 1 
2   153. H 32 2 
1   154. H 32 1 
2   156. H 3 1 
m157. H 3 m 
1
158. H 3 1 c159. H 3 c 
1162. H -3 m 
1   163. H -3 c 
1   164. H -3 1 
m   165. H -3 1 
c



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[ccp4bb] Question about P3, H3 and R3 space groups

[Nicholas Keep]

I have an answer from Jeremy Cockcroft the author of the 'Birkbeck' 
Tables. Actually Jeremy has been at UCL for a decade or so and they are 
hosted from their


Nick

In answer to the question regarding the use of R and H for trigonal 
space groups, the letters refer to two distinct types of lattice 
centring symmetry operation, namely +(⅓,⅔,⅔), +(⅔,⅓,⅓) and +(⅓,⅔,0), 
+(⅔,⅓,0), respectively. For the subset of rhombohedral space groups, the 
symbol R should always be used.When the alternative unit cell with a=b=c 
and α=β=γ is chosen, this cell corresponds to a primitive Bravais 
lattice, but the label P is not used as this would result in confusion 
with non-rhombohedral space groups. (The choice of symmetry operators 
for rhombohedral space groups is wholly dependent of the choice of unit 
cell, i.e. hexagonal versus rhombohedral, so there is no ambiguity if 
the unit cell is specified.)


For the non-rhombohedral space groups, it may occasionally be convenient 
to choose a larger H-centred unit cell that is not the usual primitive P 
one.(The use of larger unit cells is quite common for systems that 
undergo phase transformations as it may enable the crystallographer to 
keep the contents of the unit cell the same in both phases.)Note that 
the use of an H-centred lattice switches the order of the symmetry 
elements in these space group symbols, e.g. P312 becomes H321.


I am not aware of any changes to this convention, which I believe has a 
long history. However, it is possible that the letter H has been used 
unwittingly for other purposes.


Jeremy Karl Cockcroft


--

NOTE NEW PHONE NUMBER JULY 2020

Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

Office G54a

Dean Email; scid...@bbk.ac.uk
Dept email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-3926-3475  (Will contact me at home if working as well as my 
office)

If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door




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[ccp4bb] Two postdoctoral research positions in structural and biophysical characterization of the human complement system

[Harma Brondijk]

 


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Re: [ccp4bb] Question about P3, H3 and R3 space groups

[George Sheldrick]

This is precisely why SHELX always used the coordinates of the general 
position (LATT+SYMM) to define the space group rather than a name or number.


George

On 22/07/20 14:15, Ian Tickle wrote:


Hi David

The problem is that the PDB incorrectly used the H lattice symbol 
(without consulting any crystallographers AFAIK) for the hexagonal 
R-centred cell when it had already been in use for many years for the 
triply-primitive setting of P3, so now we have this confusion between 
MX & XRD/powder usage. It's probably now too late to do anything about 
it.  Simply put: in XRD/powder software H3 is #143 as originally 
specified in IUCr Int. Tab.; in MX software H3 is #146.


What should have been used are the Hermann-Mauguin symbols for the two 
R3 cells: R3:r and R3:h (see the syminfo.lib file).


This is a constant confusion between the standard symbol (i.e. one of 
the 230 space-groups in their standard settings) and the setting 
symbols.  Other common examples are space group #5 with standard 
symbol C2 which has a number of alternative settings A121, B112, C121, 
I121 etc., and standard symbol P21212 with settings P22121, P21221 and 
P21212, all of which are equally valid.  The conventional IUCr choice 
of setting is determined by the relative cell lengths (as far as 
possible c >= b >= a) and the cell angle (which in monoclinic cells 
should always be chosen >= 90 and closest to 90).  In practical 
crystallography it's the setting symbol that matters; the standard 
symbol is relevant only for classification, so in practice only the 
setting symbols should be used/


Cheers

--  Ian


On Wed, 22 Jul 2020 at 12:32, David Vizarraga Revuelto 
mailto:dvr...@ibmb.csic.es>> wrote:


Dear all,

Let me ask a question about the P3,H3, R3 space group annotations.
I had the idea that H3 was the recommended annotation for the
hexagonal representation of R3 (space group number 146). However,
in the Birbeck space groups web page (attached) H3 is associated
with the space group number 143 corresponding to P3. Similarly for
all the other H groups assigned in the page. Moreover in the
web page none of the R space groups is assigned to an H annotation.

H3 corresponds to 143 or  to 146?
Is there a space group 154 annotated as H32 1 2?

Many thanks.



"Note that the figure showing the relationship between primitive
and R-centred rhomohedral cells with hexagonal axes is clickable

Rhombohedral with Hexagonal axes
146. /R/ 3    148.
/R/ -3    155.
/R/ 3 2   160.
/R/ 3 /m/ 161.
/R/ 3 /c/ 166.
/R/ -3 /m/ 
167. /R/ -3 /c/ 
  
H-centred Trigonal
143. /H/ 3    144.
/H/ 3_1   145.
/H/ 3_2   147.
/H/ -3    149.
/H/ 3 2 1 150.
/H/ 3 1 2 
151. /H/ 3_1  2 1 
152. /H/ 3_1  1 2
  153. /H/ 3_2  2
1 154. /H/ 3_2
 1 2  156. /H/ 3
1 /m/ 157. /H/ 3
/m/ 1 
158. /H/ 3 1 /c/ 
159. /H/ 3 /c/ 1 
162. /H/ -3 /m/ 1 
163. /H/ -3 /c/ 1
  164. /H/ -3 1
/m/   165.
/H/ -3 1 /c/ 




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This message was 

Re: [ccp4bb] Question about P3, H3 and R3 space groups

[Ian Tickle]

Hi David

The problem is that the PDB incorrectly used the H lattice symbol (without
consulting any crystallographers AFAIK) for the hexagonal R-centred cell
when it had already been in use for many years for the triply-primitive
setting of P3, so now we have this confusion between MX & XRD/powder
usage.  It's probably now too late to do anything about it.  Simply put: in
XRD/powder software H3 is #143 as originally specified in IUCr Int. Tab.;
in MX software H3 is #146.

What should have been used are the Hermann-Mauguin symbols for the two R3
cells: R3:r and R3:h (see the syminfo.lib file).

This is a constant confusion between the standard symbol (i.e. one of the
230 space-groups in their standard settings) and the setting symbols.
Other common examples are space group #5 with standard symbol C2 which has
a number of alternative settings A121, B112, C121, I121 etc., and standard
symbol P21212 with settings P22121, P21221 and P21212, all of which are
equally valid.  The conventional IUCr choice of setting is determined by
the relative cell lengths (as far as possible c >= b >= a) and the cell
angle (which in monoclinic cells should always be chosen >= 90 and closest
to 90).  In practical crystallography it's the setting symbol that matters;
the standard symbol is relevant only for classification, so in practice
only the setting symbols should be used/

Cheers

--  Ian


On Wed, 22 Jul 2020 at 12:32, David Vizarraga Revuelto 
wrote:

> Dear all,
>
> Let me ask a question about the P3,H3, R3 space group annotations.
> I had the idea that H3 was the recommended annotation for the hexagonal
> representation of R3 (space group number 146). However, in the Birbeck
> space groups web page (attached) H3 is associated with the space group
> number 143 corresponding to P3. Similarly for all the other H groups
> assigned in the page. Moreover in the web page none of the R space groups
> is assigned to an H annotation.
>
> H3 corresponds to 143 or  to 146?
> Is there a space group 154 annotated as H32 1 2?
>
> Many thanks.
>
>
>
> "Note that the figure showing the relationship between primitive and
> R-centred rhomohedral cells with hexagonal axes is clickable
>
> Rhombohedral with Hexagonal axes
> 146. *R* 3  148. *R* -3
>  155. *R* 3 2
>  160. *R* 3 *m*
>  161. *R* 3 *c*
>  166. *R* -3 *m*
> 
> 167. *R* -3 *c* 
> H-centred Trigonal
> 143. *H* 3  144. *H* 31
>  145. *H* 32
>  147. *H* -3
>  149. *H* 3 2 1
>  150. *H* 3 1 2
> 
> 151. *H* 31 2 1  152. *H*
>  31 1 2  153. *H* 32 2 1
>  154. *H* 32 1 2
>  156. *H* 3 1 *m*
>  157. *H* 3 *m* 1
> 
> 158. *H* 3 1 *c*  159. *H*
>  3 *c* 1  162. *H* -3 *m*
>  1  163. *H* -3 *c* 1
>  164. *H* -3 1 *m*
>  165. *H* -3 1 *c*
> 
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Question about P3, H3 and R3 space groups

[Eleanor Dodson]

This does seem confusing!
Maybe the International tables have changed, but in my copy spacegroup 143
is labelled P3

Spacegroup 146 is equivalent to P3 with translations 1/3,2/3.2/3  and
2/3,1/3,1/3 is called rhombehedral
This can be indexed with.  "a=b=c in the rhombehedral setting" and labelled
R3, but it is usually and more conveniently indexed in " the hexagonal
setting with a=b, and gamma = 120", and with the translations to alternate
origins 1/3,2/3.2/3  and 2/3,1/3,1/3 labeled R 3:H
See this  extract from $CLIBD/syminfo.lib

  begin_spacegroup

number  146

basisop x,y,z

symbol ccp4 146

symbol Hall ' R 3'

symbol xHM  'R 3 :H'

symbol old  'H 3'

symbol laue '-P 3' '-3'

symbol patt '-R 3' '-3'

symbol pgrp ' P 3' '3'

hklasu ccp4 '(h>=0 and k>0) or (h=0 and k=0 and l>=0)'

mapasu ccp4 0<=x<=2/3; 0<=y<=2/3; 0<=z<1/3

mapasu zero 0<=x<=1/3; 0<=y<=1/3; 0<=z<1

mapasu nonz 0<=x<=1/3; 0<=y<=1/3; 0<=z<1

cheshire 0<=x<=2/3; 0<=y<=2/3; 0<=z<=0

symop x,y,z

symop -y,x-y,z

symop -x+y,-x,z

cenop x,y,z

cenop x+2/3,y+1/3,z+1/3

cenop x+1/3,y+2/3,z+2/3

end_spacegroup

On Wed, 22 Jul 2020 at 12:32, David Vizarraga Revuelto 
wrote:

> Dear all,
>
> Let me ask a question about the P3,H3, R3 space group annotations.
> I had the idea that H3 was the recommended annotation for the hexagonal
> representation of R3 (space group number 146). However, in the Birbeck
> space groups web page (attached) H3 is associated with the space group
> number 143 corresponding to P3. Similarly for all the other H groups
> assigned in the page. Moreover in the web page none of the R space groups
> is assigned to an H annotation.
>
> H3 corresponds to 143 or  to 146?
> Is there a space group 154 annotated as H32 1 2?
>
> Many thanks.
>
>
>
> "Note that the figure showing the relationship between primitive and
> R-centred rhomohedral cells with hexagonal axes is clickable
>
> Rhombohedral with Hexagonal axes
> 146. *R* 3  148. *R* -3
>  155. *R* 3 2
>  160. *R* 3 *m*
>  161. *R* 3 *c*
>  166. *R* -3 *m*
> 
> 167. *R* -3 *c* 
> H-centred Trigonal
> 143. *H* 3  144. *H* 31
>  145. *H* 32
>  147. *H* -3
>  149. *H* 3 2 1
>  150. *H* 3 1 2
> 
> 151. *H* 31 2 1  152. *H*
>  31 1 2  153. *H* 32 2 1
>  154. *H* 32 1 2
>  156. *H* 3 1 *m*
>  157. *H* 3 *m* 1
> 
> 158. *H* 3 1 *c*  159. *H*
>  3 *c* 1  162. *H* -3 *m*
>  1  163. *H* -3 *c* 1
>  164. *H* -3 1 *m*
>  165. *H* -3 1 *c*
> 
>
> --
>
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[ccp4bb] Question about P3, H3 and R3 space groups

[David Vizarraga Revuelto]

Dear all,

Let me ask a question about the P3,H3, R3 space group annotations.
I had the idea that H3 was the recommended annotation for the hexagonal
representation of R3 (space group number 146). However, in the Birbeck
space groups web page (attached) H3 is associated with the space group
number 143 corresponding to P3. Similarly for all the other H groups
assigned in the page. Moreover in the web page none of the R space groups
is assigned to an H annotation.

H3 corresponds to 143 or  to 146?
Is there a space group 154 annotated as H32 1 2?

Many thanks.



"Note that the figure showing the relationship between primitive and
R-centred rhomohedral cells with hexagonal axes is clickable

Rhombohedral with Hexagonal axes
146. *R* 3  148. *R* -3
 155. *R* 3 2
 160. *R* 3 *m*
 161. *R* 3 *c*
 166. *R* -3 *m*

167. *R* -3 *c* 
H-centred Trigonal
143. *H* 3  144. *H* 31
 145. *H* 32
 147. *H* -3
 149. *H* 3 2 1
 150. *H* 3 1 2

151. *H* 31 2 1  152. *H* 31
 1 2  153. *H* 32 2 1
 154. *H* 32 1 2
 156. *H* 3 1 *m*
 157. *H* 3 *m* 1

158. *H* 3 1 *c*  159. *H*
 3 *c* 1  162. *H* -3 *m* 1
 163. *H* -3 *c* 1
 164. *H* -3 1 *m*
 165. *H* -3 1 *c*




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Re: [ccp4bb] CCP4I TERMINATION STATUS 0 "child process exited abnormally"

[Gildea, Richard (DLSLtd,RAL,LSCI)]

Dear Adewumi Adeyeye,

Please could you let me know (off list) the full xia2 command you were trying 
to run, and I can see if I can reproduce the issue.

Cheers,

Richard

Dr Richard Gildea
Data Analysis Scientist
Tel: +441235 77 8078

Diamond Light Source Ltd.
Diamond House
Harwell Science & Innovation Campus
Didcot
Oxfordshire
OX11 0DE

From: CCP4 bulletin board  on behalf of Adewumi Adeyeye 
<42fef00af26b-dmarc-requ...@jiscmail.ac.uk>
Sent: 22 July 2020 10:31
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] CCP4I TERMINATION STATUS 0 "child process exited abnormally"

Dear all,
I need assistance with solving my protein structure.
I have attempted (using remote access)  to integrate my diffraction images (.h5 
format) using xia2 but I keep getting the following error message:

The program run with command: xia2 /dls/i04/data/2020/
has failed with error message
child process exited abnormally


#CCP4I TERMINATION STATUS 0 "child process exited abnormally"

I will appreciate suggestions on how to overcome this.

Thanks.

Adewumi Adeyeye, (PhD Candidate)
Department of Biochemistry, Genetics, and Microbiology
Structural Biology Group,
Room 3-7, Agricultural Sciences Building,
University of Pretoria
c/o University & Lynnwood Roads
Hatfield
Pretoria
0083

Cell: +27630996979
South Africa



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Re: [ccp4bb] CCP4I TERMINATION STATUS 0 "child process exited abnormally"

[David Waterman]

Dear Adewumi Adeyeye,

The ccp4i interface to xia2 is no longer supported and I suspect it might
be completely broken. You should be able to process your data using the
ccp4i2 interface though.

Best wishes
-- David


On Wed, 22 Jul 2020 at 10:32, Adewumi Adeyeye <
42fef00af26b-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear all,
> I need assistance with solving my protein structure.
> I have attempted (using remote access)  to integrate my diffraction images
> (.h5 format) using xia2 but I keep getting the following error message:
>
> The program run with command: xia2 /dls/i04/data/2020/
> has failed with error message
> child process exited abnormally
>
>
> #CCP4I TERMINATION STATUS 0 "child process exited abnormally"
>
> I will appreciate suggestions on how to overcome this.
>
> Thanks.
>
> Adewumi Adeyeye, (PhD Candidate)
> Department of Biochemistry, Genetics, and Microbiology
> Structural Biology Group,
> Room 3-7, Agricultural Sciences Building,
> University of Pretoria
> c/o University & Lynnwood Roads
> Hatfield
> Pretoria
> 0083
>
> Cell: +27630996979
> South Africa
>
> 
>
> 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
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[ccp4bb] CCP4I TERMINATION STATUS 0 "child process exited abnormally"

[Adewumi Adeyeye]

Dear all,
I need assistance with solving my protein structure.
I have attempted (using remote access)  to integrate my diffraction images (.h5 
format) using xia2 but I keep getting the following error message:

The program run with command: xia2 /dls/i04/data/2020/  
has failed with error message
child process exited abnormally


#CCP4I TERMINATION STATUS 0 "child process exited abnormally"

I will appreciate suggestions on how to overcome this. 

Thanks.

Adewumi Adeyeye, (PhD Candidate)
Department of Biochemistry, Genetics, and Microbiology
Structural Biology Group,
Room 3-7, Agricultural Sciences Building,
University of Pretoria
c/o University & Lynnwood Roads
Hatfield
Pretoria
0083

Cell: +27630996979
South Africa



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Re: [ccp4bb] request for basic crystallography online classes

[venkata narayana Are]

Dr. Natesh,

Thank you very much for your suggestion and for sharing the Online
crystallography certificate course link.

Sincerely,
Venkat

On Wed, Jul 22, 2020 at 11:20 AM Natesh Ramanathan 
wrote:

> Dear Venkata,
>
> Check with Birkbeck online crystallography certificate course here:
> http://www.bbk.ac.uk/study/2020/postgraduate/programmes/TPCCRPRO_C/.
>
> Best wishes,
> Natesh
>
> On Wed, 22 Jul 2020 at 09:22, venkata narayana Are <
> venkat.sai.biochemis...@gmail.com> wrote:
>
>> Dear Sir,
>>
>> My self Venkat completed Ph.D. in Biochemistry (structural biology) later
>> on joined in a short project where I learned cell biology and virology. I
>> have solved 15 structures during my Ph.D., further I wanting to learn
>> membrane protein receptors structural biology and other complex protein
>> structural biology.
>>
>> Here my request is, I wanted to attend crystallography lectures for
>> clearing my basic concept. could you please suggest me any online classes
>> or courses which are in running or going to start.
>>
>> Sincerely looking forward for your reply.
>>
>> Sincerely,
>> Venkat
>>
>> --
>>
>> *Venkata Narayana Are*
>>
>> C/o Dr. Debasis Nayak
>>
>> IIT, Indore, Madhya Pradesh - 452013
>>
>> Mobile No: 08435214885
>>
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>
>
> --
> --
> "Live Simply and do Serious Things .. "
> - Dorothy Mary Crowfoot Hodgkin OM, FRS
>
> "In Science truth always wins"
> - Max Ferdinand Perutz OM FRS
> --
> Dr. Ramanathan Natesh
> Assistant Professor,
> School of Biology,
> Indian Institute of Science Education and Research Thiruvananthapuram
> (IISER-TVM),
> Maruthamala P.O., Vithura,
> Thiruvananthapuram,  695551, Kerala, India
>
> nat...@iisertvm.ac.in
> http://faculty.iisertvm.ac.in/natesh
>
> *Researcher ID*: http://www.researcherid.com/rid/C-4488-2008
> *ORCID*: http://orcid.org/-0002-1145-5962
> Vidwan-ID : 94134: http://iisertvm.irins.org/profile/94134
> *PUBLONS*: https://publons.com/author/1520837/ramanathan-natesh#profile
>
> Office Ph. 0091- 471-2778087
>
>

-- 

*Venkata Narayana Are*

Postdoctoral fellow,

C/o Dr. Debasis Nayak

IIT, Indore, Madhya Pradesh - 452013

Mobile No: 08435214885



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