Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[James Holton]

Clearly, the code can change without anyone knowing!

For this reason, and others, I try to remember to do it manually and to 
check.  In cases of pseudo-symmetry, for example P21 with a 90.2 deg 
beta angle and high tNCS, the software may or may not decide it should 
pick free flags in the P222 setting, but it probably "should".


To do it manually, you want to re-index to the higher space group using 
"reindex"

Then pick your free flags
Use "cad" with "outlim" feature to symmetry-expand the data
Use "cad" again to change the space group back
One final run through "cad" to clean things up and make sure you have 
the right asymmetric unit.


That's what I do, anyway,

-James Holton
MAD Scientist

On 8/31/2021 3:04 AM, Eleanor Dodson wrote:

Espec. Jan & Kay,

I had better check this out - ville wrote the code I believe, and I 
have never actually checked the distribution!

Cheers Eleanor

On Tue, 31 Aug 2021 at 08:01, Jan Dohnalek > wrote:


This is good to know indeed.
Will improve my teaching now, I also did not know this is now done
automatically. Thanks for pointing it out.

Jan


On Mon, Aug 30, 2021 at 9:44 PM Kay Diederichs
mailto:kay.diederi...@uni-konstanz.de>> wrote:

Dear Eleanor,

Thanks for pointing out that CCP4 FreeRflag selects the test
set in the highest possible symmetry for the crystal class! I
didn't know that.

The following sentences (which are somewhat difficult to
understand for me) in
https://www.ccp4.ac.uk/html/freerflag.html
 appear to
document that:
"The FreeR_flag is randomly and uniformly distributed
reflexion-by-reflexion, but, additionally, if the keyword
NOSYM is not set, all reflections that are equivalent by the
symmetry of the point group of the twin lattice (assuming the
data is twinned), obtain the same flag. This includes both the
possibility of merohedral and pseudomerohedral twinning. In
the latter case, the obliquity parameter can be set using the
keyword OBL."

I wonder since which CCP4 version (or date) this is the
default behaviour.

best wishes,
Kay

On Mon, 30 Aug 2021 18:28:23 +0100, Eleanor Dodson
mailto:eleanor.dod...@york.ac.uk>>
wrote:

>Back to FreeR factors - Phenix, and I believe FreeRflag now
select FreeRs
>in the highest possible symmetry for the crystal class - eh
P6/mmm for a
>trigonal crystal, and expand the set to fill the actual space
group. This
>means the Free R assignment is suitable if later the crystal
symmetry is
>reassigned. But this was not always done in the past so if
you are trying
>to reuse free/work assignments from an old project there are
possibilities
>of not getting this. Maybe the best solution is to just
generate a new Free
>R set ?
>Eleanor
>
...



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


This message was issued to members of
www.jiscmail.ac.uk/CCP4BB ,
a mailing list hosted by www.jiscmail.ac.uk
, terms & conditions are available
at https://www.jiscmail.ac.uk/policyandsecurity/




-- 
Jan Dohnalek, Ph.D

Institute of Biotechnology
Academy of Sciences of the Czech Republic
Biocev
Prumyslova 595
252 50 Vestec near Prague
Czech Republic

Tel. +420 325 873 758



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








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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Antwort: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Peer Mittl]

Dear Herman,

What you write "Or is the disordered chain enclosed in the 4 
non-disordered chains, with only crystal contacts between the 
non-disordered chains? " seems to be the case. The 4 chains form a 3221 
lattice with a "pocket" on the 2-fold. One domain of the protein fits 
nicely into this "pocket". Since the pocket is symmetric but the domain 
is not, it can bind the 5th chain in both orientations. The second 
domain of the 5th pocket does not form any crystal contacts.


In my opinion twin refinement on a frustrated crystal lattice (almost 
crystallographic NCS) should end up in significantly improved Rfactors. 
Otherwise the is no justification to tret the crystallographic symmetry 
as NCS.


Best,
Peer

Am 01.09.2021 um 09:14 schrieb Schreuder, Herman /DE:


Dear Peer,

I must admit that from the beginning I was not happy to have 5 chains 
“twinned”, while in fact only one chain is “twinned”, e.g. on a 
special position. However, a twin fraction different from 0.5 
suggested the existence of twin domains and not a random distribution 
of A and B conformations.


On the other hand, given that only 20% of the asymmetric unit is 
twinned, with tNCS present and imperfect experimental data, the twin 
fraction obtained might not be very accurate and a twin fraction of 
0.5 could be within the error margin. The low Rfactors you obtain 
without twinning also point into this direction.


What I would do is have a critical look at the crystal packing to see 
if there are reasons why larger twin domains with the rogue chain only 
in one conformation would form. E.g. are there direct crystallographic 
contacts between these disordered that may force the disordered chain 
next to a chain in the “A” conformation to adopt the A conformation as 
well. Or is the disordered chain enclosed in the 4 non-disordered 
chains, with only crystal contacts between the non-disordered chains? 
If there is no compelling reason why neighboring disordered chains 
would adopt the same conformation, I would assume statistical disorder 
and not twinning.


My 2 cts,

Herman

*Von:* mi...@bioc.uzh.ch 
*Gesendet:* Dienstag, 31. August 2021 17:46
*An:* Schreuder, Herman /DE 
*Cc:* CCP4BB@JISCMAIL.AC.UK
*Betreff:* Antwort: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Antwort: Re: 
[ccp4bb] chain on 2-fold axis?


Dear Herman, Kay, Eleanor and CCp4C

At the beginning I was very enthusiastic about the twinning option, 
but meanwhile the enthusiasm has vanished. I basically get the same 
Rfactors after refining the structure in P32 with 5 chains in Refmac 
(test reflections selected in resolution shells with sftools straight 
from the beginning).


Refinement with tight NCS restrains on 4 chains and twinning results 
in Rf/Rfree 24.2/30.0, without twinning I get 27.0/32.5. With slightly 
relaxed NCS restrains for the side chains and no twinning its 
24.3/31.8. A Rfree difference of 2% is that sufficient to confirm 
twinning?


What bothers me even more is the difference ED for the "extra" chain 
(the on on the special position in P3221). After refienement with 
twinning the difference density is slightly reduced but it is still 
present. Furthermore, I can replace the "extra" chain by a 180° 
rotated copy and the refinemnt ends up in basically the same Rfactors. 
I attached two screen shots from the superposition of the initial 
structure (all atoms in wheat) on the rotated structure (blue 
Ca-trace) with the corresponding ED maps.


All the best,
Peer

-"CCP4 bulletin board" <mailto:CCP4BB@JISCMAIL.AC.UK>> schrieb: -

An: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
Von: "Schreuder, Herman /DE"
Gesendet von: "CCP4 bulletin board"
Datum: 27.08.2021 16:37
Betreff: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] 
chain on 2-fold axis?



Dear Lijun and others,

As Kay rightly pointed out, twinning is fundamentally different from 
e.g. disorder or alternative conformations. However, it does not 
depend on a chain or side chain rapidly jumping between two states, 
but whether they are within coherent length of each other. Since most 
data are collected from frozen crystals, no side chain will be rapidly 
jumping between two states. They will be frozen either conformation A 
or conformation B and since these conformations are randomly 
distributed throughout the crystal, they are in general within 
coherent length of each other and causing interference of their 
diffracted X-ray’s, so their complex structure factors are added.


However, for twinned crystals, the twin domains (twin pieces as you 
call it), behave as independent crystals and their intensities are 
added and not their (complex) structure factors.


I did not realize it when I first looked at the thread but the correct 
treatment of these crystals will depend on whether there are twin 
domains present in the crystals, or whether the two orientations of 
the disorder

[ccp4bb] AW: Antwort: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Schreuder, Herman /DE]

Dear Peer,

I must admit that from the beginning I was not happy to have 5 chains 
“twinned”, while in fact only one chain is “twinned”, e.g. on a special 
position. However, a twin fraction different from 0.5 suggested the existence 
of twin domains and not a random distribution of A and B conformations.

On the other hand, given that only 20% of the asymmetric unit is twinned, with 
tNCS present and imperfect experimental data, the twin fraction obtained might 
not be very accurate and a twin fraction of 0.5 could be within the error 
margin. The low Rfactors you obtain without twinning also point into this 
direction.

What I would do is have a critical look at the crystal packing to see if there 
are reasons why larger twin domains with the rogue chain only in one 
conformation would form. E.g. are there direct crystallographic contacts 
between these disordered that may force the disordered chain next to a chain in 
the “A” conformation to adopt the A conformation as well. Or is the disordered 
chain enclosed in the 4 non-disordered chains, with only crystal contacts 
between the non-disordered chains? If there is no compelling reason why 
neighboring disordered chains would adopt the same conformation, I would assume 
statistical disorder and not twinning.

My 2 cts,
Herman

Von: mi...@bioc.uzh.ch 
Gesendet: Dienstag, 31. August 2021 17:46
An: Schreuder, Herman /DE 
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: Antwort: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] 
chain on 2-fold axis?

Dear Herman, Kay, Eleanor and CCp4C

At the beginning I was very enthusiastic about the twinning option, but 
meanwhile the enthusiasm has vanished. I basically get the same Rfactors after 
refining the structure in P32 with 5 chains in Refmac (test reflections 
selected in resolution shells with sftools straight from the beginning).

Refinement with tight NCS restrains on 4 chains and twinning results in 
Rf/Rfree 24.2/30.0, without twinning I get 27.0/32.5. With slightly relaxed NCS 
restrains for the side chains and no twinning its 24.3/31.8. A Rfree difference 
of 2% is that sufficient to confirm twinning?

What bothers me even more is the difference ED for the "extra" chain (the on on 
the special position in P3221). After refienement with twinning the difference 
density is slightly reduced but it is still present. Furthermore, I can replace 
the "extra" chain by a 180° rotated copy and the refinemnt ends up in basically 
the same Rfactors. I attached two screen shots from the superposition of the 
initial structure (all atoms in wheat) on the rotated structure (blue Ca-trace) 
with the corresponding ED maps.

All the best,
Peer

-"CCP4 bulletin board" 
mailto:CCP4BB@JISCMAIL.AC.UK>> schrieb: -
An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Von: "Schreuder, Herman /DE"
Gesendet von: "CCP4 bulletin board"
Datum: 27.08.2021 16:37
Betreff: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 
2-fold axis?


Dear Lijun and others,

As Kay rightly pointed out, twinning is fundamentally different from e.g. 
disorder or alternative conformations. However, it does not depend on a chain 
or side chain rapidly jumping between two states, but whether they are within 
coherent length of each other. Since most data are collected from frozen 
crystals, no side chain will be rapidly jumping between two states. They will 
be frozen either conformation A or conformation B and since these conformations 
are randomly distributed throughout the crystal, they are in general within 
coherent length of each other and causing interference of their diffracted 
X-ray’s, so their complex structure factors are added.

However, for twinned crystals, the twin domains (twin pieces as you call it), 
behave as independent crystals and their intensities are added and not their 
(complex) structure factors.

I did not realize it when I first looked at the thread but the correct 
treatment of these crystals will depend on whether there are twin domains 
present in the crystals, or whether the two orientations of the disordered 
chain are randomly distributed throughout the crystal. Given that the two 
orientations have different twin fractions, my bet is that the twin supporters 
are right.

Best,
Herman





Von: Lijun Liu mailto:lijunli...@gmail.com>>
Gesendet: Freitag, 27. August 2021 15:57
An: Schreuder, Herman /DE 
mailto:herman.schreu...@sanofi.com>>
Cc: ccp4bb@jiscmail.ac.uk<mailto:ccp4bb@jiscmail.ac.uk>
Betreff: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

Dear Herman:



if you say “twinned” chains, then it already means same thing of the two and 
the side chain interactions could not be different (as you can see only one 
copy in the output coordinates), unless you talking about borders between twin 
pieces.



In this situation, the only I could imagine to be if P3221, it would have to 
make 

Re: [ccp4bb] Antwort: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Eleanor Dodson]

I dont think you expect much better R factors with twinning or without -
the fact is the "crystal"  is not perfect . Sometimes it is worth screening
other crystals from the batch - smaller ones may not be twinned at all..
Have you looked back atthe images? Gerard suggested there might be lattice
translocation..
Eleanor

On Tue, 31 Aug 2021 at 16:46, Peer Mittl  wrote:

> Dear Herman, Kay, Eleanor and CCp4C
>
> At the beginning I was very enthusiastic about the twinning option, but
> meanwhile the enthusiasm has vanished. I basically get the same Rfactors
> after refining the structure in P32 with 5 chains in Refmac (test
> reflections selected in resolution shells with sftools straight from the
> beginning).
>
> Refinement with tight NCS restrains on 4 chains and twinning results in
> Rf/Rfree 24.2/30.0, without twinning I get 27.0/32.5. With slightly relaxed
> NCS restrains for the side chains and no twinning its 24.3/31.8. A Rfree
> difference of 2% is that sufficient to confirm twinning?
>
> What bothers me even more is the difference ED for the "extra" chain (the
> on on the special position in P3221). After refienement with twinning the
> difference density is slightly reduced but it is still present.
> Furthermore, I can replace the "extra" chain by a 180° rotated copy and the
> refinemnt ends up in basically the same Rfactors. I attached two screen
> shots from the superposition of the initial structure (all atoms in wheat)
> on the rotated structure (blue Ca-trace) with the corresponding ED maps.
>
> All the best,
> Peer
>
> -"CCP4 bulletin board"  schrieb: -
> An: CCP4BB@JISCMAIL.AC.UK
> Von: "Schreuder, Herman /DE"
> Gesendet von: "CCP4 bulletin board"
> Datum: 27.08.2021 16:37
> Betreff: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on
> 2-fold axis?
>
>
>  Dear Lijun and others,
>
>  As Kay rightly pointed out, twinning is fundamentally different from e.g.
> disorder or alternative conformations. However, it does not depend on a
> chain or side chain rapidly jumping  between two states, but whether they
> are within coherent length of each other. Since most data are collected
> from frozen crystals, no side chain will be rapidly jumping between two
> states. They will be frozen either conformation A or conformation B and
> since  these conformations are randomly distributed throughout the crystal,
> they are in general within coherent length of each other and causing
> interference of their diffracted X-ray’s, so their complex structure
> factors are added.
>
>  However, for twinned crystals, the twin domains (twin pieces as you call
> it), behave as independent crystals and their intensities are added and not
> their (complex) structure factors.
>
>  I did not realize it when I first looked at the thread but the correct
> treatment of these crystals will depend on whether there are twin domains
> present in the crystals, or whether the  two orientations of the disordered
> chain are randomly distributed throughout the crystal. Given that the two
> orientations have different twin fractions, my bet is that the twin
> supporters are right.
>
>  Best,
>  Herman
>
>
>
>
>
>  Von: Lijun Liu 
>  Gesendet: Freitag, 27. August 2021 15:57
>  An: Schreuder, Herman /DE 
>  Cc: ccp4bb@jiscmail.ac.uk
>  Betreff: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold
> axis?
>
>  Dear Herman:
>
>
>
>  if you say “twinned” chains, then it already means same thing of the two
> and the side chain interactions could not be different (as you can see only
> one copy in the output coordinates), unless you talking about borders
> between twin pieces.
>
>
>
>  In this situation, the only I could imagine to be if P3221, it would have
> to make that chain very very rapidly jump between two states in the same
> asu, which can be easily proven wrong.
>
>
>
>  I do agree if refined under P3221 without restraining the two strictly,
> side chain interactions may show differences —— data always not perfect!
>
>
>
>  Lijun
>
>  Sent from my iPhone
>
>
>
>
>   On Aug 27, 2021, at 8:12 AM, Schreuder, Herman /DE <
> herman.schreu...@sanofi.com> wrote:
>
>  
>  Dear Lijun,
>  with this argument I agree: the interactions between the two orientations
> of the “twinned” chain and the neighboring molecules will be different and
> the interacting side chains will  almost certainly have different
> orientations, which necessitates a twinning of the whole structure.
>  Best,
>  Herman
>
>
>
>  Von: CCP4 bulletin board  Im Auftrag von Lijun Liu
>  Gesendet: Freitag, 27. August 2021 14:22
>

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Eleanor Dodson]

Espec. Jan & Kay,

I had better check this out - ville wrote the code I believe, and I have
never actually checked the distribution!
Cheers Eleanor

On Tue, 31 Aug 2021 at 08:01, Jan Dohnalek  wrote:

> This is good to know indeed.
> Will improve my teaching now, I also did not know this is now done
> automatically. Thanks for pointing it out.
>
> Jan
>
>
> On Mon, Aug 30, 2021 at 9:44 PM Kay Diederichs <
> kay.diederi...@uni-konstanz.de> wrote:
>
>> Dear Eleanor,
>>
>> Thanks for pointing out that CCP4 FreeRflag selects the test set in the
>> highest possible symmetry for the crystal class! I didn't know that.
>>
>> The following sentences (which are somewhat difficult to understand for
>> me) in https://www.ccp4.ac.uk/html/freerflag.html appear to document
>> that:
>> "The FreeR_flag is randomly and uniformly distributed
>> reflexion-by-reflexion, but, additionally, if the keyword NOSYM is not set,
>> all reflections that are equivalent by the symmetry of the point group of
>> the twin lattice (assuming the data is twinned), obtain the same flag. This
>> includes both the possibility of merohedral and pseudomerohedral twinning.
>> In the latter case, the obliquity parameter can be set using the keyword
>> OBL."
>>
>> I wonder since which CCP4 version (or date) this is the default behaviour.
>>
>> best wishes,
>> Kay
>>
>> On Mon, 30 Aug 2021 18:28:23 +0100, Eleanor Dodson <
>> eleanor.dod...@york.ac.uk> wrote:
>>
>> >Back to FreeR factors - Phenix, and I believe FreeRflag now select FreeRs
>> >in the highest possible symmetry for the crystal class - eh P6/mmm for a
>> >trigonal crystal, and expand the set to fill the actual space group. This
>> >means the Free R assignment is suitable if later the crystal symmetry is
>> >reassigned. But this was not always done in the past so if you are trying
>> >to reuse free/work assignments from an old project there are
>> possibilities
>> >of not getting this. Maybe the best solution is to just generate a new
>> Free
>> >R set ?
>> >Eleanor
>> >
>> ...
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
>> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
>> available at https://www.jiscmail.ac.uk/policyandsecurity/
>>
>
>
> --
> Jan Dohnalek, Ph.D
> Institute of Biotechnology
> Academy of Sciences of the Czech Republic
> Biocev
> Prumyslova 595
> 252 50 Vestec near Prague
> Czech Republic
>
> Tel. +420 325 873 758
>
> --
>
> 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:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Jan Dohnalek]

This is good to know indeed.
Will improve my teaching now, I also did not know this is now done
automatically. Thanks for pointing it out.

Jan


On Mon, Aug 30, 2021 at 9:44 PM Kay Diederichs <
kay.diederi...@uni-konstanz.de> wrote:

> Dear Eleanor,
>
> Thanks for pointing out that CCP4 FreeRflag selects the test set in the
> highest possible symmetry for the crystal class! I didn't know that.
>
> The following sentences (which are somewhat difficult to understand for
> me) in https://www.ccp4.ac.uk/html/freerflag.html appear to document that:
> "The FreeR_flag is randomly and uniformly distributed
> reflexion-by-reflexion, but, additionally, if the keyword NOSYM is not set,
> all reflections that are equivalent by the symmetry of the point group of
> the twin lattice (assuming the data is twinned), obtain the same flag. This
> includes both the possibility of merohedral and pseudomerohedral twinning.
> In the latter case, the obliquity parameter can be set using the keyword
> OBL."
>
> I wonder since which CCP4 version (or date) this is the default behaviour.
>
> best wishes,
> Kay
>
> On Mon, 30 Aug 2021 18:28:23 +0100, Eleanor Dodson <
> eleanor.dod...@york.ac.uk> wrote:
>
> >Back to FreeR factors - Phenix, and I believe FreeRflag now select FreeRs
> >in the highest possible symmetry for the crystal class - eh P6/mmm for a
> >trigonal crystal, and expand the set to fill the actual space group. This
> >means the Free R assignment is suitable if later the crystal symmetry is
> >reassigned. But this was not always done in the past so if you are trying
> >to reuse free/work assignments from an old project there are possibilities
> >of not getting this. Maybe the best solution is to just generate a new
> Free
> >R set ?
> >Eleanor
> >
> ...
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>


-- 
Jan Dohnalek, Ph.D
Institute of Biotechnology
Academy of Sciences of the Czech Republic
Biocev
Prumyslova 595
252 50 Vestec near Prague
Czech Republic

Tel. +420 325 873 758



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Kay Diederichs]

Dear Eleanor,

Thanks for pointing out that CCP4 FreeRflag selects the test set in the highest 
possible symmetry for the crystal class! I didn't know that.

The following sentences (which are somewhat difficult to understand for me) in 
https://www.ccp4.ac.uk/html/freerflag.html appear to document that:
"The FreeR_flag is randomly and uniformly distributed reflexion-by-reflexion, 
but, additionally, if the keyword NOSYM is not set, all reflections that are 
equivalent by the symmetry of the point group of the twin lattice (assuming the 
data is twinned), obtain the same flag. This includes both the possibility of 
merohedral and pseudomerohedral twinning. In the latter case, the obliquity 
parameter can be set using the keyword OBL."

I wonder since which CCP4 version (or date) this is the default behaviour.

best wishes,
Kay

On Mon, 30 Aug 2021 18:28:23 +0100, Eleanor Dodson  
wrote:

>Back to FreeR factors - Phenix, and I believe FreeRflag now select FreeRs
>in the highest possible symmetry for the crystal class - eh P6/mmm for a
>trigonal crystal, and expand the set to fill the actual space group. This
>means the Free R assignment is suitable if later the crystal symmetry is
>reassigned. But this was not always done in the past so if you are trying
>to reuse free/work assignments from an old project there are possibilities
>of not getting this. Maybe the best solution is to just generate a new Free
>R set ?
>Eleanor
>
...



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Kay Diederichs]

Dear Andrew,

what I meant is "Everything else being equal, bad data result in a larger 
Rfree-Rwork gap than good data". Of course the gap also depends on the 
resolution, and other factors.

best wishes,
Kay

On Mon, 30 Aug 2021 16:59:12 +0100, Andrew Leslie - MRC LMB 
 wrote:

>Dear Kay and Jon,
>
>I cannot remember Ian Tickles original posting on this (assuming that it was 
>made to the bulletin board), but surely the resolution of the data is also a 
>very important factor in the danger of over-fitting. The lower the resolution, 
>the worse the experimental data to refined parameter ratio becomes, and the 
>more likely it is to obtain an overfitted model, regardless of how accurate 
>that data might be. Perhaps this is why Kay said “generally I agree that the 
>accuracy of the data is inversely related to the danger of overfitting”, or 
>did you have something else in mind Kay?
>
>Cheers,
>
>Andrew
>
>> On 30 Aug 2021, at 13:59, Kay Diederichs  
>> wrote:
>> 
>> Hi Jon,
>> 
>> generally I agree that the accuracy of the data is inversely related to the 
>> danger of overfitting, and that selection in shells is not necessary.
>> But if twinning is suspected, as here, and/or a choice between high and low 
>> symmetry spacegroup has to be made, one has to make sure that
>> potentially symmetry-related reflections are _either_ labelled as test _or_ 
>> as work; a mixture will artificially down-bias Rfree.
>> 
>> Selecting the test set in the highest possible symmetry (which is what 
>> Phenix does) is a good solution. This test set should be symmetry-expanded 
>> when trying the low-symmetry spacegroup (if one wants to compare R values). 
>> The latter is not necessary when working with thin shells - but that has 
>> other disadvantages.
>> 
>> best wishes,
>> Kay
>> 
>> On Sun, 29 Aug 2021 14:32:34 +, Jon Cooper  
>> wrote:
>> 
>>> Hello Engin, we discussed this a year or two ago in relation to NCS when 
>>> Ian Tickle convinced me that since overfitting is due errors in the data, 
>>> there is no reason to expect these errors to be correlated by NCS and 
>>> picking the R-free set uniformally or in shells doesn't matter. No doubt my 
>>> incompetence, but I can't see why twinning would be different.
>>> 
>>> Cheers, Jon.C.
>>> 
>>> Sent from ProtonMail mobile
>>> 
>>>  Original Message 
>>> On 29 Aug 2021, 05:32, Engin Özkan wrote:
>>> 
 Hi,
 
 I believe this is taken care of automatically if you use phenix to pick
 your free reflections.
 
 From http://www.phenix-online.org/documentation/tutorials/twinning.html
 
 "When a test set is designed, care must be taken that free and work
 reflections are not related by a twin law. The R-free set assignment in
 phenix.refine and phenix.reflection_file_converter is designed with this
 in mind: the free reflections are chosen to obey the highest possible
 symmetry of the lattice."
 
 I believe this applies to all datasets, just in case there may be twinning.
 
 Engin
 
>> ...
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> 
>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
>> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
>> https://www.jiscmail.ac.uk/policyandsecurity/
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
>list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
>https://www.jiscmail.ac.uk/policyandsecurity/



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Eleanor Dodson]

Back to FreeR factors - Phenix, and I believe FreeRflag now select FreeRs
in the highest possible symmetry for the crystal class - eh P6/mmm for a
trigonal crystal, and expand the set to fill the actual space group. This
means the Free R assignment is suitable if later the crystal symmetry is
reassigned. But this was not always done in the past so if you are trying
to reuse free/work assignments from an old project there are possibilities
of not getting this. Maybe the best solution is to just generate a new Free
R set ?
Eleanor


On Mon, 30 Aug 2021 at 16:59, Andrew Leslie - MRC LMB <
and...@mrc-lmb.cam.ac.uk> wrote:

> Dear Kay and Jon,
>
> I cannot remember Ian Tickles original posting on this (assuming that it
> was made to the bulletin board), but surely the resolution of the data is
> also a very important factor in the danger of over-fitting. The lower the
> resolution, the worse the experimental data to refined parameter ratio
> becomes, and the more likely it is to obtain an overfitted model,
> regardless of how accurate that data might be. Perhaps this is why Kay said
> “generally I agree that the accuracy of the data is inversely related to
> the danger of overfitting”, or did you have something else in mind Kay?
>
> Cheers,
>
> Andrew
>
> > On 30 Aug 2021, at 13:59, Kay Diederichs 
> wrote:
> >
> > Hi Jon,
> >
> > generally I agree that the accuracy of the data is inversely related to
> the danger of overfitting, and that selection in shells is not necessary.
> > But if twinning is suspected, as here, and/or a choice between high and
> low symmetry spacegroup has to be made, one has to make sure that
> > potentially symmetry-related reflections are _either_ labelled as test
> _or_ as work; a mixture will artificially down-bias Rfree.
> >
> > Selecting the test set in the highest possible symmetry (which is what
> Phenix does) is a good solution. This test set should be symmetry-expanded
> when trying the low-symmetry spacegroup (if one wants to compare R values).
> > The latter is not necessary when working with thin shells - but that has
> other disadvantages.
> >
> > best wishes,
> > Kay
> >
> > On Sun, 29 Aug 2021 14:32:34 +, Jon Cooper <
> jon.b.coo...@protonmail.com> wrote:
> >
> >> Hello Engin, we discussed this a year or two ago in relation to NCS
> when Ian Tickle convinced me that since overfitting is due errors in the
> data, there is no reason to expect these errors to be correlated by NCS and
> picking the R-free set uniformally or in shells doesn't matter. No doubt my
> incompetence, but I can't see why twinning would be different.
> >>
> >> Cheers, Jon.C.
> >>
> >> Sent from ProtonMail mobile
> >>
> >>  Original Message 
> >> On 29 Aug 2021, 05:32, Engin Özkan wrote:
> >>
> >>> Hi,
> >>>
> >>> I believe this is taken care of automatically if you use phenix to pick
> >>> your free reflections.
> >>>
> >>> From
> http://www.phenix-online.org/documentation/tutorials/twinning.html
> >>>
> >>> "When a test set is designed, care must be taken that free and work
> >>> reflections are not related by a twin law. The R-free set assignment in
> >>> phenix.refine and phenix.reflection_file_converter is designed with
> this
> >>> in mind: the free reflections are chosen to obey the highest possible
> >>> symmetry of the lattice."
> >>>
> >>> I believe this applies to all datasets, just in case there may be
> twinning.
> >>>
> >>> Engin
> >>>
> > ...
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
> > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Andrew Leslie - MRC LMB]

Dear Kay and Jon,

I cannot remember Ian Tickles original posting on this (assuming that it was 
made to the bulletin board), but surely the resolution of the data is also a 
very important factor in the danger of over-fitting. The lower the resolution, 
the worse the experimental data to refined parameter ratio becomes, and the 
more likely it is to obtain an overfitted model, regardless of how accurate 
that data might be. Perhaps this is why Kay said “generally I agree that the 
accuracy of the data is inversely related to the danger of overfitting”, or did 
you have something else in mind Kay?

Cheers,

Andrew

> On 30 Aug 2021, at 13:59, Kay Diederichs  
> wrote:
> 
> Hi Jon,
> 
> generally I agree that the accuracy of the data is inversely related to the 
> danger of overfitting, and that selection in shells is not necessary.
> But if twinning is suspected, as here, and/or a choice between high and low 
> symmetry spacegroup has to be made, one has to make sure that
> potentially symmetry-related reflections are _either_ labelled as test _or_ 
> as work; a mixture will artificially down-bias Rfree.
> 
> Selecting the test set in the highest possible symmetry (which is what Phenix 
> does) is a good solution. This test set should be symmetry-expanded when 
> trying the low-symmetry spacegroup (if one wants to compare R values). 
> The latter is not necessary when working with thin shells - but that has 
> other disadvantages.
> 
> best wishes,
> Kay
> 
> On Sun, 29 Aug 2021 14:32:34 +, Jon Cooper  
> wrote:
> 
>> Hello Engin, we discussed this a year or two ago in relation to NCS when Ian 
>> Tickle convinced me that since overfitting is due errors in the data, there 
>> is no reason to expect these errors to be correlated by NCS and picking the 
>> R-free set uniformally or in shells doesn't matter. No doubt my 
>> incompetence, but I can't see why twinning would be different.
>> 
>> Cheers, Jon.C.
>> 
>> Sent from ProtonMail mobile
>> 
>>  Original Message 
>> On 29 Aug 2021, 05:32, Engin Özkan wrote:
>> 
>>> Hi,
>>> 
>>> I believe this is taken care of automatically if you use phenix to pick
>>> your free reflections.
>>> 
>>> From http://www.phenix-online.org/documentation/tutorials/twinning.html
>>> 
>>> "When a test set is designed, care must be taken that free and work
>>> reflections are not related by a twin law. The R-free set assignment in
>>> phenix.refine and phenix.reflection_file_converter is designed with this
>>> in mind: the free reflections are chosen to obey the highest possible
>>> symmetry of the lattice."
>>> 
>>> I believe this applies to all datasets, just in case there may be twinning.
>>> 
>>> Engin
>>> 
> ...
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
> https://www.jiscmail.ac.uk/policyandsecurity/



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Kay Diederichs]

Hi Jon,

generally I agree that the accuracy of the data is inversely related to the 
danger of overfitting, and that selection in shells is not necessary.
But if twinning is suspected, as here, and/or a choice between high and low 
symmetry spacegroup has to be made, one has to make sure that
potentially symmetry-related reflections are _either_ labelled as test _or_ as 
work; a mixture will artificially down-bias Rfree.

Selecting the test set in the highest possible symmetry (which is what Phenix 
does) is a good solution. This test set should be symmetry-expanded when trying 
the low-symmetry spacegroup (if one wants to compare R values). 
The latter is not necessary when working with thin shells - but that has other 
disadvantages.

best wishes,
Kay

On Sun, 29 Aug 2021 14:32:34 +, Jon Cooper  
wrote:

>Hello Engin, we discussed this a year or two ago in relation to NCS when Ian 
>Tickle convinced me that since overfitting is due errors in the data, there is 
>no reason to expect these errors to be correlated by NCS and picking the 
>R-free set uniformally or in shells doesn't matter. No doubt my incompetence, 
>but I can't see why twinning would be different.
>
>Cheers, Jon.C.
>
>Sent from ProtonMail mobile
>
> Original Message 
>On 29 Aug 2021, 05:32, Engin Özkan wrote:
>
>> Hi,
>>
>> I believe this is taken care of automatically if you use phenix to pick
>> your free reflections.
>>
>> From http://www.phenix-online.org/documentation/tutorials/twinning.html
>>
>> "When a test set is designed, care must be taken that free and work
>> reflections are not related by a twin law. The R-free set assignment in
>> phenix.refine and phenix.reflection_file_converter is designed with this
>> in mind: the free reflections are chosen to obey the highest possible
>> symmetry of the lattice."
>>
>> I believe this applies to all datasets, just in case there may be twinning.
>>
>> Engin
>>
...



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Jon Cooper]

Hello Engin, we discussed this a year or two ago in relation to NCS when Ian 
Tickle convinced me that since overfitting is due errors in the data, there is 
no reason to expect these errors to be correlated by NCS and picking the R-free 
set uniformally or in shells doesn't matter. No doubt my incompetence, but I 
can't see why twinning would be different.

Cheers, Jon.C.

Sent from ProtonMail mobile

 Original Message 
On 29 Aug 2021, 05:32, Engin Özkan wrote:

> Hi,
>
> I believe this is taken care of automatically if you use phenix to pick
> your free reflections.
>
> From http://www.phenix-online.org/documentation/tutorials/twinning.html
>
> "When a test set is designed, care must be taken that free and work
> reflections are not related by a twin law. The R-free set assignment in
> phenix.refine and phenix.reflection_file_converter is designed with this
> in mind: the free reflections are chosen to obey the highest possible
> symmetry of the lattice."
>
> I believe this applies to all datasets, just in case there may be twinning.
>
> Engin
>
> On 8/27/21 11:12 AM, Jeffrey B Bonanno wrote:
>> Hi Dirk and Kay,
>>
>> Excellent, many thanks for the refresher!
>>
>> jbb
>>
>> Jeffrey B. Bonanno, Ph.D.
>> Department of Biochemistry
>> Albert Einstein College of Medicine
>> 1300 Morris Park Avenue
>> Bronx, NY 10461
>> off. 718-430-2452 fax. 718-430-8565
>> email jeffrey.bona...@einsteinmed.org
>>
>>
>> -Original Message-----
>> From: CCP4 bulletin board  On Behalf Of Dirk Kostrewa
>> Sent: Friday, August 27, 2021 12:06 PM
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold 
>> axis?
>>
>> 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.
>>
>> Dear Jeffrey,
>>
>> just using thin shells of reflections for the test set might not be enough 
>> to eliminate any correlation to working set reflections. The distance of the 
>> test set reflections in reciprocal space, after applying the NCS rotations 
>> in reciprocal space, to any reflections of the working set should be large 
>> enough to be uncorrelated. A typical maximum distance for correlation in 
>> reciprocal space is the first zero (root) of the Fourier transform of the 
>> approximated spherical shape of the protein molecule, the so-called 
>> G-function (see [1) and [2]). However, this means, that shells should be 
>> thicker than 2 times this distance to blindly exclude any potential 
>> correlation between test set and working set reflection in reciprocal space. 
>> This would be way too expensive!
>>
>> An better way to select uncorrelated reflections is described in [3] (same 
>> reference that Kay has given), where for each test set reflection, after 
>> applying the NCS rotations in reciprocal space, the distances to the working 
>> set reflections are taken into account, and test and working set reflections 
>> are chosen such that their distances are large enough to be uncorrelated.
>>
>> Best regards,
>>
>> Dirk.
>>
>> [1] Rossmann & Blow, Acta Cryst, 15, 24 -31 (1962)
>>
>> [2] Main & Rossmann, Acta Cryst, 21, 67-72 (1966)
>>
>> [3] Fabiola, Korostelev & Chapman, Acta Cryst, D62, 227-238 (2006)
>>
>> On 8/27/21 4:47 PM, Kay Diederichs wrote:
>>> Hi Jeffrey,
>>>
>>> good question. Both twinning and NCS may couple reflections across free and 
>>> working sets, and this should be avoided by proper selection - otherwise 
>>> Rfree is biased towards Rwork. Selecting thin shells should be a good 
>>> option, and can be done in SFTOOLS (or DATAMAN, or SHELXPRO).
>>>
>>> How much does it matter? Actually I started to search the literature after 
>>> reading your question, and expected that one of Z. Dauter's papers would 
>>> enlighten me, but until a minute ago couldn't find the one(s) that I 
>>> thought existed. But I found Fabiola et al., Acta Cryst. (2006). D62, 
>>> 227-238 which is relevant for the coupling by NCS. Ah I just found 
>>> Smietanska et al., Acta Cryst. (2020). D76, 653-667 where they indeed 
>>> selected thin shells.
>>>
>>> Best wishes,
>>> Kay
>>>
>>> On Fri, 27 Aug 2021 13:24:05 +, Jeffrey B Bonanno 
>>>  wro

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Engin Özkan]

Hi,

I believe this is taken care of automatically if you use phenix to pick 
your free reflections.



From http://www.phenix-online.org/documentation/tutorials/twinning.html


"When a test set is designed, care must be taken that free and work 
reflections are not related by a twin law. The R-free set assignment in 
phenix.refine and phenix.reflection_file_converter is designed with this 
in mind: the free reflections are chosen to obey the highest possible 
symmetry of the lattice."


I believe this applies to all datasets, just in case there may be twinning.

Engin

On 8/27/21 11:12 AM, Jeffrey B Bonanno wrote:

Hi Dirk and Kay,

Excellent, many thanks for the refresher!

jbb

Jeffrey B. Bonanno, Ph.D.
Department of Biochemistry
Albert Einstein College of Medicine
1300 Morris Park Avenue
Bronx, NY 10461
off. 718-430-2452 fax. 718-430-8565
email jeffrey.bona...@einsteinmed.org


-Original Message-
From: CCP4 bulletin board  On Behalf Of Dirk Kostrewa
Sent: Friday, August 27, 2021 12:06 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

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.

Dear Jeffrey,

just using thin shells of reflections for the test set might not be enough to 
eliminate any correlation to working set reflections. The distance of the test 
set reflections in reciprocal space, after applying the NCS rotations in 
reciprocal space, to any reflections of the working set should be large enough 
to be uncorrelated. A typical maximum distance for correlation in reciprocal 
space is the first zero (root) of the Fourier transform of the approximated 
spherical shape of the protein molecule, the so-called G-function (see [1) and 
[2]). However, this means, that shells should be thicker than 2 times this 
distance to blindly exclude any potential correlation between test set and 
working set reflection in reciprocal space. This would be way too expensive!

An better way to select uncorrelated reflections is described in [3] (same 
reference that Kay has given), where for each test set reflection, after 
applying the NCS rotations in reciprocal space, the distances to the working 
set reflections are taken into account, and test and working set reflections 
are chosen such that their distances are large enough to be uncorrelated.

Best regards,

Dirk.

[1] Rossmann & Blow, Acta Cryst, 15, 24 -31 (1962)

[2] Main & Rossmann, Acta Cryst, 21, 67-72 (1966)

[3] Fabiola, Korostelev & Chapman, Acta Cryst, D62, 227-238 (2006)

On 8/27/21 4:47 PM, Kay Diederichs wrote:

Hi Jeffrey,

good question. Both twinning and NCS may couple reflections across free and 
working sets, and this should be avoided by proper selection - otherwise Rfree 
is biased towards Rwork. Selecting thin shells should be a good option, and can 
be done in SFTOOLS (or DATAMAN, or SHELXPRO).

How much does it matter? Actually I started to search the literature after 
reading your question, and expected that one of Z. Dauter's papers would 
enlighten me, but until a minute ago couldn't find the one(s) that I thought 
existed. But I found Fabiola et al., Acta Cryst. (2006). D62, 227-238 which is 
relevant for the coupling by NCS. Ah I just found Smietanska et al., Acta 
Cryst. (2020). D76, 653-667 where they indeed selected thin shells.

Best wishes,
Kay

On Fri, 27 Aug 2021 13:24:05 +, Jeffrey B Bonanno 
 wrote:


Hi Kay,

Can you also comment on Rfree set selection? It seems thin shell might be 
preferred in these cases?

jbb

Jeffrey B. Bonanno, Ph.D.
Department of Biochemistry
Albert Einstein College of Medicine
1300 Morris Park Avenue
Bronx, NY 10461
off. 718-430-2452 fax. 718-430-8565
email jeffrey.bona...@einsteinmed.org

##
##

To unsubscribe from the CCP4BB list, click the following link:
https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.
jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1d
ata=04%7C01%7Cjeffrey.bonanno%40EINSTEINMED.ORG%7C34839cf0455841166ca2
08d96974a30a%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637656772499
344795%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJ
BTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=XIDw7gK4YhuU02YwVY4F3DyeH
LvPfvamkOvqOnREXWM%3Dreserved=0

This message was issued to members of
https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.j
iscmail.ac.uk%2FCCP4BBdata=04%7C01%7Cjeffrey.bonanno%40EINSTEINME
D.ORG%7C34839cf0455841166ca208d96974a30a%7C9c01f0fd65e040c089a82dfd51e
62025%7C0%7C0%7C637656772499344795%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4
wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sda
ta=%2BNJFcTsWh8ejWN6j02s%2BhM

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Edward Berry]

upper limit for the molecular weight of this molecule?

David Cobessi solved a structure with heme on a crystallographic 2-fold.
https://www.ncbi.nlm.nih.gov/pubmed/11752777
Heme is almost, but not quite, 2-fold symmetric.
eab


Peer Mittl wrote on 8/27/2021 9:55 AM:

Dear Vaheh,

I agree with you, at least in your last statement. I guess we all agree that certain molecules can 
occupy special positions on true rotation axis. Strictly, this is only possible if the molecule 
obeys the rotation symmetry. For water molecules on 2-folds you already have to make assumptions 
about the "invisible" protons. I guess, many of us have seen even larger and asymmetric 
solvent molecules, such as glycerol, MPD or buffer molecules on special positions, which locally 
break the crystal symmetry. The work around for this issue would be to define two alternative 
conformations for this molecule, because these conformations do not "see" each other, as 
pointed out by Herman. But where is the upper limit for the molecular weight of this molecule?

I (and perhaps most other crystallographers) would not refine such a case as a 
twinned structure in a lower symmetry space group, because the major part of 
the AU obeys the crystal symmetry. Furthermore, there is a fundamental 
difference between crystallographic symmetry and the symmetry of a twin law. 
The crystallographic symmetry covers the entire crystal, whereas the twin law 
just relates twin domains locally. Refining a true P3221 structure as a twinned 
P32 structure is simply the wrong thing to do.

All the best,
Peer



-"CCP4 bulletin board"  schrieb: -
An: CCP4BB@JISCMAIL.AC.UK
Von: "Oganesyan, Vaheh"
Gesendet von: "CCP4 bulletin board"
Datum: 27.08.2021 13:56
Betreff: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?


  How P3221 can be an option if it assumes chain on axis? I guess I’m missing something, but per my belief only those sg will be possible for which there is no axis going through the extra molecule. P1 sg looks the only correct option here  in my humble opinion.

  Democracy (voting) depends on science. However, the reverse is not, 
thankfully.
   
  Vaheh
   
  
  
  From: CCP4 bulletin board   On Behalf Of Peer Mittl

  Sent: Friday, August 27, 2021 6:32 AM
  To: CCP4BB@JISCMAIL.AC.UK
  Subject: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?
 
  Dear Herman,
  
  The answer probably depends on the impact of the "extra" chain on the

  sublattice. If there is no impact the "true" space group is P3221 with
  one chain on the special position. If the swapping of the extra chain
  influences the sublattice P32 (or C2 or P1, as pointed out by Kay)
  twinned to P3221 might be the better description.
  
  All the best,

  Peer
  
  On 27.08.2021 10:56, Schreuder, Herman /DE wrote:

  >
  > Dear Peer and Eleanor,
  >
  > This is indeed what I am suspecting: If the “twinning operator” in P32
  > puts 4 out of 5 protein chains on top of symmetry mates, is the “true”
  > space group then P32, with 5 twinned chains, or P3221 with 4 normal
  > chains and 1 chain on a special position? I would vote for the latter.
  >
  > Best,
  >
  > Herman
  >
  > *Von:* CCP4 bulletin board  *Im Auftrag von
  > *Peer Mittl
  > *Gesendet:* Freitag, 27. August 2021 10:17
  > *An:* CCP4BB@JISCMAIL.AC.UK
  > *Betreff:* Re: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?
  >
  > Dear Eleanor,
  >
  > I indeed used r/tefmac for the refinement and it came up with the values
  > HKL (a=0.56), KH-L (a=0.44). It would be interesting to see if a
  > refinement in P3221 would come up with the same occupancies for the
  > alternative conformations for the "extra" chain on the 2-fold axis. It
  > seems as if the "well-ordered" chains (2 in P3221, 4 in P32) form a
  > sublattice with P3221 symmetry and it's just the "extra" chain, which
  > generates the twinning.
  >
  > All the best,
  > Peer
  >
  > On 26.08.2021 18:09, Eleanor Dodson wrote:
  > > Motto =mitti in predictive text!
  > >
  > > On Thu, 26 Aug 2021 at 16:52, Eleanor Dodson
  > > mailto:eleanor.dod...@york.ac.uk
  > <mailto:eleanor.dod...@york.ac.uk%20%3cmailto:eleanor.dod...@york.ac.uk>>>
  > wrote:
  > >
  > > Great, motto. I think you have nailed it! Did you use tefmac for
  > > twinned refinement? And if so what did it suggest the twin
  > >  fraction is?
  > >
  > > On Thu, 26 Aug 2021 at 16:30, Peer Mittl  <mailto:mi...@bioc.uzh.ch%0b>> <mailto:mi...@bioc.uzh.ch
  > <mailto:mi...@bioc.uzh.ch>>> wrote:
  > >
  > > Yes, the data indeed seems to be twinned and the tNCS has
  > > masked the twinning statistics, which is why I haven't
  &

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Jeffrey B Bonanno]

Hi Dirk and Kay,

Excellent, many thanks for the refresher!

jbb

Jeffrey B. Bonanno, Ph.D.
Department of Biochemistry
Albert Einstein College of Medicine
1300 Morris Park Avenue
Bronx, NY 10461
off. 718-430-2452 fax. 718-430-8565
email jeffrey.bona...@einsteinmed.org


-Original Message-
From: CCP4 bulletin board  On Behalf Of Dirk Kostrewa
Sent: Friday, August 27, 2021 12:06 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

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.

Dear Jeffrey,

just using thin shells of reflections for the test set might not be enough to 
eliminate any correlation to working set reflections. The distance of the test 
set reflections in reciprocal space, after applying the NCS rotations in 
reciprocal space, to any reflections of the working set should be large enough 
to be uncorrelated. A typical maximum distance for correlation in reciprocal 
space is the first zero (root) of the Fourier transform of the approximated 
spherical shape of the protein molecule, the so-called G-function (see [1) and 
[2]). However, this means, that shells should be thicker than 2 times this 
distance to blindly exclude any potential correlation between test set and 
working set reflection in reciprocal space. This would be way too expensive!

An better way to select uncorrelated reflections is described in [3] (same 
reference that Kay has given), where for each test set reflection, after 
applying the NCS rotations in reciprocal space, the distances to the working 
set reflections are taken into account, and test and working set reflections 
are chosen such that their distances are large enough to be uncorrelated.

Best regards,

Dirk.

[1] Rossmann & Blow, Acta Cryst, 15, 24 -31 (1962)

[2] Main & Rossmann, Acta Cryst, 21, 67-72 (1966)

[3] Fabiola, Korostelev & Chapman, Acta Cryst, D62, 227-238 (2006)

On 8/27/21 4:47 PM, Kay Diederichs wrote:
> Hi Jeffrey,
>
> good question. Both twinning and NCS may couple reflections across free and 
> working sets, and this should be avoided by proper selection - otherwise 
> Rfree is biased towards Rwork. Selecting thin shells should be a good option, 
> and can be done in SFTOOLS (or DATAMAN, or SHELXPRO).
>
> How much does it matter? Actually I started to search the literature after 
> reading your question, and expected that one of Z. Dauter's papers would 
> enlighten me, but until a minute ago couldn't find the one(s) that I thought 
> existed. But I found Fabiola et al., Acta Cryst. (2006). D62, 227-238 which 
> is relevant for the coupling by NCS. Ah I just found Smietanska et al., Acta 
> Cryst. (2020). D76, 653-667 where they indeed selected thin shells.
>
> Best wishes,
> Kay
>
> On Fri, 27 Aug 2021 13:24:05 +, Jeffrey B Bonanno 
>  wrote:
>
>> Hi Kay,
>>
>> Can you also comment on Rfree set selection? It seems thin shell might be 
>> preferred in these cases?
>>
>> jbb
>>
>> Jeffrey B. Bonanno, Ph.D.
>> Department of Biochemistry
>> Albert Einstein College of Medicine
>> 1300 Morris Park Avenue
>> Bronx, NY 10461
>> off. 718-430-2452 fax. 718-430-8565
>> email jeffrey.bona...@einsteinmed.org
> ##
> ##
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.
> jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1d
> ata=04%7C01%7Cjeffrey.bonanno%40EINSTEINMED.ORG%7C34839cf0455841166ca2
> 08d96974a30a%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637656772499
> 344795%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJ
> BTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=XIDw7gK4YhuU02YwVY4F3DyeH
> LvPfvamkOvqOnREXWM%3Dreserved=0
>
> This message was issued to members of 
> https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.j
> iscmail.ac.uk%2FCCP4BBdata=04%7C01%7Cjeffrey.bonanno%40EINSTEINME
> D.ORG%7C34839cf0455841166ca208d96974a30a%7C9c01f0fd65e040c089a82dfd51e
> 62025%7C0%7C0%7C637656772499344795%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4
> wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sda
> ta=%2BNJFcTsWh8ejWN6j02s%2BhMcXl9a9yOAyOjtHf410I68%3Dreserved=0, 
> a mailing list hosted by 
> https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.j
> iscmail.ac.uk%2Fdata=04%7C01%7Cjeffrey.bonanno%40EINSTEINMED.ORG%
> 7C34839cf0455841166ca208d96974a30a%7C9c01f0fd65e040c089a82dfd51e62025%
> 7C0%7C0%7C63765

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Dirk Kostrewa]

Dear Jeffrey,

just using thin shells of reflections for the test set might not be 
enough to eliminate any correlation to working set reflections. The 
distance of the test set reflections in reciprocal space, after applying 
the NCS rotations in reciprocal space, to any reflections of the working 
set should be large enough to be uncorrelated. A typical maximum 
distance for correlation in reciprocal space is the first zero (root) of 
the Fourier transform of the approximated spherical shape of the protein 
molecule, the so-called G-function (see [1) and [2]). However, this 
means, that shells should be thicker than 2 times this distance to 
blindly exclude any potential correlation between test set and working 
set reflection in reciprocal space. This would be way too expensive!


An better way to select uncorrelated reflections is described in [3] 
(same reference that Kay has given), where for each test set reflection, 
after applying the NCS rotations in reciprocal space, the distances to 
the working set reflections are taken into account, and test and working 
set reflections are chosen such that their distances are large enough to 
be uncorrelated.


Best regards,

Dirk.

[1] Rossmann & Blow, Acta Cryst, 15, 24 -31 (1962)

[2] Main & Rossmann, Acta Cryst, 21, 67-72 (1966)

[3] Fabiola, Korostelev & Chapman, Acta Cryst, D62, 227-238 (2006)

On 8/27/21 4:47 PM, Kay Diederichs wrote:

Hi Jeffrey,

good question. Both twinning and NCS may couple reflections across free and 
working sets, and this should be avoided by proper selection - otherwise Rfree 
is biased towards Rwork. Selecting thin shells should be a good option, and can 
be done in SFTOOLS (or DATAMAN, or SHELXPRO).

How much does it matter? Actually I started to search the literature after 
reading your question, and expected that one of Z. Dauter's papers would 
enlighten me, but until a minute ago couldn't find the one(s) that I thought 
existed. But I found Fabiola et al., Acta Cryst. (2006). D62, 227–238 which is 
relevant for the coupling by NCS. Ah I just found Smietanska et al., Acta 
Cryst. (2020). D76, 653-667 where they indeed selected thin shells.

Best wishes,
Kay

On Fri, 27 Aug 2021 13:24:05 +, Jeffrey B Bonanno 
 wrote:


Hi Kay,

Can you also comment on Rfree set selection? It seems thin shell might be 
preferred in these cases?

jbb

Jeffrey B. Bonanno, Ph.D.
Department of Biochemistry
Albert Einstein College of Medicine
1300 Morris Park Avenue
Bronx, NY 10461
off. 718-430-2452 fax. 718-430-8565
email jeffrey.bona...@einsteinmed.org



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/


--

***
Dirk Kostrewa
Gene Center Munich
Department of Biochemistry, AG Hopfner
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76998
E-mail: dirk.kostr...@lmu.de
kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Kay Diederichs]

Hi Jeffrey,

good question. Both twinning and NCS may couple reflections across free and 
working sets, and this should be avoided by proper selection - otherwise Rfree 
is biased towards Rwork. Selecting thin shells should be a good option, and can 
be done in SFTOOLS (or DATAMAN, or SHELXPRO).

How much does it matter? Actually I started to search the literature after 
reading your question, and expected that one of Z. Dauter's papers would 
enlighten me, but until a minute ago couldn't find the one(s) that I thought 
existed. But I found Fabiola et al., Acta Cryst. (2006). D62, 227–238 which is 
relevant for the coupling by NCS. Ah I just found Smietanska et al., Acta 
Cryst. (2020). D76, 653-667 where they indeed selected thin shells.

Best wishes,
Kay

On Fri, 27 Aug 2021 13:24:05 +, Jeffrey B Bonanno 
 wrote:

>Hi Kay,
>
>Can you also comment on Rfree set selection? It seems thin shell might be 
>preferred in these cases?
>
>jbb
>
>Jeffrey B. Bonanno, Ph.D.
>Department of Biochemistry
>Albert Einstein College of Medicine
>1300 Morris Park Avenue
>Bronx, NY 10461
>off. 718-430-2452 fax. 718-430-8565
>email jeffrey.bona...@einsteinmed.org



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Schreuder, Herman /DE]

Dear Lijun and others,

As Kay rightly pointed out, twinning is fundamentally different from e.g. 
disorder or alternative conformations. However, it does not depend on a chain 
or side chain rapidly jumping between two states, but whether they are within 
coherent length of each other. Since most data are collected from frozen 
crystals, no side chain will be rapidly jumping between two states. They will 
be frozen either conformation A or conformation B and since these conformations 
are randomly distributed throughout the crystal, they are in general within 
coherent length of each other and causing interference of their diffracted 
X-ray’s, so their complex structure factors are added.

However, for twinned crystals, the twin domains (twin pieces as you call it), 
behave as independent crystals and their intensities are added and not their 
(complex) structure factors.

I did not realize it when I first looked at the thread but the correct 
treatment of these crystals will depend on whether there are twin domains 
present in the crystals, or whether the two orientations of the disordered 
chain are randomly distributed throughout the crystal. Given that the two 
orientations have different twin fractions, my bet is that the twin supporters 
are right.

Best,
Herman



Von: Lijun Liu 
Gesendet: Freitag, 27. August 2021 15:57
An: Schreuder, Herman /DE 
Cc: ccp4bb@jiscmail.ac.uk
Betreff: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

Dear Herman:

if you say “twinned” chains, then it already means same thing of the two and 
the side chain interactions could not be different (as you can see only one 
copy in the output coordinates), unless you talking about borders between twin 
pieces.

In this situation, the only I could imagine to be if P3221, it would have to 
make that chain very very rapidly jump between two states in the same asu, 
which can be easily proven wrong.

I do agree if refined under P3221 without restraining the two strictly, side 
chain interactions may show differences —— data always not perfect!

Lijun
Sent from my iPhone


On Aug 27, 2021, at 8:12 AM, Schreuder, Herman /DE 
mailto:herman.schreu...@sanofi.com>> wrote:

Dear Lijun,
with this argument I agree: the interactions between the two orientations of 
the “twinned” chain and the neighboring molecules will be different and the 
interacting side chains will almost certainly have different orientations, 
which necessitates a twinning of the whole structure.
Best,
Herman

Von: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
Im Auftrag von Lijun Liu
Gesendet: Freitag, 27. August 2021 14:22
An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Betreff: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

I believe it is a twin from P32.




  1.  Not like the assignment of double conformations with partial occupancies 
to small part of asu, for examples, a side chain of lysin or a small fragment 
of a protein, which have both conformations stayed in the same specific asu at 
the same time.  For this p3221 asu, if one copy of that chain occupies the part 
of the asu, the other so-called conformation will not appear in the same asu at 
the same time, so the conformation and occupancy issue was arisen from 
different cell units, it is a twin from p32.
  2.  Talking about the asu of p3221, it holds 3 chains, the chain of interest 
assigned as 2 conformations related by a strict 2-fold.  Since you believe and 
have reduced to P3221, then you should restrain the two overall strictly (since 
absolutely most of these atoms are not on special positions) and not to refine 
the two 0.5 occupancies either, respecting the crystallographic 2-fold.  This 
is equivalent to perfect twin from p32 theoretically (although refinement with 
twin mode in p32 and none-twin mode in p3221 may give difference even large).  
If you refined and resulted in occupancies away from 0.5, the symmetry was 
proven to be broken, which supports P32 twinning.

Lijun

Sent from my iPhone



On Aug 27, 2021, at 6:56 AM, Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>> wrote:

How P3221 can be an option if it assumes chain on axis? I guess I’m missing 
something, but per my belief only those sg will be possible for which there is 
no axis going through the extra molecule. P1 sg looks the only correct option 
here in my humble opinion.
Democracy (voting) depends on science. However, the reverse is not, thankfully.

Vaheh

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Peer Mittl
Sent: Friday, August 27, 2021 6:32 AM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

Dear Herman,

The answer probably depends on the impact of the "extra" chain on the
sublattice. If there is no impact the "true" space group is P3221 with
one chain on the special

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Lijun Liu]

Dear Herman:  

if you say “twinned” chains, then it already means same thing of the two and 
the side chain interactions could not be different (as you can see only one 
copy in the output coordinates), unless you talking about borders between twin 
pieces.

In this situation, the only I could imagine to be if P3221, it would have to 
make that chain very very rapidly jump between two states in the same asu, 
which can be easily proven wrong.

I do agree if refined under P3221 without restraining the two strictly, side 
chain interactions may show differences —— data always not perfect!

Lijun

Sent from my iPhone

> On Aug 27, 2021, at 8:12 AM, Schreuder, Herman /DE 
>  wrote:
> 
> 
> Dear Lijun,
> with this argument I agree: the interactions between the two orientations of 
> the “twinned” chain and the neighboring molecules will be different and the 
> interacting side chains will almost certainly have different orientations, 
> which necessitates a twinning of the whole structure.
> Best,
> Herman
>  
> Von: CCP4 bulletin board  Im Auftrag von Lijun Liu
> Gesendet: Freitag, 27. August 2021 14:22
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?
>  
> I believe it is a twin from P32.
> 
> 
> Not like the assignment of double conformations with partial occupancies to 
> small part of asu, for examples, a side chain of lysin or a small fragment of 
> a protein, which have both conformations stayed in the same specific asu at 
> the same time.  For this p3221 asu, if one copy of that chain occupies the 
> part of the asu, the other so-called conformation will not appear in the same 
> asu at the same time, so the conformation and occupancy issue was arisen from 
> different cell units, it is a twin from p32.
> Talking about the asu of p3221, it holds 3 chains, the chain of interest 
> assigned as 2 conformations related by a strict 2-fold.  Since you believe 
> and have reduced to P3221, then you should restrain the two overall strictly 
> (since absolutely most of these atoms are not on special positions) and not 
> to refine the two 0.5 occupancies either, respecting the crystallographic 
> 2-fold.  This is equivalent to perfect twin from p32 theoretically (although 
> refinement with twin mode in p32 and none-twin mode in p3221 may give 
> difference even large).  If you refined and resulted in occupancies away from 
> 0.5, the symmetry was proven to be broken, which supports P32 twinning.
> Lijun
>  
> Sent from my iPhone
> 
> 
> On Aug 27, 2021, at 6:56 AM, Oganesyan, Vaheh 
>  wrote:
> 
> 
> How P3221 can be an option if it assumes chain on axis? I guess I’m missing 
> something, but per my belief only those sg will be possible for which there 
> is no axis going through the extra molecule. P1 sg looks the only correct 
> option here in my humble opinion.
> Democracy (voting) depends on science. However, the reverse is not, 
> thankfully.
>  
> Vaheh
>  
> From: CCP4 bulletin board  On Behalf Of Peer Mittl
> Sent: Friday, August 27, 2021 6:32 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?
>  
> Dear Herman,
> 
> The answer probably depends on the impact of the "extra" chain on the 
> sublattice. If there is no impact the "true" space group is P3221 with 
> one chain on the special position. If the swapping of the extra chain 
> influences the sublattice P32 (or C2 or P1, as pointed out by Kay) 
> twinned to P3221 might be the better description.
> 
> All the best,
> Peer
> 
> On 27.08.2021 10:56, Schreuder, Herman /DE wrote:
> >
> > Dear Peer and Eleanor,
> >
> > This is indeed what I am suspecting: If the “twinning operator” in P32 
> > puts 4 out of 5 protein chains on top of symmetry mates, is the “true” 
> > space group then P32, with 5 twinned chains, or P3221 with 4 normal 
> > chains and 1 chain on a special position? I would vote for the latter.
> >
> > Best,
> >
> > Herman
> >
> > *Von:* CCP4 bulletin board  *Im Auftrag von 
> > *Peer Mittl
> > *Gesendet:* Freitag, 27. August 2021 10:17
> > *An:* CCP4BB@JISCMAIL.AC.UK
> > *Betreff:* Re: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?
> >
> > Dear Eleanor,
> >
> > I indeed used r/tefmac for the refinement and it came up with the values
> > HKL (a=0.56), KH-L (a=0.44). It would be interesting to see if a
> > refinement in P3221 would come up with the same occupancies for the
> > alternative conformations for the "extra" chain on the 2-fold axis. It
> > seems as if the "well-ordered" chains (2 in P3221, 4 in P32)

[ccp4bb] Antwort: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Peer Mittl]

Dear Vaheh,

I agree with you, at least in your last statement. I guess we all agree that 
certain molecules can occupy special positions on true rotation axis. Strictly, 
this is only possible if the molecule obeys the rotation symmetry. For water 
molecules on 2-folds you already have to make assumptions about the "invisible" 
protons. I guess, many of us have seen even larger and asymmetric solvent 
molecules, such as glycerol, MPD or buffer molecules on special positions, 
which locally break the crystal symmetry. The work around for this issue would 
be to define two alternative conformations for this molecule, because these 
conformations do not "see" each other, as pointed out by Herman. But where is 
the upper limit for the molecular weight of this molecule?

I (and perhaps most other crystallographers) would not refine such a case as a 
twinned structure in a lower symmetry space group, because the major part of 
the AU obeys the crystal symmetry. Furthermore, there is a fundamental 
difference between crystallographic symmetry and the symmetry of a twin law. 
The crystallographic symmetry covers the entire crystal, whereas the twin law 
just relates twin domains locally. Refining a true P3221 structure as a twinned 
P32 structure is simply the wrong thing to do. 

All the best,
Peer



-"CCP4 bulletin board"  schrieb: -
An: CCP4BB@JISCMAIL.AC.UK
Von: "Oganesyan, Vaheh" 
Gesendet von: "CCP4 bulletin board" 
Datum: 27.08.2021 13:56
Betreff: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

   
 How P3221 can be an option if it assumes chain on axis? I guess I’m missing 
something, but per my belief only those sg will be possible for which there is 
no axis going through the extra molecule. P1 sg looks the only correct option 
here  in my humble opinion.
 Democracy (voting) depends on science. However, the reverse is not, 
thankfully. 
  
 Vaheh
  
 
 
 From: CCP4 bulletin board   On Behalf Of Peer Mittl
 Sent: Friday, August 27, 2021 6:32 AM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

 Dear Herman,
 
 The answer probably depends on the impact of the "extra" chain on the 
 sublattice. If there is no impact the "true" space group is P3221 with 
 one chain on the special position. If the swapping of the extra chain 
 influences the sublattice P32 (or C2 or P1, as pointed out by Kay) 
 twinned to P3221 might be the better description.
 
 All the best,
 Peer
 
 On 27.08.2021 10:56, Schreuder, Herman /DE wrote:
 >
 > Dear Peer and Eleanor,
 >
 > This is indeed what I am suspecting: If the “twinning operator” in P32 
 > puts 4 out of 5 protein chains on top of symmetry mates, is the “true” 
 > space group then P32, with 5 twinned chains, or P3221 with 4 normal 
 > chains and 1 chain on a special position? I would vote for the latter.
 >
 > Best,
 >
 > Herman
 >
 > *Von:* CCP4 bulletin board  *Im Auftrag von 
 > *Peer Mittl
 > *Gesendet:* Freitag, 27. August 2021 10:17
 > *An:* CCP4BB@JISCMAIL.AC.UK
 > *Betreff:* Re: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?
 >
 > Dear Eleanor,
 >
 > I indeed used r/tefmac for the refinement and it came up with the values
 > HKL (a=0.56), KH-L (a=0.44). It would be interesting to see if a
 > refinement in P3221 would come up with the same occupancies for the
 > alternative conformations for the "extra" chain on the 2-fold axis. It
 > seems as if the "well-ordered" chains (2 in P3221, 4 in P32) form a
 > sublattice with P3221 symmetry and it's just the "extra" chain, which
 > generates the twinning.
 >
 > All the best,
 > Peer
 >
 > On 26.08.2021 18:09, Eleanor Dodson wrote:
 > > Motto =mitti in predictive text!
 > >
 > > On Thu, 26 Aug 2021 at 16:52, Eleanor Dodson
 > > mailto:eleanor.dod...@york.ac.uk 
 > <mailto:eleanor.dod...@york.ac.uk%20%3cmailto:eleanor.dod...@york.ac.uk>>> 
 > wrote:
 > >
 > > Great, motto. I think you have nailed it! Did you use tefmac for
 > > twinned refinement? And if so what did it suggest the twin
 > >  fraction is?
 > >
 > > On Thu, 26 Aug 2021 at 16:30, Peer Mittl  <mailto:mi...@bioc.uzh.ch%0b>> <mailto:mi...@bioc.uzh.ch 
 > <mailto:mi...@bioc.uzh.ch>>> wrote:
 > >
 > > Yes, the data indeed seems to be twinned and the tNCS has
 > > masked the twinning statistics, which is why I haven't
 > > considered it so far.
 > >
 > > I have not tried twinned refinement in C2 and P1 yet, but
 > > refining 4 chains in P32 with twinning yields a difference ED
 > > map that clearly indicates one (and just on!) orientation for
 > > the 5th chain. Thank you all for your suggestions.
 > >
 &

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Jeffrey B Bonanno]

Hi Kay,

Can you also comment on Rfree set selection? It seems thin shell might be 
preferred in these cases?

jbb

Jeffrey B. Bonanno, Ph.D.
Department of Biochemistry
Albert Einstein College of Medicine
1300 Morris Park Avenue
Bronx, NY 10461
off. 718-430-2452 fax. 718-430-8565
email jeffrey.bona...@einsteinmed.org

-Original Message-
From: CCP4 bulletin board  On Behalf Of Kay Diederichs
Sent: Friday, August 27, 2021 9:16 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

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.

Dear Herman,

there is no freedom to choose between twinned-P32 (5 chains) and 
untwinned-P3221 (2 chains plus 0.5 chain in two orientations) or even vote; it 
is either one or the other, and there should be a difference in R values.
Why? A twin operator leads to addition of intensities whereas a spacegroup 
operator leads to addition of (complex) structure factors. They are not 
exchangeable. Both produce symmetry, but the math is different, and thus the 
resulting intensities are different.
The correct spacegroup can only be found by trying all possibilities, and 
comparing R values. However, for a meaningful comparison of R values, one has 
to restrain the NCS (and one cannot strictly compare twinned refinement results 
with untwinned refinement, as noted earlier).

best wishes,
Kay

On Fri, 27 Aug 2021 08:56:38 +, Schreuder, Herman /DE 
 wrote:

>Dear Peer and Eleanor,
>
>This is indeed what I am suspecting: If the "twinning operator" in P32 puts 4 
>out of 5 protein chains on top of symmetry mates, is the "true" space group 
>then P32, with 5 twinned chains, or P3221 with 4 normal chains and 1 chain on 
>a special position? I would vote for the latter.
>
>Best,
>Herman
>
>Von: CCP4 bulletin board  Im Auftrag von Peer 
>Mittl
>Gesendet: Freitag, 27. August 2021 10:17
>An: CCP4BB@JISCMAIL.AC.UK
>Betreff: Re: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?
>
>Dear Eleanor,
>
>I indeed used r/tefmac for the refinement and it came up with the 
>values HKL (a=0.56), KH-L (a=0.44). It would be interesting to see if a 
>refinement in P3221 would come up with the same occupancies for the 
>alternative conformations for the "extra" chain on the 2-fold axis. It 
>seems as if the "well-ordered" chains (2 in P3221, 4 in P32) form a 
>sublattice with P3221 symmetry and it's just the "extra" chain, which 
>generates the twinning.
>
>All the best,
>Peer
>
>On 26.08.2021 18:09, Eleanor Dodson wrote:
>> Motto =mitti in predictive text!
>>
>> On Thu, 26 Aug 2021 at 16:52, Eleanor Dodson 
>> > <mailto:eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk%20%3cmailto:eleanor.dod...@york.ac.uk>>>
>>  wrote:
>>
>> Great, motto. I think you have nailed it! Did you use tefmac for 
>> twinned refinement? And if so what did it suggest the twin  fraction 
>> is?
>>
>> On Thu, 26 Aug 2021 at 16:30, Peer Mittl <mailto:mi...@bioc.uzh.ch%0b>> <mailto:mi...@bioc.uzh.ch>> wrote:
>>
>> Yes, the data indeed seems to be twinned and the tNCS has masked the 
>> twinning statistics, which is why I haven't considered it so far.
>>
>> I have not tried twinned refinement in C2 and P1 yet, but refining 4 
>> chains in P32 with twinning yields a difference ED map that clearly 
>> indicates one (and just on!) orientation for the 5th chain. Thank you 
>> all for your suggestions.
>>
>> Have a nice evening,
>> Peer
>>
>> -"CCP4 bulletin board" <mailto:CCP4BB@JISCMAIL.AC.UK%0b>> <mailto:CCP4BB@JISCMAIL.AC.UK>> 
>schrieb: -
>> An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
>> <mailto:CCP4BB@JISCMAIL.AC.UK>
>> Von: "Kay Diederichs"
>> Gesendet von: "CCP4 bulletin board"
>> Datum: 26.08.2021 16:41
>> Betreff: Re: [ccp4bb] chain on 2-fold axis?
>>
>> Dear Peer,
>>
>> I suspect that the true spacegroup has lower symmetry than P3221, and 
>> that there may be twinning masked by tNCS.
>> Subgroups of P3221 are C2 and P32 (
>> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstr
>> ucbio.biologie.unikonstanz.de%2Fxdswiki%2Findex.php%2FSpace_group_det
>> ermination%23Subgroup_and_supergroup_relations_of_these_space_groups&
>> amp;data=04%7C01%7Cjeffrey.bonanno%40EINSTEINMED.ORG%7C8cb9aec600e747
&

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Kay Diederichs]

Dear Herman,

there is no freedom to choose between twinned-P32 (5 chains) and 
untwinned-P3221 (2 chains plus 0.5 chain in two orientations) or even vote; it 
is either one or the other, and there should be a difference in R values. 
Why? A twin operator leads to addition of intensities whereas a spacegroup 
operator leads to addition of (complex) structure factors. They are not 
exchangeable. Both produce symmetry, but the math is different, and thus the 
resulting intensities are different. 
The correct spacegroup can only be found by trying all possibilities, and 
comparing R values. However, for a meaningful comparison of R values, one has 
to restrain the NCS (and one cannot strictly compare twinned refinement results 
with untwinned refinement, as noted earlier).

best wishes,
Kay

On Fri, 27 Aug 2021 08:56:38 +, Schreuder, Herman /DE 
 wrote:

>Dear Peer and Eleanor,
>
>This is indeed what I am suspecting: If the "twinning operator" in P32 puts 4 
>out of 5 protein chains on top of symmetry mates, is the "true" space group 
>then P32, with 5 twinned chains, or P3221 with 4 normal chains and 1 chain on 
>a special position? I would vote for the latter.
>
>Best,
>Herman
>
>Von: CCP4 bulletin board  Im Auftrag von Peer Mittl
>Gesendet: Freitag, 27. August 2021 10:17
>An: CCP4BB@JISCMAIL.AC.UK
>Betreff: Re: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?
>
>Dear Eleanor,
>
>I indeed used r/tefmac for the refinement and it came up with the values
>HKL (a=0.56), KH-L (a=0.44). It would be interesting to see if a
>refinement in P3221 would come up with the same occupancies for the
>alternative conformations for the "extra" chain on the 2-fold axis. It
>seems as if the "well-ordered" chains (2 in P3221, 4 in P32) form a
>sublattice with P3221 symmetry and it's just the "extra" chain, which
>generates the twinning.
>
>All the best,
>Peer
>
>On 26.08.2021 18:09, Eleanor Dodson wrote:
>> Motto =mitti in predictive text!
>>
>> On Thu, 26 Aug 2021 at 16:52, Eleanor Dodson
>> > >>
>>  wrote:
>>
>> Great, motto. I think you have nailed it! Did you use tefmac for
>> twinned refinement? And if so what did it suggest the twin
>>  fraction is?
>>
>> On Thu, 26 Aug 2021 at 16:30, Peer Mittl > > wrote:
>>
>> Yes, the data indeed seems to be twinned and the tNCS has
>> masked the twinning statistics, which is why I haven't
>> considered it so far.
>>
>> I have not tried twinned refinement in C2 and P1 yet, but
>> refining 4 chains in P32 with twinning yields a difference ED
>> map that clearly indicates one (and just on!) orientation for
>> the 5th chain. Thank you all for your suggestions.
>>
>> Have a nice evening,
>> Peer
>>
>> -"CCP4 bulletin board" > > schrieb: 
>-
>> An: CCP4BB@JISCMAIL.AC.UK 
>> 
>> Von: "Kay Diederichs"
>> Gesendet von: "CCP4 bulletin board"
>> Datum: 26.08.2021 16:41
>> Betreff: Re: [ccp4bb] chain on 2-fold axis?
>>
>> Dear Peer,
>>
>> I suspect that the true spacegroup has lower symmetry than
>> P3221, and that there may be twinning masked by tNCS.
>> Subgroups of P3221 are C2 and P32 (
>> https://strucbio.biologie.unikonstanz.de/xdswiki/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_groups
>> >
>> )
>> and of course P1.
>> What I'd do is process the data, and solve (use the best chain
>> of the refined P3221 model for MR) and refine the structure in
>> these spacegroups.
>> Inspect the results: If P1 is clearly better than P32 and C2,
>> P1 is correct.
>> If C2 (P32) is clearly better than P32 (C2), then P1 should
>> give the same R-values as the better one; if so, P1 can be
>> discarded.
>> Try this with and without twin refinement - although it's hard
>> to compare R-values of non-twinned and twinned refinements.
>>
>> The automatic way to do this is with Zanuda. If you run that
>> locally, you can make refmac do twin refinement.
>>
>> For all resulting structures, I'd also feed the resulting
>> Fcalc (!) into pointless. That should reveal that the packing
>> is indeed close to P3221.
>>
>> Best wishes,
>> Kay
>>
>>
>> On Thu, 26 Aug 2021 11:54:06 +0200, Peer Mittl
>> > >>
>>  wrote:
>>
>> >Der CCP4 community,
>> >
>> >Is there a refinement program that can 

[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Schreuder, Herman /DE]

Dear Lijun,
with this argument I agree: the interactions between the two orientations of 
the “twinned” chain and the neighboring molecules will be different and the 
interacting side chains will almost certainly have different orientations, 
which necessitates a twinning of the whole structure.
Best,
Herman

Von: CCP4 bulletin board  Im Auftrag von Lijun Liu
Gesendet: Freitag, 27. August 2021 14:22
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

I believe it is a twin from P32.



  1.  Not like the assignment of double conformations with partial occupancies 
to small part of asu, for examples, a side chain of lysin or a small fragment 
of a protein, which have both conformations stayed in the same specific asu at 
the same time.  For this p3221 asu, if one copy of that chain occupies the part 
of the asu, the other so-called conformation will not appear in the same asu at 
the same time, so the conformation and occupancy issue was arisen from 
different cell units, it is a twin from p32.
  2.  Talking about the asu of p3221, it holds 3 chains, the chain of interest 
assigned as 2 conformations related by a strict 2-fold.  Since you believe and 
have reduced to P3221, then you should restrain the two overall strictly (since 
absolutely most of these atoms are not on special positions) and not to refine 
the two 0.5 occupancies either, respecting the crystallographic 2-fold.  This 
is equivalent to perfect twin from p32 theoretically (although refinement with 
twin mode in p32 and none-twin mode in p3221 may give difference even large).  
If you refined and resulted in occupancies away from 0.5, the symmetry was 
proven to be broken, which supports P32 twinning.

Lijun

Sent from my iPhone


On Aug 27, 2021, at 6:56 AM, Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>> wrote:

How P3221 can be an option if it assumes chain on axis? I guess I’m missing 
something, but per my belief only those sg will be possible for which there is 
no axis going through the extra molecule. P1 sg looks the only correct option 
here in my humble opinion.
Democracy (voting) depends on science. However, the reverse is not, thankfully.

Vaheh

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Peer Mittl
Sent: Friday, August 27, 2021 6:32 AM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

Dear Herman,

The answer probably depends on the impact of the "extra" chain on the
sublattice. If there is no impact the "true" space group is P3221 with
one chain on the special position. If the swapping of the extra chain
influences the sublattice P32 (or C2 or P1, as pointed out by Kay)
twinned to P3221 might be the better description.

All the best,
Peer

On 27.08.2021 10:56, Schreuder, Herman /DE wrote:
>
> Dear Peer and Eleanor,
>
> This is indeed what I am suspecting: If the “twinning operator” in P32
> puts 4 out of 5 protein chains on top of symmetry mates, is the “true”
> space group then P32, with 5 twinned chains, or P3221 with 4 normal
> chains and 1 chain on a special position? I would vote for the latter.
>
> Best,
>
> Herman
>
> *Von:* CCP4 bulletin board 
> mailto:CCP4BB@JISCMAIL.AC.UK>> *Im Auftrag von
> *Peer Mittl
> *Gesendet:* Freitag, 27. August 2021 10:17
> *An:* CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
> *Betreff:* Re: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?
>
> Dear Eleanor,
>
> I indeed used r/tefmac for the refinement and it came up with the values
> HKL (a=0.56), KH-L (a=0.44). It would be interesting to see if a
> refinement in P3221 would come up with the same occupancies for the
> alternative conformations for the "extra" chain on the 2-fold axis. It
> seems as if the "well-ordered" chains (2 in P3221, 4 in P32) form a
> sublattice with P3221 symmetry and it's just the "extra" chain, which
> generates the twinning.
>
> All the best,
> Peer
>
> On 26.08.2021 18:09, Eleanor Dodson wrote:
> > Motto =mitti in predictive text!
> >
> > On Thu, 26 Aug 2021 at 16:52, Eleanor Dodson
> > mailto:eleanor.dod...@york.ac.uk
<mailto:eleanor.dod...@york.ac.uk%20%3cmailto:eleanor.dod...@york.ac.uk%20%0b>> 
<mailto:eleanor.dod...@york.ac.uk%20%3cmailto:eleanor.dod...@york.ac.uk>>>
> wrote:
> >
> > Great, motto. I think you have nailed it! Did you use tefmac for
> > twinned refinement? And if so what did it suggest the twin
> >  fraction is?
> >
> > On Thu, 26 Aug 2021 at 16:30, Peer Mittl mailto:mi...@bioc.uzh.ch%0b>> <mailto:mi...@bioc.uzh.ch%0b>> 
<mailto:mi...@bioc.uzh.ch
<mailto:mi...@bioc.uzh.ch%20%0b>> <mailto:mi...@bioc.uzh.ch>>

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Lijun Liu]

I believe it is a twin from P32.

Not like the assignment of double conformations with partial occupancies to 
small part of asu, for examples, a side chain of lysin or a small fragment of a 
protein, which have both conformations stayed in the same specific asu at the 
same time.  For this p3221 asu, if one copy of that chain occupies the part of 
the asu, the other so-called conformation will not appear in the same asu at 
the same time, so the conformation and occupancy issue was arisen from 
different cell units, it is a twin from p32.
Talking about the asu of p3221, it holds 3 chains, the chain of interest 
assigned as 2 conformations related by a strict 2-fold.  Since you believe and 
have reduced to P3221, then you should restrain the two overall strictly (since 
absolutely most of these atoms are not on special positions) and not to refine 
the two 0.5 occupancies either, respecting the crystallographic 2-fold.  This 
is equivalent to perfect twin from p32 theoretically (although refinement with 
twin mode in p32 and none-twin mode in p3221 may give difference even large).  
If you refined and resulted in occupancies away from 0.5, the symmetry was 
proven to be broken, which supports P32 twinning.
Lijun

Sent from my iPhone

> On Aug 27, 2021, at 6:56 AM, Oganesyan, Vaheh 
>  wrote:
> 
> 
> How P3221 can be an option if it assumes chain on axis? I guess I’m missing 
> something, but per my belief only those sg will be possible for which there 
> is no axis going through the extra molecule. P1 sg looks the only correct 
> option here in my humble opinion.
> Democracy (voting) depends on science. However, the reverse is not, 
> thankfully.
>  
> Vaheh
>  
> From: CCP4 bulletin board  On Behalf Of Peer Mittl
> Sent: Friday, August 27, 2021 6:32 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?
>  
> Dear Herman,
> 
> The answer probably depends on the impact of the "extra" chain on the 
> sublattice. If there is no impact the "true" space group is P3221 with 
> one chain on the special position. If the swapping of the extra chain 
> influences the sublattice P32 (or C2 or P1, as pointed out by Kay) 
> twinned to P3221 might be the better description.
> 
> All the best,
> Peer
> 
> On 27.08.2021 10:56, Schreuder, Herman /DE wrote:
> >
> > Dear Peer and Eleanor,
> >
> > This is indeed what I am suspecting: If the “twinning operator” in P32 
> > puts 4 out of 5 protein chains on top of symmetry mates, is the “true” 
> > space group then P32, with 5 twinned chains, or P3221 with 4 normal 
> > chains and 1 chain on a special position? I would vote for the latter.
> >
> > Best,
> >
> > Herman
> >
> > *Von:* CCP4 bulletin board  *Im Auftrag von 
> > *Peer Mittl
> > *Gesendet:* Freitag, 27. August 2021 10:17
> > *An:* CCP4BB@JISCMAIL.AC.UK
> > *Betreff:* Re: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?
> >
> > Dear Eleanor,
> >
> > I indeed used r/tefmac for the refinement and it came up with the values
> > HKL (a=0.56), KH-L (a=0.44). It would be interesting to see if a
> > refinement in P3221 would come up with the same occupancies for the
> > alternative conformations for the "extra" chain on the 2-fold axis. It
> > seems as if the "well-ordered" chains (2 in P3221, 4 in P32) form a
> > sublattice with P3221 symmetry and it's just the "extra" chain, which
> > generates the twinning.
> >
> > All the best,
> > Peer
> >
> > On 26.08.2021 18:09, Eleanor Dodson wrote:
> > > Motto =mitti in predictive text!
> > >
> > > On Thu, 26 Aug 2021 at 16:52, Eleanor Dodson
> > > mailto:eleanor.dod...@york.ac.uk 
> > <mailto:eleanor.dod...@york.ac.uk%20%3cmailto:eleanor.dod...@york.ac.uk>>> 
> > wrote:
> > >
> > > Great, motto. I think you have nailed it! Did you use tefmac for
> > > twinned refinement? And if so what did it suggest the twin
> > >  fraction is?
> > >
> > > On Thu, 26 Aug 2021 at 16:30, Peer Mittl  > <mailto:mi...@bioc.uzh.ch%0b>> <mailto:mi...@bioc.uzh.ch 
> > <mailto:mi...@bioc.uzh.ch>>> wrote:
> > >
> > > Yes, the data indeed seems to be twinned and the tNCS has
> > > masked the twinning statistics, which is why I haven't
> > > considered it so far.
> > >
> > > I have not tried twinned refinement in C2 and P1 yet, but
> > > refining 4 chains in P32 with twinning yields a difference ED
> > > map that clearly indicates one (and just on!) orientation for
> > > the 5th chain. Than

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Eleanor Dodson]

P1 is always a "correct" answer but this data says there is a three fold
axis.
Twinning generates an apparent  2 fold in the diffraction pattern, and with
four of the five molecules obeying that 2fold, and  twin factors 0.56/0.44
that will appear pretty exact..

And the NC transl;ation disguises the twin analyses..
So it isnt as weird as Mitti first thought ..
 Eleanor
(I have seen this behavior before - we processed data as I422 then realised
about 15% of the residues could not obey the 4 fold axis, and we had to
back off to I222...)

On Fri, 27 Aug 2021 at 12:56, Oganesyan, Vaheh <
vaheh.oganes...@astrazeneca.com> wrote:

> How P3221 can be an option if it assumes chain on axis? I guess I’m
> missing something, but per my belief only those sg will be possible for
> which there is no axis going through the extra molecule. P1 sg looks the
> only correct option here in my humble opinion.
>
> Democracy (voting) depends on science. However, the reverse is not,
> thankfully.
>
>
>
> Vaheh
>
>
>
> *From:* CCP4 bulletin board  * On Behalf Of *Peer
> Mittl
> *Sent:* Friday, August 27, 2021 6:32 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on
> 2-fold axis?
>
>
>
> Dear Herman,
>
> The answer probably depends on the impact of the "extra" chain on the
> sublattice. If there is no impact the "true" space group is P3221 with
> one chain on the special position. If the swapping of the extra chain
> influences the sublattice P32 (or C2 or P1, as pointed out by Kay)
> twinned to P3221 might be the better description.
>
> All the best,
> Peer
>
> On 27.08.2021 10:56, Schreuder, Herman /DE wrote:
> >
> > Dear Peer and Eleanor,
> >
> > This is indeed what I am suspecting: If the “twinning operator” in P32
> > puts 4 out of 5 protein chains on top of symmetry mates, is the “true”
> > space group then P32, with 5 twinned chains, or P3221 with 4 normal
> > chains and 1 chain on a special position? I would vote for the latter.
> >
> > Best,
> >
> > Herman
> >
> > *Von:* CCP4 bulletin board  *Im Auftrag von
> > *Peer Mittl
> > *Gesendet:* Freitag, 27. August 2021 10:17
> > *An:* CCP4BB@JISCMAIL.AC.UK
> > *Betreff:* Re: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?
> >
> > Dear Eleanor,
> >
> > I indeed used r/tefmac for the refinement and it came up with the values
> > HKL (a=0.56), KH-L (a=0.44). It would be interesting to see if a
> > refinement in P3221 would come up with the same occupancies for the
> > alternative conformations for the "extra" chain on the 2-fold axis. It
> > seems as if the "well-ordered" chains (2 in P3221, 4 in P32) form a
> > sublattice with P3221 symmetry and it's just the "extra" chain, which
> > generates the twinning.
> >
> > All the best,
> > Peer
> >
> > On 26.08.2021 18:09, Eleanor Dodson wrote:
> > > Motto =mitti in predictive text!
> > >
> > > On Thu, 26 Aug 2021 at 16:52, Eleanor Dodson
> > > mailto:eleanor.dod...@york.ac.uk
> mailto:eleanor.dod...@york.ac.uk%20%0b>> <
> mailto:eleanor.dod...@york.ac.uk%20%3cmailto:eleanor.dod...@york.ac.uk
> mailto:eleanor.dod...@york.ac.uk>>>>
> > wrote:
> > >
> > > Great, motto. I think you have nailed it! Did you use tefmac for
> > > twinned refinement? And if so what did it suggest the twin
> > >  fraction is?
> > >
> > > On Thu, 26 Aug 2021 at 16:30, Peer Mittl  > <mailto:mi...@bioc.uzh.ch%0b
> >> <mailto:mi...@bioc.uzh.ch
> > <mailto:mi...@bioc.uzh.ch >>>
> wrote:
> > >
> > > Yes, the data indeed seems to be twinned and the tNCS has
> > > masked the twinning statistics, which is why I haven't
> > > considered it so far.
> > >
> > > I have not tried twinned refinement in C2 and P1 yet, but
> > > refining 4 chains in P32 with twinning yields a difference ED
> > > map that clearly indicates one (and just on!) orientation for
> > > the 5th chain. Thank you all for your suggestions.
> > >
> > > Have a nice evening,
> > > Peer
> > >
> > > -"CCP4 bulletin board"  > <mailto:CCP4BB@JISCMAIL.AC.UK%0b
> >> <mailto:CCP4BB@JISCMAIL.AC.UK
> > <mailto:CCP4BB@JISCMAIL.AC.UK
> >>> schrieb: -
> > > An: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK
> >
> > <mailto:CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK
> mailto:CCP4BB@JISCMAIL.AC.UK>>>
> 

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Oganesyan, Vaheh]

How P3221 can be an option if it assumes chain on axis? I guess I'm missing 
something, but per my belief only those sg will be possible for which there is 
no axis going through the extra molecule. P1 sg looks the only correct option 
here in my humble opinion.
Democracy (voting) depends on science. However, the reverse is not, thankfully.

Vaheh

From: CCP4 bulletin board  On Behalf Of Peer Mittl
Sent: Friday, August 27, 2021 6:32 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

Dear Herman,

The answer probably depends on the impact of the "extra" chain on the
sublattice. If there is no impact the "true" space group is P3221 with
one chain on the special position. If the swapping of the extra chain
influences the sublattice P32 (or C2 or P1, as pointed out by Kay)
twinned to P3221 might be the better description.

All the best,
Peer

On 27.08.2021 10:56, Schreuder, Herman /DE wrote:
>
> Dear Peer and Eleanor,
>
> This is indeed what I am suspecting: If the "twinning operator" in P32
> puts 4 out of 5 protein chains on top of symmetry mates, is the "true"
> space group then P32, with 5 twinned chains, or P3221 with 4 normal
> chains and 1 chain on a special position? I would vote for the latter.
>
> Best,
>
> Herman
>
> *Von:* CCP4 bulletin board 
> mailto:CCP4BB@JISCMAIL.AC.UK>> *Im Auftrag von
> *Peer Mittl
> *Gesendet:* Freitag, 27. August 2021 10:17
> *An:* CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
> *Betreff:* Re: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?
>
> Dear Eleanor,
>
> I indeed used r/tefmac for the refinement and it came up with the values
> HKL (a=0.56), KH-L (a=0.44). It would be interesting to see if a
> refinement in P3221 would come up with the same occupancies for the
> alternative conformations for the "extra" chain on the 2-fold axis. It
> seems as if the "well-ordered" chains (2 in P3221, 4 in P32) form a
> sublattice with P3221 symmetry and it's just the "extra" chain, which
> generates the twinning.
>
> All the best,
> Peer
>
> On 26.08.2021 18:09, Eleanor Dodson wrote:
> > Motto =mitti in predictive text!
> >
> > On Thu, 26 Aug 2021 at 16:52, Eleanor Dodson
> > mailto:eleanor.dod...@york.ac.uk
<mailto:eleanor.dod...@york.ac.uk%20%3cmailto:eleanor.dod...@york.ac.uk%20%0b>> 
<mailto:eleanor.dod...@york.ac.uk%20%3cmailto:eleanor.dod...@york.ac.uk>>>
> wrote:
> >
> > Great, motto. I think you have nailed it! Did you use tefmac for
> > twinned refinement? And if so what did it suggest the twin
> >  fraction is?
> >
> > On Thu, 26 Aug 2021 at 16:30, Peer Mittl mailto:mi...@bioc.uzh.ch%0b>> <mailto:mi...@bioc.uzh.ch%0b>> 
<mailto:mi...@bioc.uzh.ch
<mailto:mi...@bioc.uzh.ch%20%0b>> <mailto:mi...@bioc.uzh.ch>>> wrote:
> >
> > Yes, the data indeed seems to be twinned and the tNCS has
> > masked the twinning statistics, which is why I haven't
> > considered it so far.
> >
> > I have not tried twinned refinement in C2 and P1 yet, but
> > refining 4 chains in P32 with twinning yields a difference ED
> > map that clearly indicates one (and just on!) orientation for
> > the 5th chain. Thank you all for your suggestions.
> >
> > Have a nice evening,
> > Peer
> >
> > -"CCP4 bulletin board" mailto:CCP4BB@JISCMAIL.AC.UK%0b>> <mailto:CCP4BB@JISCMAIL.AC.UK%0b>> 
<mailto:CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK%20%0b>> <mailto:CCP4BB@JISCMAIL.AC.UK>>> schrieb: 
-
> > An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
> > <mailto:CCP4BB@JISCMAIL.AC.UK>
> <mailto:CCP4BB@JISCMAIL.AC.UK 
> <mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK%20%3cmailto:CCP4BB@JISCMAIL.AC.UK>>>
> > Von: "Kay Diederichs"
> > Gesendet von: "CCP4 bulletin board"
> > Datum: 26.08.2021 16:41
> > Betreff: Re: [ccp4bb] chain on 2-fold axis?
> >
> > Dear Peer,
> >
> > I suspect that the true spacegroup has lower symmetry than
> > P3221, and that there may be twinning masked by tNCS.
> > Subgroups of P3221 are C2 and P32 (
> >
> https://strucbio.biologie.unikonstanz.de/xdswiki/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_groups<https://strucbio.biologie.unikonstanz.de/xdswiki/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_groups>
> <https://strucbio.biologie.unikonstanz.de/xdswiki/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_gro

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Peer Mittl]

Dear Herman,

The answer probably depends on the impact of the "extra" chain on the 
sublattice. If there is no impact the "true" space group is P3221 with 
one chain on the special position. If the swapping of the extra chain 
influences the sublattice P32 (or C2 or P1, as pointed out by Kay) 
twinned to P3221 might be the better description.


All the best,
Peer

On 27.08.2021 10:56, Schreuder, Herman /DE wrote:


Dear Peer and Eleanor,

This is indeed what I am suspecting: If the “twinning operator” in P32 
puts 4 out of 5 protein chains on top of symmetry mates, is the “true” 
space group then P32, with 5 twinned chains, or P3221 with 4 normal 
chains and 1 chain on a special position? I would vote for the latter.


Best,

Herman

*Von:* CCP4 bulletin board  *Im Auftrag von 
*Peer Mittl

*Gesendet:* Freitag, 27. August 2021 10:17
*An:* CCP4BB@JISCMAIL.AC.UK
*Betreff:* Re: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

Dear Eleanor,

I indeed used r/tefmac for the refinement and it came up with the values
HKL (a=0.56), KH-L (a=0.44). It would be interesting to see if a
refinement in P3221 would come up with the same occupancies for the
alternative conformations for the "extra" chain on the 2-fold axis. It
seems as if the "well-ordered" chains (2 in P3221, 4 in P32) form a
sublattice with P3221 symmetry and it's just the "extra" chain, which
generates the twinning.

All the best,
Peer

On 26.08.2021 18:09, Eleanor Dodson wrote:
> Motto =mitti in predictive text!
>
> On Thu, 26 Aug 2021 at 16:52, Eleanor Dodson
> mailto:eleanor.dod...@york.ac.uk 
>> 
wrote:

>
> Great, motto. I think you have nailed it! Did you use tefmac for
> twinned refinement? And if so what did it suggest the twin
>  fraction is?
>
> On Thu, 26 Aug 2021 at 16:30, Peer Mittl > >> wrote:

>
> Yes, the data indeed seems to be twinned and the tNCS has
> masked the twinning statistics, which is why I haven't
> considered it so far.
>
> I have not tried twinned refinement in C2 and P1 yet, but
> refining 4 chains in P32 with twinning yields a difference ED
> map that clearly indicates one (and just on!) orientation for
> the 5th chain. Thank you all for your suggestions.
>
> Have a nice evening,
> Peer
>
> -"CCP4 bulletin board" > >> schrieb: -
> An: CCP4BB@JISCMAIL.AC.UK  
>

> Von: "Kay Diederichs"
> Gesendet von: "CCP4 bulletin board"
> Datum: 26.08.2021 16:41
> Betreff: Re: [ccp4bb] chain on 2-fold axis?
>
> Dear Peer,
>
> I suspect that the true spacegroup has lower symmetry than
> P3221, and that there may be twinning masked by tNCS.
> Subgroups of P3221 are C2 and P32 (
> 
https://strucbio.biologie.unikonstanz.de/xdswiki/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_groups 

> 
>

> )
> and of course P1.
> What I'd do is process the data, and solve (use the best chain
> of the refined P3221 model for MR) and refine the structure in
> these spacegroups.
> Inspect the results: If P1 is clearly better than P32 and C2,
> P1 is correct.
> If C2 (P32) is clearly better than P32 (C2), then P1 should
> give the same R-values as the better one; if so, P1 can be
> discarded.
> Try this with and without twin refinement - although it's hard
> to compare R-values of non-twinned and twinned refinements.
>
> The automatic way to do this is with Zanuda. If you run that
> locally, you can make refmac do twin refinement.
>
> For all resulting structures, I'd also feed the resulting
> Fcalc (!) into pointless. That should reveal that the packing
> is indeed close to P3221.
>
> Best wishes,
> Kay
>
>
> On Thu, 26 Aug 2021 11:54:06 +0200, Peer Mittl
> mailto:mi...@bioc.uzh.ch 
>> wrote:

>
> >Der CCP4 community,
> >
> >Is there a refinement program that can handle protein
> monomers sitting
> >on crystallographic 2-folds?
> >
> >This is probably a strange question but we have the following
> situation.
> >We have a 2.6 Ang datasets in SG P3221 (Rpim=4%, Isa=19.6)
> and a clear
> >molrep solution with 2 chains, albeit with tNCS (0/0/0.5)
> that can be
> >refined to around 27/33% Rfactor. According to Vm a third
> chain could be
> >present. So far so good, but there is clear difference ED for
> 

[ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

[Schreuder, Herman /DE]

Dear Peer and Eleanor,

This is indeed what I am suspecting: If the "twinning operator" in P32 puts 4 
out of 5 protein chains on top of symmetry mates, is the "true" space group 
then P32, with 5 twinned chains, or P3221 with 4 normal chains and 1 chain on a 
special position? I would vote for the latter.

Best,
Herman

Von: CCP4 bulletin board  Im Auftrag von Peer Mittl
Gesendet: Freitag, 27. August 2021 10:17
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

Dear Eleanor,

I indeed used r/tefmac for the refinement and it came up with the values
HKL (a=0.56), KH-L (a=0.44). It would be interesting to see if a
refinement in P3221 would come up with the same occupancies for the
alternative conformations for the "extra" chain on the 2-fold axis. It
seems as if the "well-ordered" chains (2 in P3221, 4 in P32) form a
sublattice with P3221 symmetry and it's just the "extra" chain, which
generates the twinning.

All the best,
Peer

On 26.08.2021 18:09, Eleanor Dodson wrote:
> Motto =mitti in predictive text!
>
> On Thu, 26 Aug 2021 at 16:52, Eleanor Dodson
>  >>
>  wrote:
>
> Great, motto. I think you have nailed it! Did you use tefmac for
> twinned refinement? And if so what did it suggest the twin
>  fraction is?
>
> On Thu, 26 Aug 2021 at 16:30, Peer Mittl mailto:mi...@bioc.uzh.ch%0b>> > wrote:
>
> Yes, the data indeed seems to be twinned and the tNCS has
> masked the twinning statistics, which is why I haven't
> considered it so far.
>
> I have not tried twinned refinement in C2 and P1 yet, but
> refining 4 chains in P32 with twinning yields a difference ED
> map that clearly indicates one (and just on!) orientation for
> the 5th chain. Thank you all for your suggestions.
>
> Have a nice evening,
> Peer
>
> -"CCP4 bulletin board" mailto:CCP4BB@JISCMAIL.AC.UK%0b>> > schrieb: 
-
> An: CCP4BB@JISCMAIL.AC.UK 
> 
> Von: "Kay Diederichs"
> Gesendet von: "CCP4 bulletin board"
> Datum: 26.08.2021 16:41
> Betreff: Re: [ccp4bb] chain on 2-fold axis?
>
> Dear Peer,
>
> I suspect that the true spacegroup has lower symmetry than
> P3221, and that there may be twinning masked by tNCS.
> Subgroups of P3221 are C2 and P32 (
> https://strucbio.biologie.unikonstanz.de/xdswiki/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_groups
> >
> )
> and of course P1.
> What I'd do is process the data, and solve (use the best chain
> of the refined P3221 model for MR) and refine the structure in
> these spacegroups.
> Inspect the results: If P1 is clearly better than P32 and C2,
> P1 is correct.
> If C2 (P32) is clearly better than P32 (C2), then P1 should
> give the same R-values as the better one; if so, P1 can be
> discarded.
> Try this with and without twin refinement - although it's hard
> to compare R-values of non-twinned and twinned refinements.
>
> The automatic way to do this is with Zanuda. If you run that
> locally, you can make refmac do twin refinement.
>
> For all resulting structures, I'd also feed the resulting
> Fcalc (!) into pointless. That should reveal that the packing
> is indeed close to P3221.
>
> Best wishes,
> Kay
>
>
> On Thu, 26 Aug 2021 11:54:06 +0200, Peer Mittl
>  >>
>  wrote:
>
> >Der CCP4 community,
> >
> >Is there a refinement program that can handle protein
> monomers sitting
> >on crystallographic 2-folds?
> >
> >This is probably a strange question but we have the following
> situation.
> >We have a 2.6 Ang datasets in SG P3221 (Rpim=4%, Isa=19.6)
> and a clear
> >molrep solution with 2 chains, albeit with tNCS (0/0/0.5)
> that can be
> >refined to around 27/33% Rfactor. According to Vm a third
> chain could be
> >present. So far so good, but there is clear difference ED for
> a third
> >chain sitting exactly on the 2-fold. Since the protein has a
> peculiar
> >shape, one can tell even its orientation. I can relax the
> symmetry to
> >P32 (or even P1) and place the missing chain with 50%
> occupancy on the
> >2-fold. This model can be refined, but I do not like this
> work around,
> >because the data is clearly P3221.
> >
> >Any hints on similar crystal pathologies and how they have
> been handled
> >would be helpful.
> >
> >All the best,
> >Peer
> >
>