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 s
Hello,
I just would guess that you have twinning and disorder of the 5th subunit
around the 2-fold axis at the same time.
The twinning in P3221 with operators HKL and KH-L (involving the full unit cell
contents) is required to explain the observed twinning fraction whereas only
the disorder ca
On Mon, Aug 30, 2021 at 08:44:03PM +0100, Kay Diederichs wrote:
> 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, bu
ing.
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 beg
-"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]
in 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] Antwor
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 don
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
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
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,
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
reass
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 p
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
pote
> 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
>> Subj
einmed.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 attachme
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: [
-
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
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 workin
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).
H
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
; 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
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 e
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
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 us
.
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
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 impa
ormal
> > 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:* CCP4
ds 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 o
etreff:* 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 c
on? 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 cam
An: 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 t
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,
s.
>
> 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 axi
(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
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_g
> *Von:* CCP4 bulletin board *Im Auftrag von *Peer
> Mittl
> *Gesendet:* Donnerstag, 26. August 2021 11:54
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [ccp4bb] chain on 2-fold axis?
>
>
>
> Der CCP4 community,
>
> Is there a refinement program that can handle protein monome
Phenix
or Buster to see if you can refine your structure with one of those programs.
Best,
Herman
Von: CCP4 bulletin board Im Auftrag von Peer Mittl
Gesendet: Donnerstag, 26. August 2021 11:54
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] chain on 2-fold axis?
Der CCP4 community,
Is there a refineme
Deer Peer,
i've got recently two proteins/crystals with the the following
phenomenon: One strand is swapped and extends into the sheet of its
symmetry mate. This happens obviously around a 2-fold axis and it was
hard to see at higher Rfrees. In both cases, only the first 10-20 amino
acids wer
Dear Peer,
Have you looked at your images to check whether there is streakiness in
some parts of the diffraction pattern? You could have a case of lattice
translocation disorder, a nuisance often associated with tNCS but for which
there are remedial methods available.
With best wishes,
Dear Peer,
This is indeed a very strange situation. If you have a molecule sitting
on a crystallographic 2-fold, it would almost certainly overlap with its
symmetry-related copy. A more exotic solution would be a 2-fold disorder
around the axis, with each chain having a 50% occupancy, but I ha
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 chain
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