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
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: [ccp
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
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
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
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
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
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
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: [
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 a
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
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).
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
re 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:
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
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
.
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
on 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@JISC
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
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)
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
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