: [ccp4bb] [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring
I agree with Harry that an ice ring should never require you to process the
data in two separate runs, and hopefully this does not become a standard
approach..
How did you present those data to aimless so it could scale the two
://www-ibmc.u-strasbg.fr/spip-arn/
En date de : Mar 9.4.19, Sam Tang a écrit :
Objet: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring
À: CCP4BB@JISCMAIL.AC.UK
Date: Mardi 9 avril 2019, 13h27
Hello again.
I
agree the get-around strategy
Parkhurst's email...
>>> >
>>> >
>>> > You can do more analysis regarding ice rings using Auspex (
>>> https://www.auspex.de/) if you already have some integrated file.
>>> >
>>> > Regarding re-integrating images, what did you use t
of reflections in proximity to ice rings.
>> Hence you should get better Rfactors without having to remove the effected
>> resolution range and the data it covers (
>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5619854/).
>> >
>> >
>> > H
ntegrated file.
>> >
>> > Regarding re-integrating images, what did you use the first time round?
>> I think if you use DIALS it got some clever implementation in it that is
>> better in estimating the errors of reflections in proximity to ice rings.
>> Hence yo
P4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of herman.schreu...@sanofi.com <herman.schreu...@sanofi.com>
> Sent: 04 April 2019 10:26:09
> To: ccp4bb
> Subject: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring
>
>
> Dear Sam,
>
>
>
/PMC5619854/).
> >
> >
> > HTH
> >
> >
> > M
> >
> >
> >
> > From: CCP4 bulletin board on behalf of
> herman.schreu...@sanofi.com
> > Sent: 04 April 2019 10:26:09
> > To: ccp4bb
> > Subje
d the data it covers
> (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5619854/).
>
>
> HTH
>
>
> M
>
>
>
> From: CCP4 bulletin board on behalf of
> herman.schreu...@sanofi.com
> Sent: 04 April 2019 10:26:09
> To: ccp4bb
&
the scaling.
>>
>>
>>
>> Best,
>>
>> Herman
>>
>>
>>
>> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag
>> von *Sam Tang
>> *Gesendet:* Donnerstag, 4. April 2019 11:01
>> *An:* CCP4BB@JISCMAIL.AC.U
H
M
From: CCP4 bulletin board on behalf of
herman.schreu...@sanofi.com
Sent: 04 April 2019 10:26:09
To: ccp4bb
Subject: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring
Dear Sam,
I would remove the ice ring and reprocess the data. Ice rings may wreak
ice
rings are causing systematic errors.
Best wishes
James
From: CCP4 bulletin board on behalf of Frank von Delft
Sent: 04 April 2019 11:39:19
To: ccp4bb
Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring
You can use sftools to set a
:01
*An:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
*Betreff:* [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring
Dear Eleanor and Eric
Thanks for your replies.
Yes indeed when we looked at the plots e.g. R factor vs resln
there was a sharp peak near 3.6 - 3.8 A
wreak
>> havoc with scaling so at minimum you have to redo the scaling.
>>
>>
>>
>> Best,
>>
>> Herman
>>
>>
>>
>> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag
>> von *Sam Tang
>> *G
@JISCMAIL.AC.UK
> *Betreff:* [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring
>
>
>
>
> Dear Eleanor and Eric
>
>
>
> Thanks for your replies.
>
>
>
> Yes indeed when we looked at the plots e.g. R factor vs resln there was a
> sharp peak near 3.6 - 3.8 A whic
@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring
Dear Eleanor and Eric
Thanks for your replies.
Yes indeed when we looked at the plots e.g. R factor vs resln there was a sharp
peak near 3.6 - 3.8 A which is where we visibly saw an ice ring on the image.
Thus our first thought
Dear Eleanor and Eric
Thanks for your replies.
Yes indeed when we looked at the plots e.g. R factor vs resln there was a
sharp peak near 3.6 - 3.8 A which is where we visibly saw an ice ring on
the image. Thus our first thought was to remove the ic ring. (either
reprocess or can we bypass this re
Look at the plots for Rfactor for your last cycle.
Is there a blip at some resoution?
And also look at the plot of v v resolution-- again are
there blips?
People have put a lot of effort in generating informative graphs so use
them!
You should see ice ring effects in the Wilson plot too..
Ele
Hi everyone again
Hmmm I think we have solved a structure in P1 space, to 2.5 A. However
after refinement the Rfree stuck at 33%-35% with Rwork around 26%. The
structure was solved by MR and current model seems to fit density well. In
Refmac log I found that at the resolution corresponding to high
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