://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
>>> >
>>> > 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 the first time
>>> round?
mity 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/).
>> >
>> >
>> > HTH
>> >
>>
gt; > 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 you should get better Rfac
P4BB@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,
>
>
>
> I would remove the
>
> >
> > HTH
> >
> >
> > M
> >
> >
> > ________
> > From: CCP4 bulletin board on behalf of
> herman.schreu...@sanofi.com
> > Sent: 04 April 2019 10:26:09
> > To: ccp4bb
> > Subject: [ccp4bb] AW: [EX
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
> S
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.UK
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 havoc
if the 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
*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 whic
may 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
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..
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
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