The comments on overloads are interesting and can be checked on your raw
images by zooming in to suspected overload reflections.
Do the maps look good. What is Rfree. When you try anisotropic refinement
what does Rfree do. Have you put Hydrogen atoms as riders?
Questions not answers, sorry
James
Dear Guto,
integration programs often ignore overloads, and most of them know the
detector cut-offs. mosflm has the option to estimate the resolution of
overloaded reflections from the none-overloaded parts. This should not
be a replacement for proper collection of a low resolution data set, but
i
Hi all,
Firstly, I’d like to say I’m really impressed with the volume, speed and detail
of the response that I have received. Thanks everyone.
Overloads
Eddie, Marc, Eleanor, Harry and Misha; thanks to all for suggesting collection
strategies and identifying the likely issue. Yesterday, I had a
png@01D4608C.2A6224F0]
Heisenberg was probably here!
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Marc
Graille
Sent: Wednesday, October 10, 2018 11:14 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Issue with high Rfree (0.25) for a high-resolution
dataset (1.05 Ang)
D
Dear Auto,with such crystals diffracting like rocks, it can be useful to collect two datasets. One at “low" resolution (up to 3A) using low exposure time and/or low dose to avoid overloads and a second at higher resolution (1A in your case) using higher dose. Then, merge those two datasets into a
Hi
I forgot something - "paired refinement" is the current gold standard for
determining a sensible resolution cut-off (see other ccp4bb discussions on the
topic).
On 10 Oct 2018, at 11:49, Harry Powell wrote:
> Hi
>
> As a referee, if I had been supplied with data processing statistics that
Hi
As a referee, if I had been supplied with data processing statistics that
indicate there is good information going to a higher resolution than that used
for refinement etc, I would want to know why the data had been cut off. "Making
life easier" wouldn't cut the mustard, I'm afraid!
Clearl
10
> 13125 Berlin
> Germany
> Phone: +49 (0)30 94793-284
> From: CCP4 bulletin board on behalf of Pavel Afonine
>
> Sent: Wednesday, October 10, 2018 11:03:49 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Issue with high Rfree (0.25) for a high-resolution
>
logie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin
Germany
Phone: +49 (0)30 94793-284
From: CCP4 bulletin board on behalf of Pavel Afonine
Sent: Wednesday, October 10, 2018 11:03:49 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Issue with high Rfree (0.25)
Hi Pavel,
Obviously higher resolution typically means a more accurate atomic model of a
crystal structure, but I also think that a 1.05 Ang structure is only going to
provide you with a great deal more insight than a 1.1 or 1.2 Ang structure in
very specific cases. Particularly if your stats
Hi Tony,
I always feel some people are too "greedy" with the resolution they want to
> achieve. I mostly find that extremely high density is a pain to work with
> as it's usually accompanied by many dual, triple conformers, a lot of noise
> in the solvent phase that is often difficult to interpret
tion stress
response<http://www.nature.com/articles/ncomms15847>
From: CCP4 bulletin board on behalf of Guto Rhys
Sent: 09 October 2018 18:12
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Issue with high Rfree (0.25) for a high-resolution dataset
(1.05 Ang)
of different restraints (for
> exemple on B-factors) in order to get the lowest Rfree.
> Best
> Wim
>
> --
> *De: *"Robbie Joosten"
> *À: *CCP4BB@JISCMAIL.AC.UK
> *Envoyé: *Mardi 9 Octobre 2018 20:02:17
> *Objet: *Re: [ccp4bb] Issue with
De: "Robbie Joosten"
À: CCP4BB@JISCMAIL.AC.UK
Envoyé: Mardi 9 Octobre 2018 20:02:17
Objet: Re: [ccp4bb] Issue with high Rfree (0.25) for a high-resolution dataset
(1.05 Ang)
Hi Hugo,
Perhaps you should play with your refinement strategy. Use a decent number of
cycles and
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Guto Rhys
[guto.r...@bristol.ac.uk]
Sent: Tuesday, October 9, 2018 6:12 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Issue with high Rfree (0.25) for a high-resolution dataset
(1.05 Ang)
Hi all,
I have a 1.05 Angstrom
Hi Hugo,
Perhaps you should play with your refinement strategy. Use a decent number of
cycles and a sensible restraint weight (something that gives you rmsZ < 1.0 and
good R-factors). Anisotropic B-factors are probably needed and make your model
as complete as your maps allow.
You could try pd
Hi all,
I have a 1.05 Angstrom dataset that I was able to phase but the refined model
only has an Rfree of approximately 0.25. The dataset includes 1800 images and,
as the crystal did not suffer significantly from radiation damage, comprises
all 360 deg. Auto-processing pipelines at diamond lig
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