...@uoxray.uoregon.edu]
Sent: Tuesday, May 24, 2011 6:33 PM
To: Schreuder, Herman R&D/DE
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] how to remove part of data with bad signal to noise ratio
On 5/24/2011 2:35 AM, herman.schreu...@sanofi-aventis.com wrote:
> Dear Clement,
>
> In ca
Of
Clement Angkawidjaja
Sent: Tuesday, May 24, 2011 11:19 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] how to remove part of data with bad signal to
noise ratio
But you have to do solvent flattening (density modification), which
people often (unintentionally?) skip for structures solved with
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Clement Angkawidjaja
> Sent: Tuesday, May 24, 2011 11:19 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] how to remove part of data with bad signal to
> noise ratio
>
> But you have to do solvent flattening
I think you are just confused. The solvent flattening is just a step to make
your map clearer. You do not carry the modified phases from solvent flattening
to refinement (and I sincerely hope you don't refine against the solvent
flattened amplitudes but against the original data!)
Herman's obse
ead to a degradation of the
> Rfree.
>
> My 2 cents,
> Herman
>
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Clement Angkawidjaja
> Sent: Tuesday, May 24, 2011 10:47 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [c
remove part of data with bad signal to
noise ratio
But you have to do solvent flattening (density modification), which
people often (unintentionally?) skip for structures solved with
molecular replacement. Please correct me if I am wrong.
Clement
On May 24, 2011, at 6:01 PM, herman.schreu...@sanofi
But you have to do solvent flattening (density modification), which people
often (unintentionally?) skip for structures solved with molecular replacement.
Please correct me if I am wrong.
Clement
On May 24, 2011, at 6:01 PM, herman.schreu...@sanofi-aventis.com wrote:
> This is not my experienc
,
Herman
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Clement Angkawidjaja
Sent: Tuesday, May 24, 2011 10:47 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] how to remove part of data with bad signal to
noise ratio
Hi Seema,
Small addition to
Hi Seema,
Small addition to the already abundant suggestions, if you have high solvent
content or significant portion of non-observable density, you normally get
higher R-free.
Clement
Clement Angkawidjaja, PhD.
G30 Assistant Professor
-
Seema, I agree completely with Eleanor. You need to take a step back
here. When you say that 'Rfree got stuck at 29-30' what makes you so
sure that this isn't the correct Rfree? Who told you that there's a
problem to be solved in the first place?
If you look at our paper (Acta Cryst., 1998. D54
I dont think there is an Rfree problem..
At 2.7A you expect quite a big difference between R and Rfree
Reducing the resolution will a) probably makethe Rfree/R difference
greater, and b) degrade the quality of your maps and model.
Eleanor
On 05/21/2011 02:28 AM, Seema Mittal wrote:
Hi Ethan,
I would also make sure that the spacegroup is correct. If you have instead
P222, P2212, etc, you might find the solution at low resolution but the
problem would become evident during advanced refinement steps, such as a
stuck high Rfree or a noisy difference map.
Good luck,
Javier.
On Sat, May 21,
Thank you all for your thoughts and suggestions in response to my query.
The rotamers, peptide omega angles, mol-probity data all are
perfectly fine. There are 3 outliers in Ramachandran plot ( may be
the ones causing the problem).
The protein has two engineered cysteines involved in disulfid
240 S. Martin Jischke Drive, West Lafayette, IN 47907
--
--
From: "Mittal, Seema"
Sent: Friday, May 20, 2011 5:28 PM
To:
Subject: [ccp4bb] how to remove pa
Hi Ethan,
You are absolutely right. As a matter of fact, I had initially
processed the data to 2.7A and it looked pretty decent with R symm
less than 10%. The maps looked good too.
The problem arose during second round of refinement. The Rfree got
stuck at around 29-30 while the Rfactor k
On Friday, May 20, 2011 02:28:26 pm Mittal, Seema wrote:
> Hi All,
>
> I am currently working on a 3A resolution dataset. The scaled file shows the
> following statistics (scroll down to the end of this email). It is P212121
> space group with R merge of 8.8%.
Your data statistics look fine.
Hi All,
I am currently working on a 3A resolution dataset. The scaled file shows the
following statistics (scroll down to the end of this email). It is P212121
space group with R merge of 8.8%.
My question is : Is there a way to selectively use only the data with I/Sigma
value of 2 and more
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