Re: [ccp4bb] Multiplicity is more than 20

[Dale Tronrud]

   Okay, I weigh in on the R factor issue...

   The free R that we calculate is only an estimate of the "true free 
R".  What we really want to know is what would the R value be if there 
there was no "bias" to the atomic model.  We make this estimate by 
pulling a subset of the data out of the refinement.  If you pull out a 
different subset you will get a somewhat different "free R estimate".


   If you run a lot of refinement with different subsets you will get a 
distribution of "free R estimates" and that distribution will have a 
standard deviation.  The smaller the number of reflections in the subset 
the larger that standard deviation will be.


   One shell of data will have only a few reflections so the standard 
deviation will be large and a particular instance may very well have a 
value for the "free R estimate" that is smaller than the working R, 
particularly when the overall R values are similar as in your refinement.


Dale Tronrud

On 9/19/2022 11:30 AM, Prasun Kumar wrote:

Hi All:

I have collected a dataset for a crystal of a 30 residues long helical 
peptide that makes a trimer in the solution. I also solved the structure 
to get a trimer. My issues start when I start preparing for a deposition.


Details about the data:

space group: I 21 3
Resolution: 1.6
Current Rfree/ Rwork: 0.21/0.19

Problems:
According to Aimless, Multiplicity: *33.9*, and I understand that the 
value should be less than or equal to 20. Does it mean that I have a lot 
of random noise or ice rings or something similar?

For the inner shell, R work is also *higher* than R free.

Please guide me in solving the above issue.

Thank You
Prasun




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[ccp4bb] RES: [ccp4bb] Multiplicity is more than 20

[Rafael Marques]

Problematic is low multiplicity, not high, I’d say...

Best


Rafael Marques da Silva
Mestre em Física Biomolecular
Universidade de São Paulo

Bacharel em Ciências Biológicas
Universidade Federal de São Carlos

phone: +55 16 99766-0021

   "A sorte acompanha uma mente bem treinada"


De: Winter, Graeme 
(DLSLtd,RAL,LSCI)<mailto:6a19cead4548-dmarc-requ...@jiscmail.ac.uk>
Enviado:segunda-feira, 19 de setembro de 2022 16:27
Para: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Assunto: Re: [ccp4bb] Multiplicity is more than 20

Hi Prasun

You just measured the reflections a lot. 33 is fine. More likely even with 
cubic space groups

I’d love to know where you got the idea of the limit from. I have data sets 
with more than 100 fold multiplicity

The R conversation I’ll leave to others

Best wishes Graeme


On 19 Sep 2022, at 20:32, Prasun Kumar  wrote:

Hi All:

I have collected a dataset for a crystal of a 30 residues long helical peptide 
that makes a trimer in the solution. I also solved the structure to get a 
trimer. My issues start when I start preparing for a deposition.

Details about the data:

space group: I 21 3
Resolution: 1.6
Current Rfree/ Rwork: 0.21/0.19

Problems:
According to Aimless, Multiplicity: 33.9, and I understand that the value 
should be less than or equal to 20. Does it mean that I have a lot of random 
noise or ice rings or something similar?
For the inner shell, R work is also higher than R free.

Please guide me in solving the above issue.

Thank You
Prasun




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Re: [ccp4bb] Multiplicity is more than 20

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Hi Prasun

You just measured the reflections a lot. 33 is fine. More likely even with 
cubic space groups

I’d love to know where you got the idea of the limit from. I have data sets 
with more than 100 fold multiplicity

The R conversation I’ll leave to others

Best wishes Graeme

On 19 Sep 2022, at 20:32, Prasun Kumar  wrote:


Hi All:

I have collected a dataset for a crystal of a 30 residues long helical peptide 
that makes a trimer in the solution. I also solved the structure to get a 
trimer. My issues start when I start preparing for a deposition.

Details about the data:

space group: I 21 3
Resolution: 1.6
Current Rfree/ Rwork: 0.21/0.19

Problems:
According to Aimless, Multiplicity: 33.9, and I understand that the value 
should be less than or equal to 20. Does it mean that I have a lot of random 
noise or ice rings or something similar?
For the inner shell, R work is also higher than R free.

Please guide me in solving the above issue.

Thank You
Prasun




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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
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[ccp4bb] Multiplicity is more than 20

[Prasun Kumar]

Hi All:

I have collected a dataset for a crystal of a 30 residues long helical peptide 
that makes a trimer in the solution. I also solved the structure to get a 
trimer. My issues start when I start preparing for a deposition.

Details about the data:

space group: I 21 3
Resolution: 1.6
Current Rfree/ Rwork: 0.21/0.19

Problems:
According to Aimless, Multiplicity: 33.9, and I understand that the value 
should be less than or equal to 20. Does it mean that I have a lot of random 
noise or ice rings or something similar?
For the inner shell, R work is also higher than R free.

Please guide me in solving the above issue.

Thank You
Prasun




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