[phenixbb] on Phenix's "Generate "Table 1" for journal"

Pavel Afonine pafonine at lbl.gov
Sat Mar 21 09:13:19 PDT 2015

Dear Smith,

most questions you asked below are normally answered as part of a basic 
crystallography training. If that's not the case for you then I suggest 
you dedicate a few months reading this book (entirely!)

Rupp, B, 2009
Biomolecular Crystallography: Principles, Practice, and Application to 
Structural Biology

then follow references therein and read corresponding papers. All 
together I'm sure this will give you answers to most questions you asked 
below and far more.

As to your more specific questions: content of Phenix generated Table 1 
depends on what inputs you provide. If it lacks Multiplicity then 
perhaps you did not give the tool information from data processing steps.

Good luck,

On 3/21/15 5:25 AM, Smith Liu wrote:
> Dear All,
> With the Phenix refine PDB and mtz file, I just prepared a "Table 1" 
> for journal with Phenix. Here I find something special, which I hope I 
> can get your advice.
> First, for the "Total reflections" and "Multiplicity", they are empty 
> (no data given). Wil you please tell me why?
> Secondly, it writes, "Statistics for the highest-resolution shell are 
> shown in parentheses". Suppose my crystal resolution is 2.5-45.6, then 
> the the highest-resolution value should be 2.5, rather than 45.6, right?
> In addition, what is the diffrence between highest-resolution shell in 
> the Table 1 and highest-resolution bin in the "Results" of Phenix refine?
> What is R-merge, R-meas,CC1/2 and CC*? I can get these data from 
> MOSFLM output mtz file. But is my images were processe by HKL, which I 
> have no experience, then how can I get the R-merge, R-meas,CC1/2 and CC*?
> I am looking forward to getting your reply.
> Smith
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