[phenixbb] For your consideration: Table 1

Pavel Afonine PAfonine at lbl.gov
Thu Jan 28 17:46:37 PST 2010

Hi Katherine,

thanks a lot for your warm words!

> I was putting the finishing touched on the first draft of a manuscript 
> today and thought to myself, wouldn't it me wonderful if PHENIX could 
> generate that all important crystallographic Table 1. 

You are the second person who suggests this (to give proper credits, the 
first was Meindert Lamers).

I guess you have all the numbers around and all you need is to know 
where to look. This is probably something that we need to address 
clearly in the documentation. So, here is the list:

- phenix.model_vs_data tool creates a plain text output the contents of 
which is very-very close to what people put into Table 1. You just need 
to format it the way you like. To run model_vs_data is easy:

phenix.model_vs_data model.pdb data.mtz

- PDB file header contains most of the numbers as well, but may not be 
as complete as model_vs_data output;

- refinement .log file contains even more.

- Comprehensive Validation option in PHENIX GUI is probably the most 
complete thing.

If you and the other PHENIX users will find it useful anyway, then I can 
add a command line too called something like "phenix.table_one model.pdb 
data.mtz". In this case I would need a template/example of how Table1 
looks like (last time I solved and published a structure completely 
myself was 9 years ago).

All the best!

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