[phenixbb] For your consideration: Table 1
pre at mrc-lmb.cam.ac.uk
Fri Jan 29 01:25:22 PST 2010
Note that if you scale the data with Scala (CCP4), there is a summary table which is intended to form the data processing part of "table 1" more or less as a cut and paste.
On 29 Jan 2010, at 01:46, Pavel Afonine wrote:
> 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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