Dear PHENIX programmers, I would like to preface this comment by saying that I love your suite of programs. I have converted to a 100% PHENIX fan girl and am dragging the rest of my lab down with me. I realize that you have a lot on your plates right now, what with all the bug fixes, updates, and bulletin board troubleshooting that you do. I am also primarily a biologist and have no comprehension of the effort required to keep everything running, but I do have a suggestion/request. 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 know the one that I am talking about with the data and refinement statistics. I am thinking a combination of PDB_EXTRACT and MOLEMAN where you input the log files from scaling and refinement and it outputs a handy-dandy test file with "parameter<tab>number that could easily be imported into your favorite spreadsheet (Open Office or Excel). I envision an interface with check boxes for the parameters you want to include and a place were you could input the resid of ligands for atom and b-factor counts. Like I said it is just a suggestion, in case you find yourselves bored and with time on your hands. Thanks for your time, Katherine -- SIPPEL,KATHERINE H Ph. D. candidate McKenna Lab Department of Biochemistry and Molecular Biology College of Medicine University of Florida
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! Pavel.
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. Phil 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! Pavel.
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participants (3)
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Pavel Afonine -
Phil Evans -
SIPPEL,KATHERINE H