[phenixbb] can phenix.refine create a diff of the current input file with the pdb from the last run before refining?

Scott Classen sclassen at lbl.gov
Thu Apr 22 10:54:53 PDT 2010

I see your point. I have a similar conundrum. It is a very minor point, and I'm sure there are many  other pressing issues for the developers.

phenix.refine model_refine_001.def  creates model_refine_001.pdb

I edit in Coot and save as model_001-coot-0.pdb

model_refine_002.def is expecting to see:
file_name = "model_refine_001.pdb"

Therefore I have to edit the def file to:

file_name = "model_refine_001-coot-0.pdb"

Perhaps there is some way to tell phenix.refine the preferred filename pattern. Like adding an addition output value (i.e. suffix).

~~~~~~~~~ snippet from theoretical def file ~~~~~~~~~~~~~~~
output {
    prefix = "model_refine"
    pdb_input_suffix = "editted"
    serial = 1
    serial_format = "%03d"

would produce:

file_name = "model_refine_001_editted.pdb"
in the next def file


On Apr 21, 2010, at 6:18 AM, Francis E Reyes wrote:

> Pavel
> Well here's a workflow. 
> phenix.refine model.pdb creates model_001.pdb .
> I edit model_001.pdb ... the question is what do I save it as? If I were to follow the convention of the model_002.def file, the suggestion is to save it as model_001.pdb (so I don't have to edit the input on model_002.def).  I run model_002.def and realize the edits that I made in model_001.pdb made my statistics worse. How do I get back model_001.pdb ? do I rerun phenix.refine model.pdb to get model_001.pdb? Seems like a lot of work / time .
> My current workflow for being able to revert is to save model_001.pdb as model_001-input.pdb and then change model_002.def to compensate. Lots of vim keystrokes, and the possibility of forgetting to edit model_XXX.def. 
> If I had a diff file that allowed me to revert back to obtain the original model_001.pdb, this would be ideal
> Does this make sense?
> F
> On Apr 21, 2010, at 7:10 AM, Pavel Afonine wrote:
>> Hi Francois,
>> you have your two PDB files: before and after phenix.refine run. So in case you did not like the refinement outcome you always have your input PDB file, the one you fed into phenix.refine. I'm not sure what exactly you mean by "--revert"... Could you please explain in more details?
>> Thanks!
>> Pavel.
>> On 4/21/10 6:02 AM, Francis E Reyes wrote:
>>> Hi all,
>>> Just a feature request that phenix.refine make a diff comparing the current input file with the pdb from the last run and then doing a refinement on the input file and then allow a phenix.refine --revert to allow the user to backtrack incase the refinement isn't suitable. 
>>> Right now I edit the pdb, save it as xxxx_001-input.pdb and specify xxxx_001-input.pdb as the input file in xxxx_002.def. 
>>> (Yes I'm using the command line, does the GUI allow this? (i.e. right click on a refinement run then click revert?) )
>>> F

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