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

[Schubert, Carsten [PRDUS]]

I think the underlying problem is that Phenix ADDS on PDB files defined
at the commandline to whatever is defined in the .def file. I mentioned
this a couple of year back to Ralf as an improvement request, but did
not get very far. If one could force Phenix only to only read the pdb
file defined on the command line and ignore the one in the *002.def file
these kind of minor headaches would go away. 

> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-
> bounces at phenix-online.org] On Behalf Of Scott Classen
> Sent: Thursday, April 22, 2010 1:55 PM
> To: PHENIX user mailing list
> Subject: Re: [phenixbb] can phenix.refine create a diff of the current
> inputfile with the pdb from the last run before refining?
> 
> 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
> 
> 
>  Scott
> 
> 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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