[phenixbb] phenix.phaser generate .sol file

Randy Read rjr27 at cam.ac.uk
Fri Oct 14 07:52:24 PDT 2011


Phaser is set up so that if you run it from a script (which is also effectively how it is run from ccp4i), it writes out a .sol file that can be read in as part of the script for a subsequent run.  Because it is run from Python in the Phenix GUI, and not from a script, it doesn't write out a .sol file in that circumstance.  Instead, the Phaser-MR GUI writes out the equivalent information in a Python pickle file, which can be used in the same way as information for a subsequent run.

Advanced users occasionally want to edit the .sol file to do things that hadn't been anticipated.  Since I want to do that sometimes myself, I can see why you would want to get the .sol files.  On the other hand, most people who understand Phaser well enough to manipulate .sol files also understand how to run it from scripts!  That's why we haven't put the ability to read and write .sol files into the Phenix GUI environment.

If there's enough of a need, we could either make it possible to read and write .sol files from the Phenix GUI, or perhaps come up with a way to manipulate the contents of the pickle files.

Best wishes,

Randy Read

On 13 Oct 2011, at 10:43, G Y wrote:

> Dear Experts,
> I run phaser in phenix with GUI and script using params.eff. For both case, I can not find .sol file in the outputs. What option or command I should used in GUI and params.eff to generate the .sol file in the outputs?
> Thanks for your kind help!
> GY
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Randy J. Read
Department of Haematology, University of Cambridge
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