Site-wide defaults for phenix.refine parameters
Hi all, Apologies if I've missed this in the documentation, but is there any way to set 'site-wide' defaults for, say, phenix.refine? That is, I'd like to modify the default parameters for phenix.refine so that occupancy refinement is turned off by default, the output.serial_format is different, geo files aren't created, always use F/SIGF not I/SIGI, etc. Cheers, Stephen P.S. I know I can change this by hand in my .def file and then propagate the .def file through subsequent rounds of refinement for a given project. It would just be nice to have my default personal preference parameters set (~/.phenix?) so I don't need to change them each time I start a new project... -- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549
On Jan 29, 2009, at 9:26 AM, Stephen Graham wrote:
Apologies if I've missed this in the documentation, but is there any way to set 'site-wide' defaults for, say, phenix.refine? That is, I'd like to modify the default parameters for phenix.refine so that occupancy refinement is turned off by default, the output.serial_format is different, geo files aren't created, always use F/SIGF not I/SIGI, etc.
This is possible to some extent with the phenix.refine GUI, although it's very much a work in progress.
P.S. I know I can change this by hand in my .def file and then propagate the .def file through subsequent rounds of refinement for a given project. It would just be nice to have my default personal preference parameters set (~/.phenix?) so I don't need to change them each time I start a new project...
Right now the (new) GUI creates a directory ("phenix") in each project that contains various meta-information, and a sub-directory "defaults" which contains any files to be used automatically. It will also read in a global defaults file if you specify one in the preferences. For the command-line version, couldn't you just alias phenix.refine to "phenix.refine ~/.phenix/refine_defaults.def"? ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
Hi Nathaniel,
For the command-line version, couldn't you just alias phenix.refine to "phenix.refine ~/.phenix/refine_defaults.def"?
Yes, that would probably be more or less perfect (I assume that, if something is defined separately in two .def files, the one which appears last on the command line would take precedence?) Thanks, Stephen -- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549
On Jan 29, 2009, at 9:49 AM, Stephen Graham wrote:
For the command-line version, couldn't you just alias phenix.refine to "phenix.refine ~/.phenix/refine_defaults.def"?
Yes, that would probably be more or less perfect (I assume that, if something is defined separately in two .def files, the one which appears last on the command line would take precedence?)
I think so. I'm not sure what the interaction between parameters specified manually on the command-line and parameters extracted from files is, however. ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
For the command-line version, couldn't you just alias phenix.refine to "phenix.refine ~/.phenix/refine_defaults.def"?
Yes, that would probably be more or less perfect (I assume that, if something is defined separately in two .def files, the one which appears last on the command line would take precedence?)
Yes, that's how it works for most parameters, I assume all you ever want to have defined in a central location. For completeness: there are some "multiple" parameters which accumulate, e.g. NCS and TLS selections. Ralf
Hi Stephen, there is a file "/phenix/phenix/refinement/__init__.params" that defines all default parameters for phenix.refine. I don't like the idea of changing it, but this is the place where if you change something then this will be global. Pavel. PS. Why you need to turn the occupancies refinement off by default? If you have alternative conformations or some atoms with partial occupancies, then I don't see any argument against of refinement their occupancies all the time you run refinement. On 1/29/2009 9:26 AM, Stephen Graham wrote:
Hi all,
Apologies if I've missed this in the documentation, but is there any way to set 'site-wide' defaults for, say, phenix.refine? That is, I'd like to modify the default parameters for phenix.refine so that occupancy refinement is turned off by default, the output.serial_format is different, geo files aren't created, always use F/SIGF not I/SIGI, etc.
Cheers,
Stephen
P.S. I know I can change this by hand in my .def file and then propagate the .def file through subsequent rounds of refinement for a given project. It would just be nice to have my default personal preference parameters set (~/.phenix?) so I don't need to change them each time I start a new project...
participants (4)
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Nathaniel Echols -
Pavel Afonine -
Ralf W. Grosse-Kunstleve -
Stephen Graham