Hi, Would it be possible to allow for running phenix validate without a map/mtz? I dont always want the RSCC information, and it would be useful to be able to get the geometry stats and sequence check without loading a map (which in the case of EM maps can be very large and will presumably slow things down a lot). Cheers, Oliver.
Hi Oliver,
Would it be possible to allow for running phenix validate without a map/mtz? I dont always want the RSCC information, and it would be useful to be able to get the geometry stats and sequence check without loading a map (which in the case of EM maps can be very large and will presumably slow things down a lot).
Sure! Just load PDB file and leave reflections/map fields empty, then hit Run. That should just do model validation. Please let us know if anything doesn't work as expected. Pavel
Hi Oliver,
Yes, but if you provide a sequence file as well, the results do not contain
the sequence check. I'll take a look into why that is the case since that
check should not require a map.
--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org
On Wed, Sep 7, 2016 at 10:49 AM, Pavel Afonine
Hi Oliver,
Would it be possible to allow for running phenix validate without a
map/mtz? I dont always want the RSCC information, and it would be useful to be able to get the geometry stats and sequence check without loading a map (which in the case of EM maps can be very large and will presumably slow things down a lot).
Sure! Just load PDB file and leave reflections/map fields empty, then hit Run. That should just do model validation. Please let us know if anything doesn't work as expected.
Pavel
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P.S.: Please use the latest nightly build (1.11rc2-2525) as things change rapidly in preparation for the upcoming official release. Pavel On 9/7/16 10:49, Pavel Afonine wrote:
Hi Oliver,
Would it be possible to allow for running phenix validate without a map/mtz? I dont always want the RSCC information, and it would be useful to be able to get the geometry stats and sequence check without loading a map (which in the case of EM maps can be very large and will presumably slow things down a lot).
Sure! Just load PDB file and leave reflections/map fields empty, then hit Run. That should just do model validation. Please let us know if anything doesn't work as expected.
Pavel
participants (3)
-
Billy Poon -
Oliver Clarke -
Pavel Afonine