polygon resolution control
Hi I was using polygon from GUI. One question I have now is how I can control the resolution limit. As I cut the resolution during refinements but polygon gave me from the uncut-high resolution. Is there any way, I can ask polygon to get statistics upto certain resolution as shown on pdb file? As always, thanks in advance. YoungJin
Hi Young-Jin, first of all, I assume you had very strong reasons for cutting off the resolution. Currently you cannot filter by resolution the input data for Polygon. But, as Sacha suggested, you can create another MTZ file with resolution-filtered data and then use that file for Polygon calculation. Two ways of doing it: - from the GUI: click on "Reflection file editor", and the rest should be obvious; - from the command line: phenix.refine model.pdb data.mtz strategy=none main.number_of_mac=0 export_final_f_model=mtz xray_data.high_res=2.5 that will create an MTZ file called like *_f_model.mtz. Use this file to run Polygon. When running Polygon with this file, make sure you load in data with correct labels (FOBS) since *_f_model.mtz contains many other data arrays. Pavel. On 1/21/10 7:15 AM, Young-Jin Cho wrote:
Hi I was using polygon from GUI. One question I have now is how I can control the resolution limit. As I cut the resolution during refinements but polygon gave me from the uncut-high resolution. Is there any way, I can ask polygon to get statistics upto certain resolution as shown on pdb file?
As always, thanks in advance.
YoungJin
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On Jan 21, 2010, at 8:04 AM, Pavel Afonine wrote:
Currently you cannot filter by resolution the input data for Polygon.
Correct - you can filter the data used for comparison, at least in newer versions than 1.5-2 (click "Filtering options", choose "d_min" from the list and enter minimum and maximum values), but to truncate the resolution of the reflections used for your structure, do what Pavel said. I'll see if it's easy to add a resolution cutoff to the Polygon/validation apps. (Pavel, could high resolution at least be an option for model_vs_data?) -Nat -------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
participants (3)
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Nathaniel Echols -
Pavel Afonine -
Young-Jin Cho