can phenix.refine output mtz with structure factors not just coeficients?
Hi, I am going to deposit a structurein the pdb but noticed that all of the mtz files from phenix.refine only contain coeficients and not reflection info. Is it as simple as running another refinement with write_maps = true instead of false? Will this right out an mtz with structure factors instead of just coeficients. I am a newbie at crystalagraphy so I appolgize if this obvious. Ideally, I would like to create an mtz with structure factors as well as a map for CNS. Is there a way to do this without runing another refinment maybe using "maps.params". Thank you very much for the help! -Yarrow output { prefix = "CIN4_refine" serial = 12 serial_format = "%03d" title = None write_eff_file = True write_geo_file = True write_final_geo_file = False write_def_file = True export_final_f_model = mtz cns write_maps = false write_map_coefficients = True pickle_fmodel = False
Hi Yarrow,
I am going to deposit a structurein the pdb but noticed that all of the mtz files from phenix.refine only contain coeficients and not reflection info.
this is expected. I'm not sure why you need a separate tool to create a data file for PDB deposition if you already have that file... The reflection data file that contains your Fobs (or Iobs), as well as free-R flags (and may be HL coefficients, if available) and that you used to run the refinement is what you should deposit to PDB.
Is it as simple as running another refinement with write_maps = true instead of false?
"write_maps = true " will output CNS/X-plor formatted electron density maps.
Will this right out an mtz with structure factors instead of just coeficients.
No.
Ideally, I would like to create an mtz with structure factors as well as a map for CNS.
Regarding an MTZ with structure factors -- see above. For the maps in X-plor/CNS format use "write_maps=true" keyword or whatever is equivalent in the GUI. Let me know if you have questions or need help with this. Pavel.
On Thu, Sep 2, 2010 at 11:57 AM,
Ideally, I would like to create an mtz with structure factors as well as a map for CNS. Is there a way to do this without runing another refinment maybe using "maps.params". Thank you very much for the help!
If you already have map coefficients, you can convert them to XPLOR format (I assume this is what you meant) like this: phenix.mtz2map refine_map_coeffs.mtz output.format=xplor although most people prefer CCP4 maps, which are the default for that command. -Nat
Thank You!!!! Exactly what I was looking for.
-Yarrow
On Thu, Sep 2, 2010 at 11:57 AM,
Ideally, I would like to create an mtz with structure factors as well as a map for CNS. Is there a way to do this without runing another refinment maybe using "maps.params". Thank you very much for the help!
If you already have map coefficients, you can convert them to XPLOR format (I assume this is what you meant) like this:
phenix.mtz2map refine_map_coeffs.mtz output.format=xplor
although most people prefer CCP4 maps, which are the default for that command.
-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (3)
-
amadrona＠uci.edu -
Nathaniel Echols -
Pavel Afonine