[phenixbb] Re: adding together

12 Sep 2025

      Oh, does phenixbb really strip off attachments under 1 KB in size?! 
Terrible. Anyway, I’m inlining it below (make sure your email client 
doesn’t mess up the indentation):

********
from iotbx import reflection_file_reader
import iotbx.pdb

def run():
   # Read your reflection data
   miller_arrays = reflection_file_reader.any_reflection_file(file_name =
     "1yjp.mtz").as_miller_arrays()
   for ma in miller_arrays:
     print (ma.info().label_string())
     if(ma.info().label_string()=="FOBS,SIGFOBS"):
       f_obs = ma
   # Get phases by computing Fcalc (for example)
   pdb_inp = iotbx.pdb.input(file_name = "1yjp.pdb")
   xrs = pdb_inp.xray_structure_simple()
   f_calc = 
f_obs.structure_factors_from_scatterers(xray_structure=xrs).f_calc()
   # Transfer phased from f_calc to f_obs
   f_obs_cmpl = f_obs.phase_transfer(phase_source = f_calc.phases())
   print(f_obs_cmpl.data()) # just to see the data are now complex array!
   # Write into MTZ
   mtz_dataset = f_calc.as_mtz_dataset(column_root_label = "Fcmpl")
   mtz_object = mtz_dataset.mtz_object()
   mtz_object.write(file_name = "data.mtz")

if __name__ == '__main__':
   run()

********

Pavel

On 9/12/25 12:04, Petrus Zwart wrote:
...
Hi Pavel,
You say 25 lines, but there are zero - can you attach the code?
P
On Fri, Sep 12, 2025 at 11:57 AM Pavel Afonine  wrote:
Hi James,
attached script shows how to do that in cctbx. ( And it is just 25
    lines
    including comments compared Claud's 173 )
It uses 1yjp as a source of sample files to run the example, you
    can get
    it using
phenix.fetch_pdb 1yjp action=all convert_to_mtz=true
Pavel
On 9/12/25 11:28, James Holton wrote:
    > Greetings Phenix developers!
    >
    > I have what I hope is a quick question.  I'm trying to add a
    stack of
    > phased structure factors together.  Specifically from separate
    runs of
    > phenix.fmodel.  Normally, I'd use sftools for this, but the
    > distributed version has a size limitation.  According to Tom's
    phenix
    > chatbot, I can use phenix.maps for adding two sets of structure
    > factors together, but it seems to only want to combine an mtz
    with a
    > pdb. There is iotbx.reflection_file_editor, but it only works
    from the
    > GUI (and I want to add 1000 mtz files together). phenix.xmanip
    looks
    > promising too, but again, seems to want a pdb and an mtz.  Is
    there a
    > recommended way to do this?
    >
    > I've already asked this on CCP4BB, but I wanted to get the
    Phenix take
    > on these kinds of manipulations.
    >
    > Thank you,
    >
    > -James Holton
    > MAD Scientist
    >
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-- 
------------------------------------------------------------------------------------------
Peter Zwart
Staff Scientist, Molecular Biophysics and Integrated Bioimaging
Berkeley Synchrotron Infrared Structural Biology
Biosciences Lead, Center for Advanced Mathematics for Energy Research 
Applications
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
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