Hi James,
Have a look at the tool:
phenix.get_struct_fact_from_md
I have not used this in some time but it does pretty much what you are
talking about. It is not a supported tool however so it may not be easy to
use.
All the best,
Tom T
On Fri, Sep 12, 2025 at 1:37 PM James Holton
Thank you for this Pavel,
Funny, I got the attachment just fine? Maybe its on P's email client side. I'm using thunderbird.
However, the code you shared seems to be taking an amplitude from one place and attaching it to a phase from another. What I want to do is the complex sum of two phased structure factors.
Specifically, I have is a stack of 1000 mtz files with FMODEL PHIMODEL in each. What I want is the phased sum of all of them, as well as the unphased sum of their squares. I've been doing the additions two at a time because that is parallelizable. My script is here: https://github.com/jmholton/altloc_diffuse/blob/main/addup_mtzs_diffuse.com It is currently using sftools for these operations: calc ( COL Fsum PHIsum ) = ( COL F1 P1 ) ( COL F2 P2 ) + calc COL I1 = COL F1 2 ** calc COL I2 = COL F2 2 ** calc J COL Isum = COL I1 COL I2 +
There does not seem to be a general-purpose math toolkit like sftools in phenix?
Much appreciate all the quick responses!
-James
On 9/12/2025 12:12 PM, Pavel Afonine wrote:
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 > _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s
--
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
phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s
-- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: [email protected] Tel: 505-431-0010