[cctbxbb] Experimental gradients

[Pavel Afonine]

Hi Kristoffer,

CCTBX is a source of building blocks for Phenix, and Phenix has real- 
and reciprocal-space refinement programs, phenix.real_space_refine and 
phenix.refine, so the answer to your question is yes.

You have not specified, but I'm assuming you are looking for gradients 
of reciprocal space refinement target (LS, ML, MLHL, etc) and real-space 
target (we have only one described here: 
https://pubmed.ncbi.nlm.nih.gov/29872004/) with respect to model 
parameters such as coordinates, ADPs (isotropic, anisotropic), 
occupancies, f' and f'', etc.

Here are a few places:

- reciprocal space:

cctbx_project/mmtbx/refinement

files:

minimization.py
occupancies.py
rigid_body.py
group.py

regression/tst_xray_fast_gradients.py
xray/boost_python/tst_xray.py
regression/tst_xray_derivatives.py

- real space:

cctbx_project/mmtbx/refinement/real_space/individual_sites.py
cctbx_project/cctbx/maptbx/tst_real_space_refinement_simple.py
cctbx_project/cctbx/maptbx/target_and_gradients.h
cctbx_project/cctbx/maptbx/real_space_refinement_simple.py

Note, these are examples of high-level code that uses target function 
and its gradients to perform various kind of refinement. You'll need to 
do some detective work to trace to the low-level code that actually 
calculates gradients. Hope that's good enough starting point for you.

Also, try grep for "gradient" and "target"! Usually tests (files tst*.py 
serve as good examples).

Good luck!
Pavel


On 10/3/23 08:13, Kristoffer Lundgren wrote:
>
> Hello all,
>
> I am wondering if it is possible to use cctbx to calculate gradients 
> from experimental data? Both in reciprocal and real space is of interest.
>
> Are there any code examples available somewhere showcasing how this 
> can be achieved?
>
> Best regards
>
> Kristoffer Lundgren
>
>
> _______________________________________________
> cctbxbb mailing list
> cctbxbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/cctbxbb
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