Installation

A step by step guide on how to install qrefine is found here:

https://github.com/qrefine/qrefine/blob/master/README.md

more details can also be found here:

https://github.com/qrefine/qrefine/wiki/Installation

Run Tests

Please run the test suite on your system before using qrefine.

Simply make a clean directory, and the change into that empty directory

mkdir clean_test_dir cd clean_test_dir

then run:

qr.test --nproc=4

where the nproc is set to the number of processors you want to use. This can be used to speed up the test set.

See more documentation: Tests

Stages

A typical workflow would take the following steps:

Step 1. Fetch the pdb of interest and structure factors from the https://www.rcsb.org/

phenix.fetch_pdb 1yjp --mtz

Step 2. Complete your pdb by adding hydrogen and by adding missing atoms

qr.finalise 1yjp.pdb

output from running this script is

1yjp_complete.pdb

Step 3. Check the overall charge of your system by running

qr.charges 1yjp_complete.pdb  verbose=true

this will print out the charge, and is a useful sanity check before running a refinement.

in this example, the output is

Charge: 0

Step 4. Another sanity check is performed by running a single point. MOPAC is used by default.

qr.restraint 1yjp_complete.pdb 1yjp.mtz

Step 5. A refinement using cctbx can quickly test that the refinement of the model is working as expected.

We also run the cctbx refinement to provide a comparison for quantum refinement.

qr.refine 1yjp_complete.pdb 1yjp.mtz > qr.log

The refined model is written to the folder

1yjp_complete_refined.pdb

adn the refinement statistics are displayed to the screen:

`` Best r_work: 0.1435 r_free: 0.1860 ``

Step 6. Another comparison that can be performed is optimization.

This will ignore the experimental data and only use the restraints.

qr.refine 1yjp_complete.pdb mode=opt > qr.log

This is useful when evaluating new qm engines to make sure they are performing well.

Step 7. Large proteins must be broken up into small manageable pieces when performing refinement or

optimization using quantum restraints.

qr.refine 1yjp_complete.pdb 1yjp.mtz clustering=true > qr.log

Step 8. You can change the qm engine if you have other qm engines installed.

qr.refine 1yjp_complete.pdb 1yjp.mtz clustering=true engine_name=pyscf