Octav dec-19

Note that you need to use a special, modified version of phenix (to write out energies and gradients):

1.     Start with a refined crystal structure, including structure factors (i.e. the pdb file and a structure factor file in cif format, downloaded from

      Convert the structure factors from cif to mtz using
Both these steps are conveniently done by

phenix.fetch_pdb --mtz pdb_id
Alternatively, if you already have downloaded the pdb and cif files, you can do:

phenix.cif_as_mtz cif_file

3.     Copy all needed files:
mmrun2, mmrun1, sedfile2, sedfile1
cp /temp4/Bio/Data/Comqumx_lib/Phenix/* .

4.     Edit the file sedfile2 by inserting:

Then, run
sed -i -f sedfile2 mmrun2

5.     Delete alternative conformations in the quantum system. Other alternative conformations can be kept.

6.     Protonate the quantum system (for example, using phenix.ReadySet). The rest of the protein can also be fully protonated, the hydrogen atoms will be kept riding.

7.     Run pdbtocomqum

8.     Run comqumtoturbo to get the Turbomole files:
control  coord

9.     Check the name of metal atoms in file coord and then run

10.  Run one test refinement to get parameters for the junctions

phenix.refine mmrun2 > mmrun2.out

mv mmrun2_1.geo mm2.geo

mv mmrun2_1.pdb pdb3

You may need to set
disable_suitability_test = True.

RuntimeError: No data for scale calculation.
Means that there are no selection of reflections for Rfree.

11.  Run comqumtophenix ! This does not work for the moment

This will generate or change the following files: pdb1, junc.cif and comqum.dat

12.  Edit sedfile1, with the residues in the quantum system, with the syntax “resseq x and chain A or resseq y and chain B or…” and the ligand parameter file (if the ligand is in the quantum system; otherwise None)

13.  Run
sed -i -f sedfile1 mmrun1

14.  Test mmrun1 by running

phenix.geometry_minimization mmrun1 > mmrun1.out

15.  You should always run with a fixed value of the weight factor (even if you want the default one). This is done in the file mmrun2 (search for fix_wxc = ). Run fixenergy_phenixin to get the default value of weight (take the first in the output of this program - there are two). ! I have not done this

16.  Remove unneccesary files and make a backup by running
cqxback This also needs to be changed

The following 19 (20 for UHF) files are needed to run comqumx:
basis            control          grad1            mm1.pdb1         mm3.pdb1                 junc.cif
mmrun2  coord            mmrun1           mos
comqum.dat       bindividual
In addition, you need the structure factor file and the parameter files for all heterocompounds. 

17.  You can add restraints on a distance between two atoms using (note the unusual units):
  atom1(1)  atom2(1)  desired_distance_in_A   force_constant_in_au
1 3  1.00 1.0

A typical force constant is 1 a.u. (which typically gives less than 0.01 � deviation at convergence)

18.  Start comqumx:
comqumx-phenix -c 200

The results are in files energy and cns.dat.

The final coordinates are in bindividual_1.pdb and coord




Extra info

To run the phenix properly, you have to modify two files in Phenix (Search for ComQum):


Weights and r/rfree for neutron data are currently not printed but easy to find in

Some inspiration about the cif files can be obtained from:

It gives cif lines and atom types.

For torsions, you have three options:


comqumtophenix should: