[phenixbb] Spermine molecule on a crystallographic two-fold axis

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Thu Mar 26 12:06:31 PDT 2009

Hi Marjolein,

> I have been trying to find in the documentation if there is a way to do this
> but I have the following problem: In a recent structure we are currently
> refining we identified a spermine molecule sitting right on a
> crystallographic two-fold axis. Spermine has internal two-fold symmetry and
> it is part of extensive crystal contacts. I just wonder how to refine this
> with Phenix. In Refmac it is easy, I put the occupancies to 0.5 and the
> program ignores the clashes of the symmetry related molecule, but that
> doesn't seem to be the way that Phenix works. Can anyone give me advise on
> this? 

Supporting the occupancy trick is on my to-do list (fairly high up).

In the meantime, could you try giving only the asymmetric unit of the
spermine? I.e. delete all duplicate atoms from your pdb file.
The restraints across the symmetry bond will not work automatically.
You have to define a "custom bond" instead, and if you also want to
restrain the angles, custom pseudo-bonds. See the
"Definition of custom bonds and angles" section.
In your case you'll have to define symmetry_operations (not shown
in the docs), e.g.:

 bond {
    action = *add
    atom_selection_1 = resname SPM and name C7
    atom_selection_2 = resname SPM and name C7
    symmetry_operation = -x,-y,z
    distance_ideal = 1.5
    sigma = 0.01

The main difficulty will be to find the correct symmetry_operation
for each custom bond. If you send my the CRYST1 card from your
PDB file and the part with the SPM residue I could help out.


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