[phenixbb] phenixbb Digest, Vol 40, Issue 31

Marjolein Thunnissen marjolein.thunnissen at mbfys.lu.se
Tue Mar 31 09:38:54 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.
> Ralf
> ------------------------------


The commands worked indeed the trick. Luckily it is actually not that
difficult to find the symmetry operators when using coot. One just has to
switch drawing symmetry atoms on and clicking on a symmetry atom, coot will
tell you in the bottom line which atom it is and which symmetry operator was
used to draw it...

Thanks again


| Marjolein Thunnissen                             Phone +46-(0)46-22 24584|
| Associate Professor                              Fax   +46-(0)46-22 24692|
| Dept of Molecular Biophysics, Lund University    http://www.mbfys.lu.se  |
| PO-Box 124 S-221 00 Lund, Sweden                                         |
|                                                                          |
|Scientific coordinator I911 (Max-lab): MAD and fixed-wavelength stations
|                      |         for macromolecular crystallography

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