[phenixbb] Cacodylate won't stay in place

Phan, Jason jason.phan at vanderbilt.edu
Mon Oct 27 08:30:31 PDT 2014

Hi Oarabile,

The pdb residue name of cacodylate is CAC. In Coot, position the density peak at the center of the screen then go to File -> Get Monomer..., type in CAC, OK, then do a real-space fit to see if the atoms still fly apart. Since cacodylate ion is in the standard CCP4 monomer library ($CCP4/lib/data/monomers/c/CAC.cif), there's no need to generate a restraints file, as long as your pdb residue name is CAC. Otherwise, use eLBow to generate restraints for the non-standard ligand for Phenix Refine to work properly.


On Oct 25, 2014, at 1:50 PM, Kgosisejo, Oarabile wrote:

Hello all,

I am trying to fit cacodylate ion in my model using Coot but it does not stay where I put it. The molecule breaks apart and some of its components attach to the peptide residues. Due to this, phenix.refine would not accept this as the input for refinement. Is there a way I can make cacodylate ion stay in its electron density and refine my structure with cacodylate ion?

I appreciate your help!

Best Regards,

Oarabile M. Kgosisejo
o.kgosisejo at usask.ca<mailto:o.kgosisejo at usask.ca>
phenixbb mailing list
phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>

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