[phenixbb] Fo-Fc omit map for ligand in the protein-ligand structure

Wei Shi wei.shi118 at gmail.com
Sun Sep 14 14:12:29 PDT 2014

Thank you so much! I guess I will do as Pavel first suggested to define a
box around the ligand and omit all the scattering inside the box (ligand
and bulk-solvent) using CCTBX. I now got CCTBX installed on my computer and
are trying to figure out ... Let me know if any of you happen to know how
to define a box and omit all the scattering using CCTBX. Thank you so much!


On Sun, Sep 14, 2014 at 12:10 PM, Nathaniel Echols <nechols at lbl.gov> wrote:

> On Sat, Sep 13, 2014 at 8:21 PM, Pavel Afonine <pafonine at lbl.gov> wrote:
>>  2. "Restraining the zero-occupancy ligand (and perhaps adjacent
>>> residues) is strongly recommended, especially if it contains heavier
>>> elements.  (The newer versions of the phenix.refine GUI have a button in
>>> the Output tab to set this up.)  Without restraints, you run the risk of
>>> refining the surrounding model into the ligand density.  As always this is
>>> worse at lower resolution - at 2.8Å I'm not sure what to expect."
>>> I am wondering how this could be done.
>> I am not sure why you may want to do this at all. If you keep the ligand
>> in PDB file and "omit" it by setting occupancies to zero then the omit map
>> you will get is useless if you ask the program to not fill bulk solvent
>> into ligand region. If you let the program to fill bulk-solvent into ligand
>> region (= ask mask calculation to ignore zero occupancy atoms) then why
>> don't you just remove the ligand from PDB file (then you don't need to
>> worry about restraining it etc.)? In fact you can even keep it in file as
>> you don't care (for map calculation purpose) where restraints will move it.
> I think you're confusing what I wrote with the bulk solvent issue.  It is
> also sometimes necessary to prevent actual atoms from being refined into
> the omit region - this is the purpose of adding harmonic restraints on the
> omitted atoms.  (As far as I know this was first suggested in Hodel et al.
> 1992, although they don't go into a great deal of detail.)  It will have no
> effect on the bulk solvent mask, which will still be extended over the
> zero-occupancy atoms.  I'm sure there are plenty of cases where the
> restraints don't make a difference, but I just spent a great deal of time
> working with a structure where they were essential.
> Wei: I've attached a slide showing how to set up the restraints.  But I
> agree with Pavel that changing the bulk solvent mask settings is dangerous.
> -Nat
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20140914/ee4c2852/attachment.htm>

More information about the phenixbb mailing list