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

Dale Tronrud detBB at daletronrud.com
Mon Sep 15 08:58:56 PDT 2014

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   An alternative you might want to consider is what I call the
"discovery map".  At some point in the refinement process there was a
map that convinced YOU that this ligand was present.  You should be
the hardest person to be convinced so that map will be both an omit
map (because the model had been refined without the ligand prior to
this) and clear enough to satisfy the reader.

   This map will have the bulk solvent issues discussed previously,
but the ligand density must have been sufficiently strong and clear to
overcome that obstacle in order for you to be convinced.

Dale Tronrud

On 9/15/2014 12:23 AM, Pavel Afonine wrote:
> Hi Wei,
> I'm glad this discussion gave you some food for thought! -:)
> If you have no programing experience with CCTBX then this may not
> be the best route to take. I mentioned CCTBX in my previous email
> just to identify this as a possible option. However the amount of
> scripting necessary to achieve this may be prohibitive for novices
> to CCTBX.
> At present we do not have tools in Phenix that compute local OMIT
> maps most optimally (and I'm not aware of such tools outside of
> Phenix). We do have great tools to calculate various kinds of OMIT
> maps but I believe they are suboptimal in contexts like yours for
> reasons I explained in one of my previous emails in this thread. In
> fact I'm preparing a manuscript that discusses this matter and
> hopefully makes my points clearer.
> Options you have are:
> 1) I'm going to add a tool that I plan to call 
> phenix.difference_omit_map (or something similar) that will
> calculate OMIT map the way I described before. With some luck it
> may be available in nightly builds by end of this week.
> 2) If you can't wait you can just follow Nat's suggestions. If
> ligand density is sufficiently strong and you use tools correctly
> you may get what you want. However if ligand density is weak the
> OMIT map may not be useful as bulk-solvent may obscure the ligand
> density..
> 3) You can send me files off list and I will calculate the OMIT map
> for you.
> All the best, Pavel
> On 9/14/14 2:12 PM, Wei Shi wrote:
>> 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!
>> Best, Wei
>> On Sun, Sep 14, 2014 at 12:10 PM, Nathaniel Echols
>> <nechols at lbl.gov <mailto:nechols at lbl.gov>> wrote:
>> On Sat, Sep 13, 2014 at 8:21 PM, Pavel Afonine <pafonine at lbl.gov 
>> <mailto: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
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