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 <[email protected]> wrote:
On Sat, Sep 13, 2014 at 8:21 PM, Pavel Afonine <[email protected]> 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