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Hi Wei,<br>
<br>
I'm glad this discussion gave you some food for thought! -:)<br>
<br>
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.<br>
<br>
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.<br>
<br>
Options you have are:<br>
<br>
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. <br>
<br>
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..<br>
<br>
3) You can send me files off list and I will calculate the OMIT map
for you.<br>
<br>
All the best,<br>
Pavel<br>
<br>
<br>
<div class="moz-cite-prefix">On 9/14/14 2:12 PM, Wei Shi wrote:<br>
</div>
<blockquote
cite="mid:CA+Sz7q7VmS1DhH735Q3d-xjyr2BL+PPryBy+v5E81wxr_hUSAQ@mail.gmail.com"
type="cite">
<div dir="ltr">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!<br>
<br>
Best, <br>
Wei <br>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Sun, Sep 14, 2014 at 12:10 PM,
Nathaniel Echols <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:nechols@lbl.gov"
target="_blank">nechols@lbl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><span class="">On Sat, Sep 13, 2014 at 8:21
PM, Pavel Afonine <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span>
wrote:</span>
<div class="gmail_extra">
<div class="gmail_quote"><span class="">
<blockquote class="gmail_quote" style="margin:0 0
0 .8ex;border-left:1px #ccc
solid;padding-left:1ex"><span>
<blockquote class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px
#ccc solid;padding-left:1ex">
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."<br>
<br>
I am wondering how this could be done.<br>
</blockquote>
<br>
</span>
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.</blockquote>
<div><br>
</div>
</span>
<div>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.</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>-Nat</div>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</blockquote>
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