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Hi Folmer,<br>
<br>
I'm not sure I understand this. Isn't it a matter of displaying
density: compute all but show on graphics only what you want?<br>
<br>
If you still want to compute density around selected atoms only then
you can do it using phenix.maps:<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/documentation/phenix_maps.htm">http://phenix-online.org/documentation/phenix_maps.htm</a><br>
<br>
see "atom_selection" keyword in map {...} scope of parameters. Of
course you can do it in the GUI too.<br>
<br>
Pavel.<br>
<br>
<blockquote
cite="mid:CAE7RQxJKQaYGWDyF_BHt9Mrdks=0zd=fxcM75fEjkOKy1P+O+g@mail.gmail.com"
type="cite">
<p>Dear Pavel, <br>
This would still yield "normal" density in the entire unit cell.
It seems to me that Tjaard wants a map covering only the ligand
(if I understand correctly).</p>
<p>Using my phone, so I can't comment on what phenix programs
would be good.</p>
<p>Venlig hilsen<br>
Folmer Fredslund<br>
(and sorry for top posting)</p>
<div class="gmail_quote">Den 06/07/2011 17.46 skrev "Pavel
Afonine" <<a moz-do-not-send="true"
href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>>:<br
type="attribution">
> Hi Tjaar,<br>
> <br>
> an easy and transparent way of doing what you want with
just one command:<br>
> <br>
> phenix.refin model.pdb data.mtz simulated_annealing=true <br>
> modify_start_model.occupancies.set=0
modify_start_model.selection="chain <br>
> A and resname LIG"<br>
> <br>
> the residual map (Fourier map coefficients) in output MTZ
file is the <br>
> map you want (that you can open and see in Coot). The
command <br>
> phenix.mtz2map will convert this map into actual CCP4 or
X-plor <br>
> formatted map:<br>
> <br>
> <a moz-do-not-send="true"
href="http://phenix-online.org/documentation/mtz2map.htm">http://phenix-online.org/documentation/mtz2map.htm</a><br>
> <br>
> You can see the content of output MTZ file using
phenix.mtz.dump command.<br>
> <br>
> You should discard the output PDB file since will contain
the ligand <br>
> with zero occupancy.<br>
> <br>
>> I would like to generate an SA-omit Fo-Fc map for a
ligand bound to <br>
>> protein.<br>
>> Using the GUI I selected the AutoBuild-Create Omit Map
module and set <br>
>> the following :<br>
>> - data.mtz<br>
>> - protein.pdb (no ligand, no solvent) = start model<br>
>> - ligand.pdb (just ligand) = omit map atoms<br>
>> - omit map type = simulated annealing<br>
>> - omit region = omit around pdb<br>
>> The resulting map (/OMIT/resolve_composite_map.mtz)
shows density for <br>
>> both the protein and the ligand. <br>
> <br>
> This should be equivalent to what I described above, and if
not then <br>
> there is a problem that we need to fix.<br>
> <br>
>> When I feed this into the CCP4 module FFT to generate
an nF1-mF2 map <br>
>> (with n=1 and m=1) I still get density for both the
protein and ligand.<br>
> <br>
> I don't know what this step does so can't comment.<br>
> <br>
> Let me know if you have any questions or need help with
this.<br>
> <br>
> Pavel.<br>
> <br>
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