<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 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 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>> _______________________________________________<br>> phenixbb mailing list<br>> <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>> <a href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
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