Dear Phenix Users,<br><div class="gmail_quote"><div><br></div><div>I have been playing around with Phenix AutoBuild GUI to generate a fo-fc sa omit map of the ligand in a protein structure, and I have the input files as follows:</div>
<div>
<br></div><div>output.mtz (data type:experimental data)</div><div>ligand.pdb (data type: omit box atoms &amp; ligands)</div><div>ligand.cif (data type: restraints of the ligand)</div><div>protein.pdb (data type: starting model)</div>

<div><br></div><div>omit map type: simulated annealing</div><div>omit region: omit around PDB fie</div><div><br></div><div>I have set the occupancies of all ligand atoms zero and deleted the ligand coordinates in my starting model. After the run finished and I checked the refined coordinates and map.mtz in COOT, I found that there was no electron density around the ligand while the protein model was in electron density, which was exactly opposite of what I wanted before. Furthermore, I have 3 Mg2+ ions in protein.pdb file, all of which moved away from where they were after the refinement run, which was not wanted either.</div>

<div><br></div><div>Could anyone tell me how to do the sa omit map of ligand correctly?</div><div><br></div><div>Thanks in advance! </div><div><br></div><div>Mengbin</div><span class="HOEnZb"><font color="#888888"><div>-- </div>
</font></span></div>Mengbin Chen<div>Department of Chemistry</div><div>University of Pennsylvania</div><br>