<div dir="ltr">Hi Manoj,<div><br></div><div>Your command is very close! I think the goal is to combine a total of 7 maps, identifying the relative weights in these 7 maps for </div><div>26 regions. This will result in 7 weights for each region, one weight for each map. The sum of weights for each region will be 1. To do this, you want to specify 26 values for "region_selection", one at a time.</div><div><br></div><div>To get one weight per map, you want to turn off "local_weighting". </div><div><br></div><div>As you are supplying only full maps, you won't be able to get any half-map output.</div><div><br></div><div>This yields the following command:</div><div><br></div><div>phenix.combine_focused_maps \</div><div>map_file=Relion_deepEmhancer_reference_.mrc \</div><div>map_file=Base_map4.mrc \</div><div>map_file=Base_map1.mrc \</div><div>map_file=Base_map2.mrc \</div><div>map_file=Base_map3.mrc \</div><div>map_file=Base_map5.mrc \</div><div>map_file=Base_map6.mrc \</div><div>model_file=test1.pdb \</div><div>region_selection="(chain P and resid 366-401)" \</div><div>region_selection="(chain P and resid 179-297) " \<br>region_selection="(chain O and resid 401-555)"\</div><div>region_selection="(chain N and resid 458-530) " \</div><div>region_selection="(chain N and resid 311-457) " \</div><div>region_selection="(chain R and resid 13-79)" \</div><div>region_selection="(chain N and resid 726-577)" \</div><div>region_selection="(chain N and resid 823-880)" \</div><div>region_selection="(chain I and resid 350-409)" \</div><div>region_selection="(chain N and resid 577-726)" \</div><div>region_selection="(chain O and resid 667-722)" \</div><div>region_selection="(chain Q and resid 264-276)" \</div><div>region_selection="(chain N and resid 928-981) " \</div><div>region_selection="(chain O and resid 926-971) " \</div><div>region_selection="(chain O and resid 875-899) " \<br>region_selection="(chain Q and resid 208-244) " \<br>region_selection="(chain O and resid 717-739) " \<br>region_selection="(chain N and resid 877-898) " \<br>region_selection="(chain M and resid 7-101) " \<br>region_selection="(chain L and resid 2047-2141)" \</div><div>region_selection=" (chain L and resid 1718-1746)" \</div><div>region_selection="(chain L and resid 2001-2025)" \</div><div>region_selection="(chain N and resid 880-900)" \</div><div>region_selection="(chain P and resid 430-440)" \</div><div>region_selection="(chain L and resid 1954-1965)" \</div><div>region_selection="(chain P and resid 131-154)" \</div><div>composite_map_file=composite_map.mrc \</div><div>local_weighting=False \</div><div>rigid_body_refinement_single_unit=False \</div><div>nproc=8 \</div><div>resolution=4.0</div><div><br></div><div>Let me know if that does not do it!</div><div><br></div><div>All the best,</div><div>Tom T</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, May 9, 2023 at 11:30 PM Manoj saxena <<a href="mailto:mks131@gmail.com">mks131@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Hi ,</div><div>I am trying the following command using PHENIX VERSION: 1.20.1-4487.</div><div>to generate a composite map from locally refined maps (cryo-EM) of my complex. I have <br></div><div>selected multiple regions each one correspond to one of the six locally refined maps that I wish to combine using this command. I would be grateful if you can suggest if this is the correct way to do it. In this test1.pdb contains the complete model. <br></div><div>One of my doubts is that if instead of selection, I supply individual model files for each map region</div><div>can they have multiple chain Ids. Asking because I was told that I would need to combine all chains and rename them as one chain (per map region) to have the correct weighted map.</div><div><br></div><div>Many thanks</div><div>Manoj<br></div><div><br></div><div><br></div><div>phenix.combine_focused_maps map_file=Relion_deepEmhancer_reference_.mrc map_file=Base_map4.mrc map_file=Base_map1.mrc map_file=Base_map2.mrc map_file=Base_map3.mrc map_file=Base_map5.mrc map_file=Base_map6.mrc model_file=test1.pdb region_selection="(chain P and resid 366-401) or (chain P and resid 179-297) or \<br> (chain O and resid 401-555) or (chain N and resid 458-530) or (chain N and resid 311-457) or (chain R and resid 13-79) or \<br> (chain N and resid 726-577) or (chain N and resid 823-880) or (chain I and resid 350-409) or (chain N and resid 577-726) or (chain O and resid 667-722) or \<br> (chain Q and resid 264-276) or (chain N and resid 928-981) or (chain O and resid 926-971) or \<br> (chain O and resid 875-899) or (chain Q and resid 208-244) or (chain O and resid 717-739) or (chain N and resid 877-898) or \<br> (chain M and resid 7-101) or (chain L and resid 2047-2141) or (chain L and resid 1718-1746) or (chain L and resid 2001-2025) or (chain N and resid 880-900) or (chain P and resid 430-440) or (chain L and resid 1954-1965) or (chain P and resid 131-154)" composite_map_file=composite_map.mrc composite_half_map_1_file=composite_half_A_map.mrc composite_half_map_2_file=composite_half_B_map.mrc local_weighting=True rigid_body_refinement_single_unit=False nproc=8 resolution=4.0</div></div>
</blockquote></div><br clear="all"><div><br></div><span class="gmail_signature_prefix">-- </span><br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr">Thomas C Terwilliger<div>Laboratory Fellow, Los Alamos National Laboratory</div><div>Senior Scientist, New Mexico Consortium</div><div>100 Entrada Dr, Los Alamos, NM 87544</div><div>Email: <a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank">tterwilliger@newmexicoconsortium.org</a></div><div>Tel: 505-431-0010</div><div><br></div></div></div></div></div></div></div></div></div></div>