Hello,<br><br>I want to generate a simulated annealing omit map around DNA molecule in my protein-DNA complex for publication. My resolution is very low - 5A. <br><br>1. I deleted the whole DNA (947 atoms of DNA against 7543 for protein part) from pdb and ran phenix.refine with simulated_annealing=True. But resulted Fo-Fc in the omitted region is very weak. Is it because of the low resolution and because big part of the model was omitted?<br>
<br>2. Next, I wanted to generate a composit_sa_omit map as in this case DNA would be deleted in small portions and the resulted map would give me a map I can use for publication:<br><br>phenix.autobuild data=inp.mtz model=whole.pdb (contains DNA) maps_only=True (to skip rebuilding) composite_omit_type=sa_omit omit_selection=DNA.pdb (contains only DNA coordinates). But the job runs too long and still it seems like it is doing rebuilding.  Is this a correct command and correct action to create a sa_omit map for the DNA in my complex?<br>
<br>Thank you a lot for the help,<br><br>Nick<br><br> <br>