On Thu, Apr 15, 2010 at 5:46 AM, Claudia Scotti <span dir="ltr">&lt;<a href="mailto:claudiascotti@hotmail.com">claudiascotti@hotmail.com</a>&gt;</span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">




<div>I&#39;m trying to rebuild a model with Autobuild. The protein has a ligand, whose density is already well defined, thus that the input for the new autobuild run includes its coordinates as well. <br><br>When I start the autobuild run, however, I see that the ligand is removed before rebuilding, which leads the program to use the ligand density to try to rebuild loops, thus introducing errors.<br>
<br>How can I keep the ligand in place, please? Or is there any alternative solutions?<br></div></blockquote><div><br></div><div>I believe the answer is to move the ligand to a separate PDB file, and add these parameters:</div>
<div><br></div><div>input_files.input_lig_file_list=ligand.pdb</div><div>input_files.keep_pdb_atoms=False</div><div><br></div><div>(Or if you&#39;re using the GUI, add the ligand PDB file and change the type to &quot;Ligands&quot;, and uncheck Settings-&gt;Input files-&gt;Keep pdb atoms.</div>
<div><br></div><div>-Nat</div></div>