On Mon, Jun 21, 2010 at 8:13 AM, Mark A Saper <span dir="ltr">&lt;<a href="mailto:saper@umich.edu">saper@umich.edu</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 style="word-wrap:break-word">Could someone explain the difference between the GUI &quot;ligand_identification&quot; routine and the documented command line &quot;find_all_ligands&quot;.  The latter appears to have more flexible input parameters. </div>
</blockquote><div><br></div><div>I believe find_all_ligands is just a frontend to LigandFit for searching for multiple different ligands, which you still need to specify.  The ligand identification program runs &quot;blind&quot;, i.e. it tries all of the most common ligands in the PDB, or all found in ATP-binding proteins, or everything in a directory you supply, etc., and would normally be used to fill mystery blobs in the maps.</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div style="word-wrap:break-word">I&#39;m not sure the GUI for ligand_identification is working correctly. </div>
</blockquote><div><br></div><div>sigh. . .</div><div><br></div><div>Yes, someone deleted a couple of essential lines of my code, so it runs in the wrong directory (and it does still run correctly, but you won&#39;t see the results in the GUI).  I&#39;ll send you the patch.</div>
<div><br></div><div>-Nat</div></div>