On Thu, Jun 13, 2013 at 11:53 AM, Mengbin Chen <span dir="ltr"><<a href="mailto:mengbinc@sas.upenn.edu" target="_blank">mengbinc@sas.upenn.edu</a>></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 dir="ltr"><div style="font-family:arial,sans-serif;font-size:13px"><font face="Arial, sans-serif">I tried the command line in Terminal, but Elbow still regularized the conformation and bonds of the ligand and the result turned out to be the same with that I ran thorough GUI. The thing is that the input pdb file has a conformation the ligand should adopt so that I do not really want energy minimization or geometry optimization to be done on it. Although I set "none" for "geometry optimization" in GUI, it unfortunately changed the ligand conformation.</font></div>
</div></blockquote><div><br></div><div>This has nothing to do with use of the GUI versus command line - the problem is that using a PDB file as the only source of chemical information is unlikely to work, especially if no hydrogens are present. �At the very least you need explicit hydrogens, and ideally you need an input file that actually defines the topology, like SMILES or MOL2 or CIF. �If it's a ligand that is already in the PDB you can just give it the three-letter code and it will extract this information automatically from the database included with Phenix.</div>
<div><br></div><div>I guess I need to add a warning to the GUI if users try to use a PDB file alone, because this problem comes up again and again.</div><div><br></div><div>-Nat</div></div>