On Fri, May 14, 2010 at 5:40 PM, xaravich ivan <span dir="ltr">&lt;<a href="mailto:xaravich.ivan@gmail.com">xaravich.ivan@gmail.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;">
Again this is pretty novice and I would apologize in advance.<br>I ran Simulated annealing omit map in PHENIX and it gave me a bunch of files. I started with a partially built model ( I would say most of it was built) and it gave me an edited pdb that I can open in coot but I the composite omit mtz file is not opening in coot. In fact I cannot open any mtz file from the phenix output /OMIT directory and cannot see any map.<br>

I am pretty clueless.<br></blockquote><div><br></div><div>Some clarification:</div><div><br></div><div>1. Which version of Phenix, and which platform?</div><div>2. GUI or command-line?</div><div>3. If you&#39;re really making a composite omit map (as opposed to a simple omit map, e.g. for a ligand), ignore the PDB file output by AutoBuild and stick to the original.</div>
<div><br></div><div>One common problem is that on Mac, if you try to open the MTZ file in Coot (using the &quot;Open MTZ&quot;, not auto-open), it will open a window to choose column labels in the file, but it opens *behind* the main window, which you need to move to the side temporarily.</div>
<div><br></div><div>-Nat</div></div>