Thanks Nat,<br>Its the latest version I downloaded less than a week back. It is in Mac OS X. I am using GUI. Basically I have made most of the model and as it was from Molecular Replacement it still has that high R free and I am sure that parts of the model has that bias and does not fit niceley. I deleted those regions and used SA_omit map in phenix GUI. It made a composite omit map by default. and it has made those number of regions of pdb and mtz files.<br>
<br>The coot is distinctly indicating that it could not open the map/mtz. even when I try to open from phenix or separately from command line.<br><br>Thanks,<br>Ivan<br><br><br><div style="visibility: hidden; display: inline;" id="avg_ls_inline_popup">
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On Fri, May 14, 2010 at 5:52 PM, Nathaniel Echols <span dir="ltr"><<a href="mailto:nechols@lbl.gov">nechols@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div></div><div class="h5">On Fri, May 14, 2010 at 5:40 PM, xaravich ivan <span dir="ltr"><<a href="mailto:xaravich.ivan@gmail.com" target="_blank">xaravich.ivan@gmail.com</a>></span> wrote:<br></div></div><div class="gmail_quote">
<div><div></div><div class="h5"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; 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></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'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 "Open MTZ", 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>
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