On Fri, May 14, 2010 at 6:45 PM, xaravich ivan <span dir="ltr"><<a href="mailto:xaravich.ivan@gmail.com">xaravich.ivan@gmail.com</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;">
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>
</blockquote><div><br></div><div>FYI, if you are generating a composite omit map, you do not need to delete anything first. �If you just want to look at a specific region, there are much faster ways to do this:</div><div>
<br></div><div>1. Specify the region to omit "Omit map options->Omit region specification", either using a PDB file containing the atoms to leave out, or an atom selection.</div><div>or</div><div>2. delete the region manually, then run phenix.refine with simulated annealing for a couple of macrocycles, and look at those maps.</div>
<div><br></div><div>As long as you have simulated annealing turned on (always a good idea for omit maps), these are approximately equivalent. �The composite omit procedure basically does (2) for every region of the model, then stitches the maps around those regions back together, so it will take ~20x longer to run.</div>
<div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">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>
</blockquote><div><br></div><div>That sounds bad. �Could you please send me (not the list!) the final MTZ file?</div><div><br></div><div>thanks,</div><div>Nat</div></div>