Thanks- got it working! I used #2 (redid the refinement).<br>-Sam<br><br><div class="gmail_quote">On Tue, Oct 27, 2009 at 5:54 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 class="im">On Oct 27, 2009, at 2:28 PM, Sam Stampfer wrote:<br>
</div><div><div></div><div class="h5">> This isn't exactly phenix-related but someone might know an easy<br>
> solution. I'm trying to open an electron density map in pymol. It<br>
> won't open .mtz files and the .xplor files I generated from ccp4i<br>
> don't seem to work either. I need to have my density as a .xplor<br>
> file in order for pymol to open it (I think). How would I generate<br>
> a .xplor file from .mtz? Or, alternately, how can I set phenix to<br>
> output a .xplor file? I've had it output to a cns file instead<br>
> of .mtz but that didn't help me get it in .xplor format.<br>
<br>
<br>
</div></div>Several solutions:<br>
<br>
1) phenix.create_maps<br>
<br>
2) output.write_maps=True in phenix.refine will generate XPLOR maps.<br>
<br>
3) In the GUI, it should create the XPLOR maps on the fly if you click<br>
one of the "Open in PyMOL" buttons.<br>
<br>
Since most of the necessary code is already floating around, I don't<br>
mind creating a utility for simply converting map coefficients, if<br>
people would find this useful, but unfortunately we don't have the<br>
ability to write CCP4-format maps yet.<br>
<br>
One thing to make sure of is that PyMOL is recognizing the input<br>
format correctly - sometimes you need to explicitly state this:<br>
<br>
PyMOL> load 2fofc.xplor, format=xplor<br>
<br>
-------------------<br>
<font color="#888888">Nathaniel Echols<br>
Lawrence Berkeley Lab<br>
510-486-5136<br>
<a href="mailto:NEchols@lbl.gov">NEchols@lbl.gov</a><br>
</font><div><div></div><div class="h5"><br>
<br>
<br>
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