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Hi Emily,<br>
<br>
step 1 - get files from PDB: <br>
<br>
phenix.fetch_pdb 1akg --mtz<br>
<br>
step 2 - compute maps:<br>
<br>
phenix.maps 1akg.{pdb,mtz}<br>
<br>
step 3 - convert map coefficients into map:<br>
<br>
phenix.mtz2map 1akg_map_coeffs.mtz<br>
<br>
Note 1: you can request to output actual maps at step 2, so step 3
isn't necessary.<br>
Note 2: all the above you can do in Phenix GUI.<br>
<br>
Let me know if you still having problems with this and I will send
step-by-step instructions how to do this using the GUI.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 5/30/15 3:05 PM, Emilia C. Arturo
(Emily) wrote:<br>
</div>
<blockquote
cite="mid:CAHB=7XjL6vHmTg9-GTX6h==xKyTTRjtNSD4K3vC978Vbx5P1Bg@mail.gmail.com"
type="cite">
<div dir="ltr">
<div style="font-size:12.8000001907349px">Hello.</div>
<div style="font-size:12.8000001907349px"><br>
</div>
<div style="font-size:12.8000001907349px">I'd like to generate a
map appropriate for viewing in PyMOL, using a model and
structure factors downloaded from the PDB. But I'm unable to
do so, and perhaps you can help me figure out what I might be
doing wrong:�</div>
<div style="font-size:12.8000001907349px"><br>
</div>
<div style="font-size:12.8000001907349px">To generate the map, I
did the following using the phenix GUI (version 1.9-1692):�</div>
<div style="font-size:12.8000001907349px">1. I used Reflection
tools > Import CIF structure factors to convert the .cif
format structure factors for PDB id 1J8U to an mtz file.</div>
<div style="font-size:12.8000001907349px">2. Then, to configure
the job to generate the CCP4 map, I loaded this mtz file, but
when I did that I got the following error:</div>
<span style="font-size:12.8000001907349px">"This reflections
file does not appear to contain any suitable map coefficients"</span>
<div style="font-size:12.8000001907349px"><br>
</div>
<div style="font-size:12.8000001907349px">I went through the
same steps again for two other PDB ids, this time generating
the mtz file by either letting phenix do it from a PDB id, or
by supplying the tool with both a .cif file with structure
factors and a pdb model file. I get the same error.</div>
<div style="font-size:12.8000001907349px"><br>
<div>Has anyone any advice?</div>
<div><br>
</div>
<div>Regards,</div>
<div>Emily.</div>
</div>
</div>
<br>
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<br>
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