<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div>Pavel, </div><div><br></div><div>The command line steps you gave worked well (i.e. I got the map I wanted) for the models in which I am interested.</div><div><br></div><div>But the GUI is still giving the same error <span style="font-size:12.8000001907349px;color:rgb(80,0,80)">"This reflections file does not appear to contain any suitable map coefficients"</span>, even for the PDB id you gave as an example (1AKG). This is what I did to use the GUI: I typed in the PDB id to the GUI 'Reflections tools' > 'Import CIF structure factors' tool, and the tool fetched the model and .cif file and output an mtz file. But when I loaded this mtz file into the GUI 'Maps' > 'FFT map coefficients' tool, I got the error. Furthermore, EVEN if I loaded the mtz file that I'd generated using the command line phenix.maps 1akg.{pdb,mtz} into the GUI maps tool, I get the same error.</div><div><br></div><div>I am fine using the command line, but I suspect that there's an issue with how the GUI is loading the mtz files for the Maps tool.</div><div><br></div><div>Regards,</div><div>Emily.</div><div><br></div><div><br></div><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div bgcolor="#FFFFFF" text="#000000">
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></div></blockquote><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div bgcolor="#FFFFFF" text="#000000">
<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<div><div class="h5"><br>
<br>
<div>On 5/30/15 3:05 PM, Emilia C. Arturo
(Emily) wrote:<br>
</div>
</div></div><blockquote type="cite"><div><div class="h5">
<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>
<fieldset></fieldset>
<br>
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