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Hi Emily,<br>
<br>
ok, let's do it step-by-step:<br>
<br>
1) Other tools -> Fetch PDB data, In Action choose "Download all
data and convert CIF to MTZ".<br>
<br>
This will give you model and reflection data.<br>
<br>
2) Maps -> Calculate maps<br>
<br>
Load model (PDB) and data (MTZ) files.<br>
<br>
3) Maps -> FFT map coefficients, load *_map_coeffs.mtz file and
run.<br>
<br>
This will give *.ccp4 maps that you need.<br>
<br>
I just did these steps and it worked for me fine.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 6/1/15 8:49 AM, Emilia C. Arturo
(Emily) wrote:<br>
</div>
<blockquote
cite="mid:CAHB=7Xj1+r3HfydW3M0VA=4pcBrDoTY2AJ90bY=1qrdXkZj2XQ@mail.gmail.com"
type="cite">
<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>
</div>
</div>
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