<div dir="ltr"><div>Paul and Pavel,</div><div><br></div><div>Thank you for bearing with me - I am still so new at this. I did some side-by-side 'experiments' with the GUI and at the command line (now I know about the reflection file editor tool, too) and now I understand what I'd done wrong, and where I misunderstood things: I see now that the 'Import CIF structure factors' tool converts the PDB data to "MTZ format", but even though I'd supplied both the structure factors and the model (because there are fields available in the GUI for both), this tool does not generate map coefficients; I could have guessed as much from the name of the tool ;-). Basically, I just needed to use 'Calculate map' after using the 'Import CIF structure factors' tool.</div><div><br></div><div>Pavel, by the way: the command line '<span style="font-size:12.8000001907349px">phenix.maps 1akg.{pdb,mtz}' does also generate a CCP4 format map, without explicitly requesting one.</span></div><div><br></div><div>I learned a lot in going through the exercise. Thank you :-)</div><div><br></div><div>Emily.</div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Jun 1, 2015 at 12:36 PM, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span> wrote:<br><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">
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.<span><font color="#888888"><br>
<br>
Pavel</font></span><div><div><br>
<br>
<div>On 6/1/15 8:49 AM, Emilia C. Arturo
(Emily) wrote:<br>
</div>
<blockquote 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><br>
<br>
<div>On 5/30/15 3:05 PM, Emilia C. Arturo (Emily)
wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div>
<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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