<div dir="ltr">Hi Elliot,<div><br></div><div>It looks like you want to calculate Fo-Fc map and have it in .mtz format. I would suggest to have a look at phenix.maps tool (living in cctbx_project/mmtbx/command_line/maps.py).</div><div><br></div><div>I believe confusion happened because .mtz format can store various things: experimental data (Fobs), map coefficients or both. You were generating fake experimental data, which cannot be displayed in Coot because it is not a map.</div><div><br></div><div>Hope it helps,</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Apr 5, 2018 at 1:24 AM, Elliot Nelson <span dir="ltr"><<a href="mailto:elliot.nelson@dtc.ox.ac.uk" target="_blank">elliot.nelson@dtc.ox.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt">Hi All,<br>
<br>
I'm trying to generate some simulated mtz files. My main aim is to test a script which looks to determine ligand occupancy (<a href="https://github.com/nelse003/exhaustive_search/blob/master/exhaustive_search.py" target="_blank">https://github.com/nelse003/<wbr>exhaustive_search/blob/master/<wbr>exhaustive_search.py</a>)
by looking at |Fo-Fc| over the ligand/ ground-state the ligand replaces. <br>
<br>
To test this I would like to generate mtz files from pdb models with a ligand occupancy that has varied between 0-1, which the above script would hopefully recover the occupancy.
<br>
<br>
I have tried to use mmtbx/examples/simulate_<wbr>experimental_data.py (<a href="https://github.com/cctbx/cctbx-playground/blob/8f23c190a9f8d2ed2b5845385f568f3233c16132/mmtbx/examples/simulate_experimental_data.py" target="_blank">https://github.com/cctbx/<wbr>cctbx-playground/blob/<wbr>8f23c190a9f8d2ed2b5845385f568f<wbr>3233c16132/mmtbx/examples/<wbr>simulate_experimental_data.py</a>
) to generate an mtz file.<br>
<br>
So far I have been able to generate mtz files using the simulate_experimental_data.py, these have the columns:<br>
<br>
H K L FOBS(+) SIGFOBS(+) FOBS(-) SIGFOBS(-)<br>
<br>
I can use this outputted mtz for running tests of my scripts ,However as this has no PHI columns, I cannot display this in coot. I have tried to add the phi column from the refined mtz of the orignal data using CAD, but have not yet managed to do this succesfully.<br>
<br>
I feel that this may be an overcomplicated, and potentially superseded way of generating simulated mtz data. Any advice on alternatives would be really useful?<br>
<br>
Apologies if this is not very clear.<br>
<br>
Thanks<span class="HOEnZb"><font color="#888888"><br>
<br>
Elliot Nelson<br>
</font></span></div>
</div>
<br>______________________________<wbr>_________________<br>
cctbxbb mailing list<br>
<a href="mailto:cctbxbb@phenix-online.org">cctbxbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/cctbxbb" rel="noreferrer" target="_blank">http://phenix-online.org/<wbr>mailman/listinfo/cctbxbb</a><br>
<br></blockquote></div><br></div>