<div dir="ltr"><div>Thanks Dr. Pavel,</div><div><br></div><div>This looks simple. </div><div><br></div><div>regards</div><div>Manoj</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Nov 15, 2015 at 11:49 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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Manoj,<br>
<br>
you can do it this way:<br>
<br>
1) remove ligand from PDB file;<br>
2) compute mFo-DFc map. This is your ligand-omit map.<br>
<br>
Some would advise to do a round of refinement between steps 1-2 above in order to remove "memory from the ligand". I'm not convinced this is critical though.<span class="HOEnZb"><font color="#888888"><br>
<br>
Pavel</font></span><div class="HOEnZb"><div class="h5"><br>
<br>
On 11/15/15 12:18, Manoj saxena wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid">
Greetings,<br>
<br>
I would be very grateful if someone can help<br>
me to explain in I can get F0-Fc omit maps of a particular<br>
ligands using Phenix.<br>
I am trying to generate an omit map<br>
for the ligands in my protein model using the<br>
composite omit map GUI feature of phenix version 1.10.1-2155.<br>
I selected my ligands by using atom selection feature under the<br>
map options(and in the omit map method I put refine). What map type I should give in the map types<br>
input to get the F0-Fc maps. Currently I may getting a map<br>
that look like my 2F0-Fc map that I got after my refinement.<br>
Also, I have no waters in my model.<br>
Can we define areas (boxes) around the ligand to generate<br>
omit map of that particular region to get output maps with densities<br>
like Fo-Fc maps.<br>
<br>
So many thanks in advance.<br>
<br>
Regards<br>
Manoj<br>
<br>
</blockquote>
<br>
</div></div></blockquote></div><br></div>