<div dir="ltr">Hi Pavel, <div><br></div><div>Thank you for your information.</div><div>I had a try with the cmd you suggested and I did get the mtz file.</div><div>While trying to use the mtz to get a real space map, I tried with "phenxi.mtz2map model.cif.mtz"</div><div>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;font-size:15px;line-height:normal;font-family:Monaco;color:rgb(242,242,242);background-color:rgba(0,0,0,0.92)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">Available map coefficients in this MTZ file:</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;font-size:15px;line-height:normal;font-family:Monaco;color:rgb(242,242,242);background-color:rgba(0,0,0,0.92)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>['FMODEL,PHIFMODEL'] (skipping, add include_fmodel=True to include)</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;font-size:15px;line-height:normal;font-family:Monaco;color:rgb(242,242,242);background-color:rgba(0,0,0,0.92)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">No model input - will output map(s) in unit cell.</span></p></div><div>After adding includ_fmodel=True. It gives the CCP4 map but it is not a real space model-map as expected.</div><div>I may not get the right way to do this. Need further help.</div><div><br></div><div>Many thanks,</div><div>Joe</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, Jan 20, 2024 at 5:07 AM Pavel Afonine <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Joe,<br>
<br>
> I am new to Phenix and using the phenix.mtriage to get the map-model <br>
> FSC results. It gives the correct results at the same time I also want <br>
> to produce the mode-map used for the FSC calculation. Is there an <br>
> option for this? If not how can I reproduce the same model-map with <br>
> another phenix command?<br>
<br>
at the moment phenix.mtriage does not have an option to output the <br>
model-generated map. However, you can get such a map using a different <br>
Phenix tool (in the command line). Example:<br>
<br>
phenix.fmodel model.pdb high_res=3.2 scattering_table=electron<br>
<br>
where model.pdb is the file with your atomic model, high_res specifies <br>
resolution of the map, and scattering_table tells to use electron form <br>
factors.<br>
<br>
This will produce an MTZ file with the Fourier map that is calculated as <br>
described in Section 2.1.1. here:<br>
<br>
<a href="https://pubmed.ncbi.nlm.nih.gov/30198894/" rel="noreferrer" target="_blank">https://pubmed.ncbi.nlm.nih.gov/30198894/</a><br>
<br>
Pavel<br>
<br>
<br>
</blockquote></div>