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<p>Hi Joe,</p>
<p>it looks like you did everything just right.. So I'm not sure
what you mean by "It gives the CCP4 map but it is not a real space
model-map as expected.". What makes you think this is not a
real-space model-calculated map? It should be, it is expected to
be..</p>
<p>Pavel<br>
</p>
<div class="moz-cite-prefix">On 1/22/24 01:53, joe.wilson2023 wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CALj5QQ4=FOGktggGiyzc=pMNZTKMaYLo4rpnV7Yqmpr0iyc9Sg@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<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"
moz-do-not-send="true" class="moz-txt-link-freetext">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" moz-do-not-send="true"
class="moz-txt-link-freetext">https://pubmed.ncbi.nlm.nih.gov/30198894/</a><br>
<br>
Pavel<br>
<br>
<br>
</blockquote>
</div>
</blockquote>
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