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Try putting a resolution=3 on the command line (change the 3 to something appropriate for you). That omission often spawns the error you see.
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<div>(I’m not convinced that a sensible default couldn’t be deduced by the programs in many instances.)
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<div>Phil Jeffrey</div>
<div>Princeton</div>
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<blockquote type="cite">On Jun 10, 2023, at 12:03 PM, Das, Abhinaba <abhinaba.das@emory.edu> wrote:<br>
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<p class="MsoNormal">Good afternoon all, <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’ve been running Phenix using the GUI however I want to segment a map using phenix.segment_and_split_map which turns out to be a command line program.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’m trying to run it using the following command: <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="p1"><span class="s1">abhinabadas@AbhinabasM1Mac ~ % phenix.segment_and_split_map \</span><o:p></o:p></p>
<p class="p1"><span class="s1">/Users/abhinabadas/Downloads/Chimera/postProcessMaskedsharpened_map.ccp4 \</span><o:p></o:p></p>
<p class="p1"><span class="s1">/Users/abhinabadas/Desktop/Test_map_2/rcsb_pdb_3J9G.fasta auto_sharpen = False \</span><o:p></o:p></p>
<p class="p1"><span class="s1">box_in_auto_sharpen = False<o:p></o:p></span></p>
<p class="p1"><span class="s1"><o:p> </o:p></span></p>
<p class="p1"><span class="s1"><o:p> </o:p></span></p>
<p class="p1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">However, it ends every time giving the error:
<o:p></o:p></span></p>
<p class="p1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
<p class="p1"><span class="s1">Read sequence from /Users/abhinabadas/Desktop/VipA-B/rcsb_pdb_3J9G.fasta</span><o:p></o:p></p>
<p class="p1"><span class="s1">Sorry: Need resolution for segment_and_split_map with sharpening<o:p></o:p></span></p>
<p class="p1"><span class="s1"><o:p> </o:p></span></p>
<p class="p1"><span class="s1"><o:p> </o:p></span></p>
<p class="p1"><span class="s1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Initially, I used the same command without using
</span></span><span class="s1">auto_sharpen = False</span><o:p></o:p></p>
<p class="p1"><span class="s1">box_in_auto_sharpen = False, </span><span class="s1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">as the map was already auto sharpened in Phenix. It gave me the same error regardless.
<o:p></o:p></span></span></p>
<p class="p1"><span class="s1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p> </o:p></span></span></p>
<p class="p1"><span class="s1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Apologies for this possibly inane question; there might be a very easy fix to it but I can’t seem to figure it out. I would greatly appreciate any insights or suggestions
to resolve this issue. Please let me know if you need any further information. Thank you for your attention and assistance.
<o:p></o:p></span></span></p>
<p class="p1"><span class="s1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p> </o:p></span></span></p>
<p class="p1"><span class="s1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Thanks, abhi</span></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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