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<p class="MsoNormal">Hi Chimera team,</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Is it possible to mask after vop. I got it to work in Chimera’s command line in the gui but when I run it from my python script it does not work. I am trying to change this working solution to this solution without ground truth:</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">WORKING SOLUTION</p>
<p class="MsoNormal"> #chimera_script.write('open ' + paths['input'] + '\n'</p>
<p class="MsoNormal"> # 'open ' + paths['ground_truth'] + '\n'</p>
<p class="MsoNormal"> # 'molmap #1 6 gridSpacing 1\n'</p>
<p class="MsoNormal"> # 'volume #1.1 level 0.1\n'</p>
<p class="MsoNormal"> # 'mask #0 #1.1\n'</p>
<p class="MsoNormal"> # 'vop resample #2 onGrid #1.1\n'</p>
<p class="MsoNormal"> # 'volume #3 save ' + paths['cleaned_map'])</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">NEW SOLUTION</p>
<p class="MsoNormal"> chimera_script.write('open ' + paths['input'] + '\n'</p>
<p class="MsoNormal"> 'vop gaussian #0 sDev 2\n'</p>
<p class="MsoNormal"> 'vop median #1 iterations 5 modelId #2.1\n'</p>
<p class="MsoNormal"> 'volume #2.1 level 0.1\n'</p>
<p class="MsoNormal"> 'mask #0 #2.1\n'</p>
<p class="MsoNormal"> 'vop resample #3 onGrid #2.1\n'</p>
<p class="MsoNormal"> 'volume #4 save ' + paths['cleaned_map'])</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">While mask after vop works with GUI command line it gets a NoneType error when doing this: subprocess.run(['/usr/local/bin/chimera', '--nogui', chimera_script.name]). It seems like this might be a bug of chimera? Since it tries to return
None to a tuple and crashes. For some reason no triangles in the new surface with vop. Here is a snippet from the depthmask.py where it crashes.</p>
<p class="MsoNormal"><img width="369" height="176" style="width:3.8437in;height:1.8281in" id="Picture_x0020_3" src="cid:image001.png@01D525AB.830ADC20"></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you,</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Ryan Harlich</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">
Mail</a> for Windows 10</p>
<p class="MsoNormal"><o:p> </o:p></p>
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