<div dir="ltr">Hi Reza,<div><br></div><div>Great! Those error messages are not the most helpful, but it's something we're trying to improve. Let us know of any other issues!</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>--</div><div><span style="font-size:12.8000001907349px">Billy K. Poon</span><br></div></div><div>Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Tel: (510) 486-5709</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org" target="_blank">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Fri, Aug 4, 2017 at 4:09 PM, Reza Khayat <span dir="ltr"><<a href="mailto:rkhayat@ccny.cuny.edu" target="_blank">rkhayat@ccny.cuny.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr" style="font-size:12pt;color:#000000;background-color:#ffffff;font-family:Calibri,Arial,Helvetica,sans-serif">
<p>Hi Bill,</p>
<p><br>
</p>
<p>That's embarrassing, having missed the difference in cell size. The Reciprocal space variant (mtz) is now working. Thanks for the help.</p><span class="">
<p><br>
</p>
<p><br>
</p>
<p>Best wishes,</p>
<p>Reza <br>
</p>
<p><br>
</p>
<div id="m_-4006719570669145066Signature">
<div name="divtagdefaultwrapper">
Reza Khayat, PhD
<div>Assistant Professor </div>
<div>City College of New York</div>
<div>Department of Chemistry</div>
<div>New York, NY 10031</div>
</div>
</div>
</span><div style="color:rgb(33,33,33)">
<hr style="display:inline-block;width:98%">
<div id="m_-4006719570669145066divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" color="#000000" face="Calibri, sans-serif"><b>From:</b> Billy Poon <<a href="mailto:bkpoon@lbl.gov" target="_blank">bkpoon@lbl.gov</a>><br>
<b>Sent:</b> Friday, August 4, 2017 4:24 PM<br>
<b>To:</b> Reza Khayat<br>
<b>Cc:</b> PHENIX user mailing list<br>
<b>Subject:</b> Re: [phenixbb] phenix.real_space_correlation</font>
<div> </div>
</div><div><div class="h5">
<div>
<div dir="ltr">Hi Reza,
<div><br>
</div>
<div>For the first error, phenix.map_model_cc should be used when you have a model and a map in real space.</div>
<div><br>
</div>
<div>For the second error, the unit cell in the model (592.359, 589.659, 590.506, 90, 90, 90) is different than the unit cell in the reflections file (278.528, 278.528, 278.528, 90, 90, 90). </div>
</div>
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<div>--</div>
<div><span style="font-size:12.8000001907349px">Billy K. Poon</span><br>
</div>
</div>
<div>Research Scientist, Molecular Biophysics and Integrated Bioimaging</div>
<div>Lawrence Berkeley National Laboratory</div>
<div>1 Cyclotron Road, M/S 33R0345</div>
<div>Berkeley, CA 94720</div>
<div>Tel: <a href="tel:(510)%20486-5709" value="+15104865709" target="_blank">(510) 486-5709</a></div>
<div>Fax: <a href="tel:(510)%20486-5909" value="+15104865909" target="_blank">(510) 486-5909</a></div>
<div>Web: <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=_kfHIIMR3VGLnuYe30Zr0ZFScLJL022yfZrkMqxcp6U&s=zFvWTkDsiaht30qxwR4S_hrkO_PpnTKvG61139Ch-2E&e=" target="_blank">https://phenix-online.org</a></div>
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<div class="gmail_quote">On Fri, Aug 4, 2017 at 1:10 PM, Reza Khayat <span dir="ltr">
<<a href="mailto:rkhayat@ccny.cuny.edu" target="_blank">rkhayat@ccny.cuny.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr" style="font-size:12pt;color:#000000;background-color:#ffffff;font-family:Calibri,Arial,Helvetica,sans-serif">
<p>Hi,</p>
<p><br>
</p>
<p>I'm having difficulty running phenix.real_space_correlation. I get the following error when comparing a pdb to a ccp4 map:</p>
<p><br>
</p>
<p>phenix.real_space_correlation ../17may31a_cryoSPARC_C1.pdb ../17may31a_cryoSPARC_C1.ccp4
<br>
------------------------------<wbr>------------------------------<wbr>-------------------<br>
Input PDB file name: ../17may31a_cryoSPARC_C1.pdb<br>
******************************<wbr>*******************<br>
Number of scatterers: 95640<br>
At special positions: 0<br>
Unit cell: (592.359, 589.659, 590.506, 90, 90, 90)<br>
Space group: P 1 (No. 1)<br>
------------------------------<wbr>------------------------------<wbr>-------------------<br>
Input map file name: ../17may31a_cryoSPARC_C1.ccp4<br>
******************************<wbr>********************<br>
Map type: CCP4-format<br>
Traceback (most recent call last):<br>
File "/opt/X-tal_suite/phenix-1.12-<wbr>2829/build/../modules/cctbx_pr<wbr>oject/mmtbx/command_line/real_<wbr>space_correlation.py", line 10, in <module><br>
command_name = "phenix.real_space_correlation<wbr>")<br>
File "/opt/X-tal_suite/phenix-1.12-<wbr>2829/modules/cctbx_project/mmt<wbr>bx/real_space_correlation.py", line 335, in cmd_run<br>
(fobs_handle.file_name, map_handle.file_name))<br>
NameError: global name 'fobs_handle' is not defined</p>
<p><br>
</p>
<p><br>
</p>
<p><br>
</p>
<p><br>
</p>
<p><br>
</p>
<p><br>
</p>
<p>I get the following error when comparing a pdb to the reflection files. <br>
</p>
<p><br>
</p>
<p>phenix.real_space_correlation ../17may31a_cryoSPARC_C1.pdb ../17may31a_cryoSPARC_C1.mtz<br>
------------------------------<wbr>------------------------------<wbr>-------------------<br>
Input PDB file name: ../17may31a_cryoSPARC_C1.pdb<br>
******************************<wbr>*******************<br>
Number of scatterers: 95640<br>
At special positions: 0<br>
Unit cell: (592.359, 589.659, 590.506, 90, 90, 90)<br>
Space group: P 1 (No. 1)<br>
------------------------------<wbr>------------------------------<wbr>-------------------<br>
Input reflection file name: ../17may31a_cryoSPARC_C1.mtz<br>
******************************<wbr>**************************<br>
Miller array info: ../17may31a_cryoSPARC_C1.mtz:F<wbr>-obs,SIGF-obs<br>
Observation type: xray.amplitude<br>
Type of data: double, size=762857<br>
Type of sigmas: double, size=762857<br>
Number of Miller indices: 762857<br>
Anomalous flag: False<br>
Unit cell: (278.528, 278.528, 278.528, 90, 90, 90)<br>
Space group: P 1 (No. 1)<br>
Systematic absences: 0<br>
Centric reflections: 0<br>
Resolution range: 278.528 3.90017<br>
Completeness in resolution range: 1<br>
Completeness with d_max=infinity: 1<br>
Wavelength: 1.0000<br>
Traceback (most recent call last):<br>
File "/opt/X-tal_suite/phenix-1.12-<wbr>2829/build/../modules/cctbx_pr<wbr>oject/mmtbx/command_line/real_<wbr>space_correlation.py", line 10, in <module><br>
command_name = "phenix.real_space_correlation<wbr>")<br>
File "/opt/X-tal_suite/phenix-1.12-<wbr>2829/modules/cctbx_project/mmt<wbr>bx/real_space_correlation.py", line 354, in cmd_run<br>
r_free_flags = r_free_flags)<br>
File "/opt/X-tal_suite/phenix-1.12-<wbr>2829/modules/cctbx_project/mmt<wbr>bx/utils/__init__.py", line 1572, in fmodel_simple<br>
ro = outliers_rejection,om=optimize<wbr>_mask)<br>
File "/opt/X-tal_suite/phenix-1.12-<wbr>2829/modules/cctbx_project/mmt<wbr>bx/utils/__init__.py", line 1559, in get_fmodel<br>
twin_law = tl)<br>
File "/opt/X-tal_suite/phenix-1.12-<wbr>2829/modules/cctbx_project/mmt<wbr>bx/utils/__init__.py", line 1507, in fmodel_manager<br>
n_resolution_bins_output = n_resolution_bins_output)<br>
File "/opt/X-tal_suite/phenix-1.12-<wbr>2829/modules/cctbx_project/mmt<wbr>bx/f_model/f_model.py", line 439, in __init__<br>
if(f_calc is None): f_calc = self.compute_f_calc(miller_arr<wbr>ay=f_obs)<br>
File "/opt/X-tal_suite/phenix-1.12-<wbr>2829/modules/cctbx_project/mmt<wbr>bx/f_model/f_model.py", line 526, in compute_f_calc<br>
exp_table_one_over_step_size = p.exp_table_one_over_step_size<wbr>)<br>
File "/opt/X-tal_suite/phenix-1.12-<wbr>2829/modules/cctbx_project/cct<wbr>bx/miller/__init__.py", line 1515, in structure_factors_from_scatter<wbr>ers<br>
algorithm=algorithm)<br>
File "/opt/X-tal_suite/phenix-1.12-<wbr>2829/modules/cctbx_project/cct<wbr>bx/xray/structure_factors/from<wbr>_scatterers.py", line 53, in __call__<br>
algorithm=algorithm) # passing algorithm allows f to decide on CPU/GPU implementation<br>
File "/opt/X-tal_suite/phenix-1.12-<wbr>2829/modules/cctbx_project/cct<wbr>bx/xray/structure_factors/from<wbr>_scatterers_fft.py", line 18, in __init__<br>
manager, xray_structure, miller_set, algorithm="fft")<br>
File "/opt/X-tal_suite/phenix-1.12-<wbr>2829/modules/cctbx_project/cct<wbr>bx/xray/structure_factors/mana<wbr>ger.py", line 233, in __init__<br>
assert xray_structure.unit_cell().is_<wbr>similar_to(miller_set.unit_cel<wbr>l())<br>
AssertionError<br>
<br>
</p>
<p><br>
</p>
<p><br>
</p>
<p><br>
</p>
<p>Any suggestions would be appreciated. </p>
<p><br>
</p>
<p>Best wishes,<br>
Reza<br>
</p>
<div id="m_-4006719570669145066m_7602904032018093528Signature">
<div name="divtagdefaultwrapper">Reza Khayat, PhD
<div>Assistant Professor </div>
<div>City College of New York</div>
<div>Department of Chemistry</div>
<div>New York, NY 10031</div>
</div>
</div>
</div>
<br>
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