<div dir="ltr">Hi Reza,<div><br></div><div>I'm afraid this needs to be fixed on our end. Can you please send me (off list) the files you used for this run?</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Apr 17, 2017 at 4:34 AM, 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 getting the following error when running phenix.find_peaks_holes</p>
<p><br>
</p>
<p>peak= -3.937 closest distance to pdb=" CB ASPCB 228 " = 2.259<br>
peak= -3.521 closest distance to pdb=" O PROCB 229 " = 2.275<br>
peak= -4.264 closest distance to pdb=" CD1 LEUCB 231 " = 4.718<br>
peak= -3.384 closest distance to pdb=" CD1 LEUCB 231 " = 5.050<br>
<br>
Traceback (most recent call last):<br>
File "/opt/X-tal_suite/phenix-dev-<wbr>2733/build/../modules/cctbx_<wbr>project/mmtbx/command_line/<wbr>find_peaks_holes.py", line 550, in <module><br>
<br>
SUMMARY OF MAP PEAKS:<br>
mFo-DFc > 3: 10775<br>
mFo-DFc > 6: 847<br>
mFo-DFc > 9: 42<br>
mFo-DFc max: 13.04<br>
mFo-DFc < -3: 6148<br>
mFo-DFc < -6: 525<br>
mFo-DFc < -9: 49<br>
mFo-DFc min: -10.40<br>
<br>
<br>
</p>
<p> run(sys.argv[1:])<br>
File "/opt/X-tal_suite/phenix-dev-<wbr>2733/build/../modules/cctbx_<wbr>project/mmtbx/command_line/<wbr>find_peaks_holes.py", line 511, in run<br>
result.save_pdb_file(file_<wbr>name="%s.pdb" % prefix, log=out)<br>
File "/opt/X-tal_suite/phenix-dev-<wbr>2733/build/../modules/cctbx_<wbr>project/mmtbx/command_line/<wbr>find_peaks_holes.py", line 173, in save_pdb_file<br>
rg = create_atom(xyz, peak, k)<br>
File "/opt/X-tal_suite/phenix-dev-<wbr>2733/build/../modules/cctbx_<wbr>project/mmtbx/command_line/<wbr>find_peaks_holes.py", line 159, in create_atom<br>
rg = iotbx.pdb.hierarchy.residue_<wbr>group(resseq=str(serial))<br>
ValueError: string is too long for target variable (maximum length is 4 characters, 5 given).<br>
<br>
</p>
<p>Is it referring to the 5 characters used for the residue name? If so, how do I correct for this? This is a PDB of a virus (60 subunits). Thanks.</p>
<p><br>
</p>
<p>Best wishes,<br>
Reza<br>
</p>
<p><br>
</p>
<div id="m_1768881860200716066Signature">
<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 dir="ltr" style="color:rgb(33,33,33)">
<hr style="display:inline-block;width:98%">
<div id="m_1768881860200716066divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> <a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-<wbr>online.org</a> <<a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-<wbr>online.org</a>> on behalf of #AHMED TOFAYEL# <<a href="mailto:TOFAYEL001@e.ntu.edu.sg" target="_blank">TOFAYEL001@e.ntu.edu.sg</a>><br>
<b>Sent:</b> Monday, April 17, 2017 12:38 AM<br>
<b>To:</b> PHENIX user mailing list<br>
<b>Subject:</b> [phenixbb] Generate a map showing local agreement between map and model</font>
<div> </div>
</div>
<div>
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<p></p>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;margin-top:0px;margin-bottom:0px">
Dear developers and users,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;margin-top:0px;margin-bottom:0px">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;margin-top:0px;margin-bottom:0px">
Is it possible to generate a map to show local agreement between cryo-EM map and the model generated using the same map? If I am not wrong, the supplementary figure S5 had accomplished the job (using Chimera), but I don't understand how to generate a similar
figure for my project. Is it possible to do with phenix?</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;margin-top:0px;margin-bottom:0px">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;margin-top:0px;margin-bottom:0px">
<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__emboj.embopress.org_content_28_6_755&d=DgMFAw&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=pvrL1zz81cKSgrwK0o2bLY-9_SY5XnNbJUoV8uk3Vng&s=7SDJ0Xn1Yw2YMcBQKaJp9dCizbRKPrs8YrFvLsfFaJw&e=" class="m_1768881860200716066OWAAutoLink" id="m_1768881860200716066LPlnk477753" target="_blank">http://emboj.embopress.org/<wbr>content/28/6/755</a><br>
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;margin-top:0px;margin-bottom:0px">
Best regards,<br>
</div>
<div id="m_1768881860200716066Signature" style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px">
<div id="m_1768881860200716066divtagdefaultwrapper"><font face="Calibri,Arial,Helvetica,sans-serif"><span id="m_1768881860200716066divtagdefaultwrapper">
<div style="margin-top:0px;margin-bottom:0px">Tofayel</div>
<div style="margin-top:0px;margin-bottom:0px">NTU Singapore</div>
</span></font></div>
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