<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" style="display:none"><!--P{margin-top:0;margin-bottom:0;} p
{margin-top:0;
margin-bottom:0}--></style>
</head>
<body 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-2733/build/../modules/cctbx_project/mmtbx/command_line/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-2733/build/../modules/cctbx_project/mmtbx/command_line/find_peaks_holes.py", line 511, in run<br>
result.save_pdb_file(file_name="%s.pdb" % prefix, log=out)<br>
File "/opt/X-tal_suite/phenix-dev-2733/build/../modules/cctbx_project/mmtbx/command_line/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-2733/build/../modules/cctbx_project/mmtbx/command_line/find_peaks_holes.py", line 159, in create_atom<br>
rg = iotbx.pdb.hierarchy.residue_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="Signature">
<div name="divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:; margin:0">
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 tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> phenixbb-bounces@phenix-online.org <phenixbb-bounces@phenix-online.org> on behalf of #AHMED TOFAYEL# <TOFAYEL001@e.ntu.edu.sg><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>
<div id="divtagdefaultwrapper" dir="ltr" style="font-size:12pt; color:#000000; font-family:Calibri,Arial,Helvetica,sans-serif">
<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="OWAAutoLink" id="LPlnk477753">http://emboj.embopress.org/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="Signature" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<div id="divtagdefaultwrapper"><font face="Calibri,Arial,Helvetica,sans-serif"><span id="divtagdefaultwrapper">
<div style="margin-top:0px; margin-bottom:0px">Tofayel</div>
<div style="margin-top:0px; margin-bottom:0px">NTU Singapore</div>
</span></font></div>
</div>
<p></p>
<div id="Signature">
<div id="divtagdefaultwrapper" style="font-size:12pt; font-family:Calibri,Arial,Helvetica,sans-serif; background-color:rgb(255,255,255)">
<p style="color:rgb(0,0,0)"><br>
</p>
<p style="color:rgb(0,0,0)"></p>
<p style="color:rgb(0,0,0)"></p>
<p style="color:rgb(0,0,0)"><span style="font-size:12pt"></span></p>
</div>
</div>
</div>
</div>
</div>
</body>
</html>