[phenixbb] Error from phenix.find_peaks_holes

Reza Khayat rkhayat at ccny.cuny.edu
Mon Apr 17 04:34:37 PDT 2017


I'm getting the following error when running phenix.find_peaks_holes

peak=   -3.937 closest distance to pdb=" CB  ASPCB 228 " =    2.259
peak=   -3.521 closest distance to pdb=" O   PROCB 229 " =    2.275
peak=   -4.264 closest distance to pdb=" CD1 LEUCB 231 " =    4.718
peak=   -3.384 closest distance to pdb=" CD1 LEUCB 231 " =    5.050

Traceback (most recent call last):
  File "/opt/X-tal_suite/phenix-dev-2733/build/../modules/cctbx_project/mmtbx/command_line/find_peaks_holes.py", line 550, in <module>

  mFo-DFc >  3:  10775
  mFo-DFc >  6:    847
  mFo-DFc >  9:     42
  mFo-DFc max:   13.04
  mFo-DFc < -3:   6148
  mFo-DFc < -6:    525
  mFo-DFc < -9:     49
  mFo-DFc min:  -10.40

  File "/opt/X-tal_suite/phenix-dev-2733/build/../modules/cctbx_project/mmtbx/command_line/find_peaks_holes.py", line 511, in run
    result.save_pdb_file(file_name="%s.pdb" % prefix, log=out)
  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
    rg = create_atom(xyz, peak, k)
  File "/opt/X-tal_suite/phenix-dev-2733/build/../modules/cctbx_project/mmtbx/command_line/find_peaks_holes.py", line 159, in create_atom
    rg = iotbx.pdb.hierarchy.residue_group(resseq=str(serial))
ValueError: string is too long for target variable (maximum length is 4 characters, 5 given).

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.

Best wishes,

Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031
From: phenixbb-bounces at phenix-online.org <phenixbb-bounces at phenix-online.org> on behalf of #AHMED TOFAYEL# <TOFAYEL001 at e.ntu.edu.sg>
Sent: Monday, April 17, 2017 12:38 AM
To: PHENIX user mailing list
Subject: [phenixbb] Generate a map showing local agreement between map and model

Dear developers and users,

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?

https://urldefense.proofpoint.com/v2/url?u=http-3A__emboj.embopress.org_content_28_6_755&d=DgIFAw&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=jCBuhFtksZ8bTlBMxgH6J9UDJ3CkcE-GQK2yZyIY3mg&m=LZIvZ8JgHwo_3w0I-NqCDKrhS__TJ6thpZTvWdfG4NU&s=T3FQWqSmDFAHT73gjSugLcoFXo_lGqfWiXoTcoe4dn4&e= <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=>

Best regards,
NTU Singapore

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