[phenixbb] Error from phenix.find_peaks_holes
Reza Khayat
rkhayat at ccny.cuny.edu
Mon Apr 17 04:34:37 PDT 2017
Hi,
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>
SUMMARY OF MAP PEAKS:
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
run(sys.argv[1:])
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
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,
Tofayel
NTU Singapore
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