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
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