Hi all
I am trying to assign secondary structure for a pdb file and get the
following error:
PyMOL>util.ss
util.ss: WARNING: This is not a "correct" secondary structure
util.ss: assignment algorithm! Please use only as a last resort.
util.ss: initiating secondary structure assignment on 224 residues.
util.ss: extracting sequence and relationships...
util.ss: analyzing phi/psi angles (slow)...
util.ss: finding hydrogen bonds...
util.ss: verifying beta sheets...
Traceback (most recent call last):
File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py",
line 136, in parse
result=apply(kw[nest][0],args[nest],kw_args[nest])
File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\util.py",
line 492, in ss
o_a1_atom = o_dict[scr_a1]
KeyError: ('', 'H', '224')
Here is the end of the pdb file. I do not quite understand the erro message.
Thank you!
ATOM 2125 N SER H 224 -11.523 14.126 16.464
ATOM 2126 H SER H 224 -11.375 13.495 17.279
ATOM 2127 CA SER H 224 -12.514 15.202 16.513
ATOM 2128 CB SER H 224 -13.644 14.934 15.514
ATOM 2129 OG SER H 224 -14.661 15.936 15.550
ATOM 2130 HG SER H 224 -15.320 15.718 14.908
ATOM 2131 C SER H 224 -13.116 15.379 17.909
ATOM 2132 OT1 SER H 224 -13.164 14.414 18.684
TER
Yunfeng
Department of Chemistry & Biochemistry
University of California
Los Angeles, CA 90095
(310)206-0553
http://www.chem.ucla.edu/~yunfeng
