Hi: When I use my initial model to build the structure, it appears some erros, the following is the scripts and log file: from modeller import * from modeller.automodel import * log.verbose() env = environ() env.io.atom_files_directory = './:../atom_files' a = automodel(env, alnfile = 'bhro_mult.ali', knowns = ('bhro_n','bhro_tm','bhro_c'), sequence = 'bhro', inifile = 'myini.pdb')
a.starting_model= 1 a.ending_model = 1 a.make()
some errors in log file: rdpdb___303E> No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " ", chain " " read_te_288W> Protein not accepted: 1 myini.pdb rdabrk__337E> Structure not read in (please consult the log file for more details): now, how does MODELLER to do this question? thanks a lot!
jinlian05@lzu.cn wrote: > When I use my initial model to build the structure, it appears some erros, the > following is the scripts and log file: ... > rdpdb___303E> No atoms were read from the specified input PDB file, since the > starting residue number and/or chain id in MODEL_SEGMENT (or > the alignment file header) was not found; > requested starting position: residue number " ", chain " "
When you provide an initial model, as you have done here, Modeller uses the information in the alignment file header to read it in. (For example, your initial model may be a multi-chain crystal structure, of which you're building only one chain.) So just edit your alignment file to add a starting residue number - for example, the alignment.ali file provided in examples/automodel/ has the following header: sequence:1fdx:1 : :54 : :ferredoxin:Peptococcus aerogenes: 2.00:-1.00 which instructs Modeller to read residues 1 through 54 from the initial model file.
Ben Webb, Modeller Caretaker
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jinlian05＠lzu.cn -
Modeller Caretaker