Is your MBL.B99990003.pdb file at "../atom_files/" directory?

Try to remove the  words "../atom_files/" and put MBL.B99990003.pdb at the same directory you are executing dope.py.

Regards,

flavio

--- On Wed, 12/21/11, si yang siyang13@gmail.com wrote:

From: si yang siyang13@gmail.com Subject: [modeller_usage] pdb code To: modeller_usage@salilab.org Date: Wednesday, December 21, 2011, 8:30 AM

Good day to all,

I have encountered a small problem during model.evaluation, the normalized dope.py requires to load a built model as indicated below: # Read a model previously generated by Modeller's automodel class

mdl = complete_pdb(env, '../atom_files/xxx.pdb'

right now the xxx should be replaced by the pdb code such as 1fdx, however my protein sequence is not yet deposited into PDB, thus it does not has pdb code, i just name it as MBL.B99990003.pdb (for example) after the atom_files:

mdl = complete_pdb(env, '../atom_files/MBL.B99990001.pdb'

However, the error stated that the pdb file is not a valid file, so do any expert provide suggestion to solve this problem??

Your response is appreciated....

Regards, Zhao Yang Institute of Bioscience UPM, 43400, Serdang Selangor, Malaysia

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