Hi,
My name is Cathy. I'm a new user of Modeller, and I'm still trying to figure out the input files to run Modeller. I'm having trouble with the atom files...I don't exactly know what is an atom file.
I tried using the .pdb file straight from the PDB. I tried changing the file content to just the "atom" section of the PDB files. And nothing seems to work.
I have the script file & alignment file in the default Modeller directory, and I set the atom file environment to a folder named "atom_files" with the 2 atom files (1pme & 1wbn). But when I try running my script, it says that atom files cannot be found in the directory atom_files. Here's the exact error message:
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Read the alignment from file : 1pme_1wbn.ali Total number of alignment positions: 388
# Code #_Res #_Segm PDB_code Name ---------------------------------------------------------------------------- --- 1 1pme 380 1 1pme 2 1wbn 360 1 1wbn runcmd______> alignment.check()
check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL \Modeller8v2\atom_files\1pme.atm 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 " 0", chain " " rdabrk__288W> Protein not accepted: 1 1pme check_a_337E> Structure not read in (please consult the log file for more details): 1 1pme
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It would be great if anyone can help me with this problem! Thank you very much for your time!
- Cathy
Cathy Chang wrote: > My name is Cathy. I'm a new user of Modeller, and I'm still trying to > figure out the input files to run Modeller. I'm having trouble with the > atom files...I don't exactly know what is an atom file. > > I tried using the .pdb file straight from the PDB. I tried changing the > file content to just the "atom" section of the PDB files. And nothing > seems to work.
An atom file is a PDB file, straight from PDB. Modeller only reads the ATOM records anyway, so you don't need to remove the other stuff (it also reads HETATM, TER and some REMARK records, but that shouldn't be a problem). You generally don't need to manually edit PDB files, unless they are non-standard in some way (e.g. weird HETATMs or modified residues).
> I have the script file & alignment file in the default Modeller > directory, and I set the atom file environment to a folder named > "atom_files" with the 2 atom files (1pme & 1wbn). But when I try running > my script, it says that atom files cannot be found in the directory > atom_files. Here's the exact error message:
I think you're misreading the log. It says that the file was found, and opened - it just couldn't find the sequence in the 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 " 0", chain " "
Your alignment sequence must match that in the PDB file, otherwise Modeller won't know how to map your template structures to your target. Your alignment file header apparently states that your sequence starts at residue number 0. Looking at the 1pme PDB structure, it's clear that the ATOM records start at residue number 16. So you should change your alignment header accordingly.
Ben Webb, Modeller Caretaker
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Cathy Chang -
Modeller Caretaker