[modeller_usage] [ question ] atom files?

["Cathy Chang" <>]

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:

 

====================

 

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

====================

It would be great if anyone can help me with this problem! Thank you very much for your time!

 

- Cathy