Hi Cathy, Please send your script and I will try to help you.

Fred

>Message: 2 >Date: Fri, 21 Jul 2006 17:00:09 +0900 >From: "Cathy Chang" aochang@ucsd.edu >Subject: [modeller_usage] [ question ] atom files? >To: modeller_usage@salilab.org >Message-ID: 002b01c6ac9b$b0438080$830ba8c0@IBMMUNCHIE >Content-Type: text/plain; charset="us-ascii" > >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 >