Hi Bozidar;

I corrected Stephane error. It was a chain identifier problem. The chain was specified in the pdb but not in the top file, and Modeler could not extrapolate. Eric

-------------------------------------------------------- Eric Feyfant, Ph.D. Department of Biological Chemistry WYETH Research 85 bolton St. Cambridge ,MA 02140

tel: (617) 665 8987 fax:(617) 665 8993 email: efeyfant@wyeth.com

>>> "Bozidar Jerkovic" bozidar@oboe.rockefeller.edu 03/20 11:51 AM >>>

Hi,

The .top file looks OK, but I would still add: SET ALIGNMENT_FORMAT = 'PIR'

What looks strange is the call: openf5__224_> Open 11 OLD SEQUENTIAL ./1G9L.atm

...after: TOP_________> 121 107 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND

...while it should be doing: check_ali___> Checking the sequence-structure alignment. Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms:

One more thing: if it fails again, move your .atm files to a directory other then one where is your .top file (keep your .ali in the same dir as your .top file). You can create atom_files dir paraller to the dir where is your .top file. Make sure you replace your ATOM_FILES_DIRECTORY then with: SET ATOM_FILES_DIRECTORY = './:../atom_files'

If all this fails, then please send me a complete .log file, .top file, all atom and .ali files and I'll run it here, and see what happens.

Thanks, Bozidar

-----Original Message----- From: Stephane Coillet-Matillon [mailto:coillet@bri.nrc.ca] Sent: Wednesday, March 20, 2002 8:11 AM To: Bozidar Cc: modeller_usage@salilab.org Subject: RE: pdb format

Hi Bozidar,

Here's what my top file looks like.

# Homology modelling by the MODELLER TOP routine 'model'.

INCLUDE #Include the predefined TOP routines

SET OUTPUT_CONTROL = 1 1 1 1 1 #uncomment to produce a large log file SET ALNFILE = 'hpabc.ali' #alignment filename SET KNOWNS = '1G9L' # codes of the templates SET SEQUENCE = 'wPABC' # code of the target SET ATOM_FILES_DIRECTORY = '.' #directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate)

CALL ROUTINE = 'model' # do homology modelling

> -----Original Message----- > From: owner-modeller_usage@salilab.org > [mailto:owner-modeller_usage@salilab.org] On Behalf Of > Stephane Coillet-Matillon > Sent: Tuesday, March 19, 2002 5:32 PM > To: modeller_usage@salilab.org > Subject: pdb format > > > > Hello Modellers, > > I've been trying to run my first modelling, but cannot get any model > so far. Instead, the log file tells me: > > Read the alignment from file : hpabc.ali > Total number of alignment positions: 144 > # Code #_Res #_Segm PDB_code Name > ---------------------------------------------------------------------- > -- > ------- > 1 1G9L 144 1 1G9L PABC > 2 wPABC 72 1 wPABC PABC > > TOP_________> 121 107 CHECK_ALIGNMENT > > check_a_343_> >> BEGINNING OF COMMAND > openf5__224_> Open 11 OLD SEQUENTIAL ./1G9L.atm > rdpdb___303E> No atoms were read from the specified input PDB file: > 1) Possibly because an incorrect/non-existent PDB file

> is specified. > 2) Possibly because the segment is specified > incorrectly in the alignment file or by the TOP variable > MODEL_SEGMENT. That is, the beginning residue number and/or chain id > in MODEL_SEGMENT may not be found in the input PDB file; MODEL_SEGMENT:1 : > To find out more, switch on maximal output by 'SET > OUTPUT_CONTROL = 1 1 1 1 2' rdabrk__288W> Protein not accepted: 1 > rdabrk__290E> Number of residues in the alignment and pdb files are > different: 144 0 > For alignment entry: 1 recover > ____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > My alignment file is: > > >P1;1G9L > structureN:1G9L:1 : :144 : :PABC:homo sapiens: : > GPLGSAAAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLAS > APPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVA > VLQAHQAKEAAQKAVNSATGVPTV* > >P1;wPABC > sequence:wPABC:1 : :144 : :PABC:wheat: : > --------------------------------------------------EPLTASMLAS > APPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVA > VL----------------------* > > Which I trust is the right way to do it. > The top file has nothing that deviates from the example file. My pdb > file was just renamed from 1G9L.pdb to 1G9L.atm, its content was not > edited or changed, and it was located in the right directory. > > So what am I missing there? > > Any suggestion welcomed! > > Thanks, > Stephane >