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(a)wyeth.com
>>> "Bozidar Jerkovic" <bozidar(a)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(a)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(a)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(a)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
>
