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
Hi,
It's hard to help you without looking at your .top file.
Thanks, Bozidar
-----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
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 >
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 >
-
Bozidar -
Bozidar Jerkovic -
Stephane Coillet-Matillon