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RE: pdb format



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:] 
Sent: Wednesday, March 20, 2002 8:11 AM
To: Bozidar
Cc: 
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: 
> [">mailto:] On Behalf Of 
> Stephane Coillet-Matillon
> Sent: Tuesday, March 19, 2002 5:32 PM
> To: 
> 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
>