Dan,
It looks like the program reading in the full sequence, all 3 segments. Try to
specify the required segment like e.g.:
MODEL_SEGMENT '1:A' '214:A',
Additionally, it could also happen that there is a problem in the PDB
file(unusual residue type or unusual bond distances, atom with empty coordinate
entry etc). Switch on full error report for a more detailed error message
SET OUTPUT_CONTROL = 1 1 1 1 1
Andras
> ----------------------------------------------------------------------
>
> Subject: ALIGN2D problem
> Date: Mon, 12 Nov 2001 16:13:19 +0200
> From: Dan Thomas Major <>
> Organization: Bar-Ilan University
> To: modeller_usage <>
>
> I'm trying to perform ALIGN2D of a target sequence with the sequence of a
> protein with with X-ray structure, but I keep on getting errors. The protein
> has several subunits, and I want to align with subunit A only.
>
> The top file is:
> READ_MODEL FILE = '1HZX.pdb', MODEL_SEGMENT '@:A' 'X:A', OUTPUT_CONTROL = 1 1
> 1 1
> SEQUENCE_TO_ALI ALIGN_CODES = '1HZX'
> READ_ALIGNMENT FILE = 'hp2y1.seq', ALIGN_CODES = ALIGN_CODES 'hp2y1', ;
> ADD_SEQUENCE = on
> READ_TOPOLOGY FILE = '/u/ch/majord/modeller/modeller6a/modlib/top_heav.lib'
> ALIGN2D
> WRITE_ALIGNMENT FILE = 'hp2y1-1HZX.ali', ALIGNMENT_FORMAT = 'PIR'
> WRITE_ALIGNMENT FILE = 'hp2y1-1HZX.pap', ALIGNMENT_FORMAT = 'PAP', ;
> ALIGNMENT_FEATURES = 'indices helix beta'
>
> The error reported is:
> ...
> # Code #_Res #_Segm PDB_code Name
> -------------------------------------------------------------------------------
>
> 1 1HZX 641 3 1HZX undefined
> 2 hp2y1 373 1 hp2y1
> TOP_________> 4 4 READ_TOPOLOGY FILE =
> '/u/ch/majord/modeller/modeller6a/mo;
> dlib/top_heav.lib'
>
> openf5__224_> Open 11 OLD SEQUENTIAL
> ${MODINSTALL6a}/modlib//as1.sim.mat
> rdrrwgh_268_> Number of residue types: 20
> dispers_247E> Internal error: 640 641
> recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
>
> Dynamically allocated memory at finish [B,kB,MB]: 23066567
> 22525.945 21.998
> Starting time : 2001/11/12
> 13:53:59.313
> Closing time : 2001/11/12
> 14:41:13.406
> Total CPU time [seconds] : 0.00
>
> Thanks, Dan
>
> --
> Dan Thomas Major (at Dr. B. Fischer's lab)
> Bar-Ilan University
> Ramat-Gan, Israel
>
>
--
,
Andras Fiser, PhD # phone: (212) 327 7216
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras