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Re: [Fwd: ALIGN2D problem]



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