Hi,
Please make sure that you define
SET ATOM_FILES_DIRECTORY = ....
One more thing: make sure that your PDB file doesn't have a chain
identifier (A, B, C, etc), or make sure that your .ali file has one
(currently it's empty), but I guess you already know this.
NB. Would you please post any questions you might have in the future on
the list first, because other people might have the same problem and may
benefit from or already have the answer as well.
Good luck,
Bozidar
-----Original Message-----
From: Krzysztof Lazarski [">mailto:]
Sent: Monday, April 15, 2002 12:45 PM
To: Bozidar Jerkovic
Cc: Andrzej Joachimiak; Andrej Sali
Subject: Reading_PDB_File
Hello,
I need a help.
My task was to see if we can model sequence with unknown structure which
has >90%
similarities (Protein Blast) to our X-Ray determined structure recently
deposited to PDB
from our Structural Genomics Project (MCSG; http://www.mcsg.anl.gov ).
The known structure name is: 1g2r. I named sequence my_ 15900466 (Where
I can find rules for assigning a
name to unknown structure?).
I tried DESCRIBE with following .top file:
--
SET OUTPUT_CONTROL = 1 1 1 1 2
SET ATOM_FILES = '1g2r', ALIGN_CODES = '1g2r'
READ_MODEL FILE = '1g2r', MODEL_SEGMENT = '@:@' 'X:X'
DESCRIBE
--
There were no problems. I've got nice report in .log file.
When I tried to run modelling .top:
--
INCLUDE
SET ATOM_FILES_DIRECTORY = './:../atom_files'
SET ATOM_FILES = '1g2r', ALIGN_CODES = '1g2r'
READ_MODEL FILE = '1g2r', MODEL_SEGMENT = '@:@' 'X:X'
SET SEGFILE = 'align-jerzy.seg'
SET KNOWNS = '1g2r'
SET SEQUENCE = 'my_15900466'
SET OUTPUT_CONTROL = 1 1 1 1 2
CALL ROUTINE = 'full_homol'
--
where align-jerzy.seg is:
--
>P1;1g2r
structureX:1g2r:1::100::::
GSHMKTRKIPLRK
SVVSNEVIDKRDL
LRIVKNKEGQVFI
DPTGKANGRGAYI
KLDNAEALEAKKK
KVFNRSFSMEVEE
SFYDELIAYVDHK
VKRRELGLE*
>P1;my_15900466
sequence:my_15900466:1 : :97 : : : : :
MKTRKIPLRKSVVSNEVIDKRDLLRIVKNKEGQVFIDPTGKANGRGAYIKLDNAEALEAK
KKKVFNRSFSMEVEESFYDELIAYVDHKVKRRELGLE*
--
It created align-jerzy.seg.ali,
but it stopped on full_homology when reading .pdb file,
which it read properly for describing protein.
Here it is 25 last lines from .log file (tail -25 ..):
--
# Code #_Res #_Segm PDB_code Name
------------------------------------------------------------------------
-------
1 1g2r 100 1 1g2r
2 my_159004 97 1 my_15900466
TOP_________> 140 107 CHECK_ALIGNMENT
check_a_343_> >> BEGINNING OF COMMAND
openf5__224_> Open 11 OLD SEQUENTIAL ./1g2r.pdb
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: 100 0
For alignment entry: 1
recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]:
4890025 4775.415 4.663
Starting time : 2002/04/15
11:20:01.978
Closing time : 2002/04/15
11:20:05.387
Total CPU time [seconds] : 3.14
--
Thank you for any suggestions, Christopher.
--
Dr. Krzysztof Lazarski, Argonne National Laboratory
9700 S. Cass Ave, Building 202, RQ106, Argonne, IL 60439
ph: 630-252-3855, e-mail: , fax: 630-252-6126