Thank you all for the answers. I've corrected the problem that Windows
gave me. Windows made some terrible things with my sequence, but
apparently nothing was going wrong. now everything is going just fine.
Darren Thompson escreveu:
You must have an unnecessary space or carriage return in your .top
file. The command not recognized happens when modeller interprets a
carriage return and the next line does not have a modeller command.
good luck!
Darren
On Tuesday, December 7, 2004, at 06:47 AM, Aline Rossi wrote:
Hi,
Im trying to make an alignment, but i receive an error:
Kind, OS, HostName, Kernel, Processor: 4, SunOS caprichosa 5.8 sun4u
Date and time of compilation : 09/12/2004 21:16:03
Job starting time (YY/MM/DD HH:MM:SS): 2004/12/07 11:29:11.627
rdactio_534E> Command not recognized:
recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]:
56755 55.4
25 0.054
Starting time :
2004/12/07 11:29:11.6
27
Closing time :
2004/12/07 11:29:13.0
97
Total CPU time [seconds] : 0.00
The .seq is:
>P1;03883
sequence:03883: : : 696 : :::-1.00:-1.00
-MMARKFELKDYRNIGIMAHIDAGKTTTTERILFHTGKIHKIGETHDGVSQMDWMEQEKERGITITSAATTAFWK
GKRINIIDTPGHVDFTVEVERSLRVLDGAVAVLDAQSGVEPQTETVWRQATNYSVPRIVYVNKMDKAGANFEASI
ESVRTKLNGNAVAIQLNIGAEADFSGLIDLVEMKAYNYDGQKEEIEYEIPIPEDLFEKASQMRLALAEAVADYDE
and so go.......
>P1;1KTV
structureX:1KTV: 1 :B : 691 :B : Elongation Factor G: The
MAVKVEYDLKRLRNIGIAAHIDAGKTTTTERILYYTGRIHKIGEVHEGAATMDFMEQERERGITITAAVTTCFWK
DHRINIIDTPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTGADLWLVI
and so go.....
And the align2d.top is:
INCLUDE
READ_MODEL FILE = '1KTV'
SEQUENCE_TO_ALI ALIGN_CODES = '1KTV'
READ_ALIGNMENT FILE = '03883.seq', ALIGN_CODES = ALIGN_CODES
'03883', ADD_SEQUENCE = on
ALIGN2D
WRITE_ALIGNMENT FILE='03883-KTV.ali', ALIGNMENT_FORMAT = 'PIR'
WRITE_ALIGNMENT FILE='03883-KTV.pap', ALIGNMENT_FORMAT = 'PAP'