Re: [modeller_usage] alignment question

[aline <aline AT lncc.br>]

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'
>
>      
>
>     Whats wrong????
>
>      
>
>     Thank you very much
>
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