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Re: multiple and not overlapping templates



Dear Dr. Andras Fiser,

Sorry for replying you late.

Thank you for your top and alignment files. They are very helpful. To compare
your top file with mine, I found that I used a comma between two knows files: 
SET KNOWNS='template1, template2' although I don't know if it really matter.

Another problem was found by using the debug option: SET OUTPUT_CONTROL= 1 1 1
1. Modeller complained that one of my template was unacceptable, probably that
was because its low resolution (2.6 or something) and too many missing atoms.
After changing to another template, I got model. Thank you for your help.

Sincerely, 

Xiao-Ping

At 07:05 PM 3/28/00 -0500, you wrote: 
>
> Dear Xiao-Ping ,
>
> It is not very fruitful, if you are not showing what exactly you are dealing
> with.
>
> As a last help I send one of mine last application for the very same topic,
> hope it helps.
> a top file and an alignment file. Structures were generataed without any
> problem.
>
> best wishes,
>
> Andras
>
> ###########################################
>
> INCLUDE
> SET OUTPUT_CONTROL= 1 1 1 1
> SET ALNFILE='tetu.pir'
> SET KNOWNS='2abc3' '2abc2' 
> SET SEQUENCE= 'tetu'
> SET STARTING_MODEL= 1              
> SET ENDING_MODEL  = 30
>                                    
> CALL ROUTINE = 'model'
>
>
> SUBROUTINE ROUTINE = 'transfer_xyz'
>
>  # SET ALIGNMENT_FORMAT = 'PIR'
> ##  READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS
> ##  MALIGN3D FIT = off, GAP_PENALTIES_3D = 0 4
>   READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUENCE
>
>   READ_TOPOLOGY   FILE = TOPLIB
>   READ_PARAMETERS FILE = PARLIB
>
>   CALL ROUTINE = 'create_topology'
>
>   TRANSFER_XYZ CLUSTER_CUT = -1.0
>   BUILD_MODEL INITIALIZE_XYZ = OFF
>
>   WRITE_MODEL FILE = MODEL
>
>   RETURN
> END_SUBROUTINE
> ##################################################
>
> >P1;2abc3
> structureX:2ezm3:55::99:::::
> ----YPSDNEEFDPHEQEDKLADPHEQCEFDCDPYPSDNEEDYPSHEQC-----------
> -----------------------------------------*
> >P1;2abc2
> structureX:2ezm2:5::48:::::
> -------------------------------------------------------SQTCY
> LSDKEYHRTCNMKHGSDFEQAPLPWDFHGKLMNYTELKS--*
> >P1;tetu
> sequence:tetu::::::::
> DCDPKLADNEEDEFDCDPNEEFDPHEDKLADPHEQCEFDCDPYPSDNEEDYPSDNEEDKL
> NSAIQGSVLTSTCERTNGGYNTSSIDLNSVIENVDGSLKYE*
>
> #################################################
>
>
> -- 
>     ,
> Andras Fiser, PhD            # phone: (212) 327 7206
> The Rockefeller University   # fax:   (212) 327 7540 
> Box 270, 1230 York Avenue    # e-mail:
> New York, NY 10021-6399, USA # http://salilab.org/~andras 



------------------------------------------------
Xiao-Ping Zhang
Department of Biochemistry
Stockholm University
106 91 Stockholm
Sweden

Phone: 46-08-162582 / 162472
Fax: 46-08-153679
e-mail: