Subject: Re: multiple and not overlapping templates
From: Xiao-Ping Zhang <>
Date: Mon, 10 Apr 2000 18:48:17 +0200
Cc: modeller_usage
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: