Re: Problem with SEQUENCE_TO_ALI

[Andras Fiser <andras@tuba>]

something funny must be going on. Using your script on an arbitrary model
coordinate file i get the proper, full sequence:

> read_model file = 'pruse1.B99990001', align_codes = 'test'
> sequence_to_ali add_sequence = off
> write_alignment file = 'dummy.ali'
> 
> dummy.ali:
> >P1;test
> structureX:test:   1 : : 521 : :undefined:undefined:-1.00:-1.00
> L*


read_model file = '1clc.B99990001', align_codes = 'test'
sequence_to_ali add_sequence = off
write_alignment file = 'dummy.ali'

dummy.ali:

>P1;test
structureX:test:  35 : : 575 : :undefined:undefined:-1.00:-1.00
IETKVSAAKITENYQFDSRIRLNSIGFIPNHSKKATIAANCSTFYVVKEDGTIVYTGTATSMFDNDTKETVYIAD
FSSVNEEGTYYLAVPGVGKSVNFKIAMNVYEDAFKTAMLGMYLLRCGTSVSATYNGIHYSHGPCHTNDAYLDYIN
GQHTKKDSTKGWHDAGDYNKYVVNAGITVGSMFLAWEHFKDQLEPVALEIPEKNNSIPDFLDELKYEIDWILTMQ
YPDGSGRVAHKVSTRNFGGFIMPENEHDERFFVPWSSAATADFVAMTAMAARIFRPYDPQYAEKCINAAKVSYEF
LKNNPANVFANQSGFSTGEYATVSDADDRLWAAAEMWETLGDEEYLRDFENRAAQFSKKIEADFDWDNVANLGMF
TYLLSERPGKNPALVQSIKDSLLSTADSIVRTSQNHGYGRTLGTTYYWGCNGTVVRQTMILQVANKISPNNDYVN
AALDAISHVFGRNYYNRSYVTGLGINPPMNPHDRRSGADGIWEPWPGYLVGGGWPGPKDWVDIQDSYQTNEIAIN
WNAALIYALAGFVNYN/*

If you can not figure out what is wrong, please send me your example.

Andras


Karl Gruber wrote:
> 
> Dear all,
> 
> I am a new user of Modeller (vers. 4h, June 16, 1997) and I hope that
> this list is still alive. I have encountered some problems running the
> scripts 'loop' and 'cluster', which I tried both with my own and the
> tutorial files.
> 
> The input and (part of the) output in the case of 'cluster' were as
> follows:
> 
> --------------------
> 
> INCLUDE
> 
> DEFINE_STRING VARIABLES = SEQUENCE MODEL CSRFILE
> 
> SET SEQUENCE = 'pruse1'            # sequence code
> SET MODEL = 'pruse1.B99990002'     # one PDB structure
> SET CSRFILE = 'pruse1.rsr'         # restraints file
> SET ID1 = 2, ID2 = 11            # cluster these models
> 
> CALL ROUTINE = 'cluster'
> 
> --------------------
> .
> .
> .
> ipdbnam_W> environment variable PDBENT undefined
> 
> chkseq__E> sequence difference between alignment and pdb :
>    STRUCTURE RES_IND  ALN_ITYP  ALN_RES  X_ITYP  X_RES  -----*-----
>            2       2         0     ####       1   ALA   ----L------
>            2       3         0     ####      17   THR   ---L-------
>            2       4         0     ####      17   THR   --L--------
>            2       5         0     ####      16   SER   -L---------
>            2       6         0     ####      12   ASN   L----------
>            2       7         0     ####       7   HSD   -----------
>            2       8         0     ####       3   ASP   -----------
>            2       9         0     ####       5   PHE   -----------
>            2      10         0     ####      16   SER   -----------
>            2      11         0     ####      20   TYR   -----------
> 
> chkseq__E> sequence difference between alignment and pdb :
>    STRUCTURE RES_IND  ALN_ITYP  ALN_RES  X_ITYP  X_RES  -----*-----
>            3       2         0     ####       1   ALA   ----L------
>            3       3         0     ####      17   THR   ---L-------
>            3       4         0     ####      17   THR   --L--------
>            3       5         0     ####      16   SER   -L---------
>            3       6         0     ####      12   ASN   L----------
>            3       7         0     ####       7   HSD   -----------
>            3       8         0     ####       3   ASP   -----------
>            3       9         0     ####       5   PHE   -----------
>            3      10         0     ####      16   SER   -----------
>            3      11         0     ####      20   TYR   -----------
> .
> . (continuing for all 10 structures)
> .
> ----------------
> 
> I modified '__cluster.top' such that the alignment is written to a file.
> Obviously only the first amino-acid was copied into the alignment array.
> 
> ----------------
> 
> >P1;pruse1_2
> structureM:pruse1.B99990002:   1 : : 521 : :model:model:-1.00:-1.00
> L*
> >P1;pruse1_3
> structureM:pruse1.B99990003:   1 : : 521 : :model:model:-1.00:-1.00
> L*
> .
> .
> .
> >P1;pruse1_11
> structureM:pruse1.B99990011:   1 : : 521 : :model:model:-1.00:-1.00
> L*
> 
> -----------------
> 
> I also tried the following script:
> 
> -----------------
> 
> read_model file = 'pruse1.B99990001', align_codes = 'test'
> sequence_to_ali add_sequence = off
> write_alignment file = 'dummy.ali'
> 
> dummy.ali:
> >P1;test
> structureX:test:   1 : : 521 : :undefined:undefined:-1.00:-1.00
> L*




> 
> -----------------
> 
> I hope that I did not overlook anything obvious!
> 
> Any help would be very much appreciated.
> 
> Yours,
> 
> Karl
> 
> ---------------------------------------------------------------------
> Karl Gruber
> Institute of Chemistry
> KFU Graz
> Heinrichstrasse 28                   e-mail: 
> A-8010 Graz                           phone: (+43 316) 380-5483
> AUSTRIA                                 fax: (+43 316) 380-9850
> ---------------------------------------------------------------------

-- 
    ,
Andras Fiser, PhD            # phone: (212) 327 7216
The Rockefeller University   # fax:   (212) 327 7540 
Box 270, 1230 York Avenue    # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras