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
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Karl Gruber
Institute of Chemistry
KFU Graz
Heinrichstrasse 28 e-mail: karl.gruber(a)uni-graz.at
A-8010 Graz phone: (+43 316) 380-5483
AUSTRIA fax: (+43 316) 380-9850
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