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:
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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.
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>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*
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I also tried the following script:
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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*
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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: karl.gruber@uni-graz.at A-8010 Graz phone: (+43 316) 380-5483 AUSTRIA fax: (+43 316) 380-9850 ---------------------------------------------------------------------