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.
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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*
-----------------
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 ---------------------------------------------------------------------
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: karl.gruber@uni-graz.at > A-8010 Graz phone: (+43 316) 380-5483 > AUSTRIA fax: (+43 316) 380-9850 > ---------------------------------------------------------------------
One more note:
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'
try to use the clustering script in this form: ################# INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1
SET ROOT_NAME = 'pruse1' # sequence code SET MODEL = 'pruse1.B99990002' # one PDB structure SET CSRFILE = 'pruse1.rsr' # restraints file SET FILE_EXT = ' ' SET FILE_ID = '.B'
SET EXPAND_CONTROL = 0000 0000 2 11 0
CALL ROUTINE = 'cluster' ######################
"expand_control" first two arguments: the starting first 4 and ending first 4 digits in the file extension (from 9999 and to 9999 in your case), the third and fourth is about the second part of the file extension: from model-2 to model-11
A "cluster.opt" named coordinate file should appear as a result. It worked for me, of course the underlying coordinate files were different.
Andras
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Andras Fiser -
Karl Gruber