Hi
I assume from your message that none of the structure coordinates are read
in. Well the problems seems to be with the "known" codes you have used in
the TOP script and the ones you hace used in the alignment. The TOP script
says that the knowns are 't2avi1' 't2avi2' 't2avi3' .... but in the .ali
file the first entry has the code as 2avi1 instead of t2avi1 (after
structureX), so MODELLER would be looking for 2avi1.atm instead of
t2avi1.atm and hence gving the error 'Structure not read in'. If you
change your alignment file there should be no problems. If you still have
the same problem try changing the codes in the comment line too (the one
after >P1). Also if you aren't using the entire sequence of the structure
in your alignment your .atm file should contain only those residues which
you are using in the alignment and you have to specify the residue numbers
appropriately in the alignment.
Hope this helps.
regards
Raghu
> Hi All,
>
> I am a newbie to Modeller, and am having a problem reading in my
> template files
> in the log I get the error message:
>
> 3 lines just before the end bit.....
> check_a_343_> >> BEGINNING OF COMMAND
> check_a_347E> Structure not read in: 1
> recover____E> ERROR_STATUS >=STOP_ON_ERROR: 1 1
>
> All my files (.ali .top .atm .log) are shown below
>
> The 8 template files are in fact all the same (so I just show 1) ,
> just with different filenames, to model different bits of the query
> sequence.
> They are called t2avi1.atm t2avi2.atm ..... t2avi8.atm
>
> I specify which of the 4 chains in the template files to use in the
> PIR alignment file
> in the 4th and 6th fields of the 2nd lines.
>
>
> My .top script file, .atm template files, and .ali PIR alignment file
> are all in /home/model/henri/
>
> # Homology modelling by the MODELLER TOP routine 'model'.
>
> INCLUDE # Include the predefined TOP
> routines
>
> SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to produce a large
> log file
> SET ALNFILE = 'avi4.ali' # alignment filename
> SET ALIGNMENT_FORMAT = 'PIR' #sets alignment format
> SET KNOWNS = 't2avi1' 't2avi2' 't2avi3' 't2avi4' 't2avi5' 't2avi6'
> 't2avi7' 't2avi8' # codes of the templates
> SET SEQUENCE = 'avi4' # code of the target
> SET ATOM_FILES_DIRECTORY = '/home/model/henri' # directories for input atom
> files
> SET STARTING_MODEL= 1 # index of the first model
> SET ENDING_MODEL = 1 # index of the last model
> # (determines how many models to
> calculate)
>
> CALL ROUTINE = 'model' # do homology modelling
>
>
> >P1;2avi1
> structureX:2avi1:3 :A:123 :A::::
> -----------------KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIK
> ESPLHGTENTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVND
> IGDDWKATRVGINIFTRL------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ---------------------------------------------------------*
> >P1;2avi2
> structureX:t2avi2:3 :A:123 :A::::
> ------------------------------------------------------------
> ------------------------------------------------------------
> -------------------------------KCSLTGKWTNDLGSNMTIGAVNSRGEFTG
> TYTTAVTATSNEIKESPLHGTENTINK---------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ----------------------------------------------------RTQPTFGF
> TVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL*
> >P1;2avi3
> structureX:t2avi3:3 :D:123 :D::::
> KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIKESPLHGTENTINK----
> ------------------------------------------------------------
> ------------------------------------------------------------
> ---------------------------------RTQPTFGFTVNWKFSESTTVFTGQCFI
> DRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL----------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ---------------------------------------------------------*
> >P1;2avi4
> structureX:t2avi4:3 :D:123 :D::::
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ---------------------------------------------------KCSLTGKWT
> NDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIKESPLHGTENTINKRTQPTFGFTVNWK
> FSE---------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> --------STTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL*
> >P1;2avi5
> structureX:t2avi5:3 :C:123 :C::::
> KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIKESPLHGTENTINK----
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ---------------RTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSV
> NDIGDDWKATRVGINIFTRL----------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ---------------------------------------------------------*
> >P1;2avi6
> structureX:t2avi6:3 :C:123 :C::::
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ---------------------------------KCSLTGKWTNDLGSNMTIGAVNSRGEF
> TGTYTTAVTATSNEIKESPLHGTENTINK-------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ----------------------------------------------------RTQPTFGF
> TVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL*
> >P1;2avi7
> structureX:t2avi7:3 :B:123 :B::::
> KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIKESPLHGTENTINKRTQP
> TFGFTVNWKFSES-----------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ---------TTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL---
> ------------------------------------------------------------
> ------------------------------------------------------------
> ---------------------------------------------------------*
> >P1;2avi8
> structureX:t2avi8:3 :B:123 :B::::
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> -----------KCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIKESPLHG
> TENTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWK
> ATRVGINIFTRL---------------------------------------------*
> >P1;avi4
> sequence:avi4:1 : :554 : ::::
> ------------------------------------------------------------
> -------------RTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVND
> IGDDWKATRVGINIFTRLRTQKEGGSGGSARKCSLTGKWDNDLGSNMTIGAVNSKGEFTG
> TYTTAVTATSNEIKESPLHGTQNTINK-SGGS------------------TTVFTGQCFI
> DRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRLRTQKEGGSGGSARKCSLTGKWD
> NDLGSNMTIGAVNSKGEFTGTYTTAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWK
> FSEGGSGSGSGSGSGRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSV
> NDIGDDWKATRVGINIFTRLRTQKEGGSGGSARKCSLTGKWDNDLGSNMTIGAVNSKGEF
> TGTYTTAVTATSNEIKESPLHGTQNTINKSGGS---------------------------
> ---------TTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRLRTQ
> KEGGSGGSAR-KCSLTGKWDNDLGSNMTIGAVNSKGEFTGTYTTAVTATSNEIKESPLHG
> TQNTINKRTQPTFGFTVNWKFSE-------------------------------------
> ---------------------------------------------------------*
>