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Re: error: Structure not read in

To: "Raghurama P. Hegde" <>
Subject: Re: error: Structure not read in
From: "Dr. Dan White" <>
Date: Mon, 11 Nov 2002 13:31:08 +0200
Cc:

Hi,

thanks for spotting my typo error!

now the files read in, but I'm having trouble getting modeller tochoose the right chain as the template for eachpart of the structural alignment.....using the chain identifiers inthe PIR second lines, in the fields after the residue numbers doesn'tseem to be working. see bleow for how I specify the chain to use inthe ali

Even weirder........., when I edit the pdb template files so each oneonly contains the one chain (A B C or D) which I specify in thealignment, the model generated still has most of the structuresuperimposed on one of the chains (looks like ther are at least 3chains in the same place in many parts of the model generated)

now I think there is something very odd happening, as the templatesare being read in ok, but the positions of the modelled residues arenot in the same place as the template chain they are being modelledon......??????????


>P1,t2avi1
structureX:t2avi1:3 :A:123 :A ::::
blah

>P1,t2avi1
structureX:t2avi1:3 :B:123 :B ::::
blah

>P1,t2avi1
structureX:t2avi1:3 :C:123 :C ::::
blah

>P1,t2avi1
structureX:t2avi1:3 :D:123 :D ::::
blah

Cheers

Dan



On Monday, November 11, 2002, at 08:21 , Raghurama P. Hegde wrote:

Hi

I assume from your message that none of the structure coordinatesare readin. Well the problems seems to be with the "known" codes you haveused inthe TOP script and the ones you hace used in the alignment. The TOPscriptsays 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 stillhavethe same problem try changing the codes in the comment line too (theoneafter >P1). Also if you aren't using the entire sequence of thestructurein your alignment your .atm file should contain only those residueswhichyou are using in the alignment and you have to specify the residuenumbers

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 inputatom

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-------------------------------------
---------------------------------------------------------*


http://www.chalkie.org.uk

Daniel James White PhD.
Cell Biology
Department of Biological and Environmental Science
University of Jyväskylä
FIN-40351
Jyväskylä
Finland

+358 414740463 (mobile)
+358 (0)14 260 4183 (office)

References:
- Re: error: Structure not read in
  - From: "Raghurama P. Hegde" <>

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