Subject: Re: [modeller_usage] structure not read in
From: "Jaimin Shah" <>
Date: Tue, 13 Jan 2004 11:54:44 +0530 (IST)
Cc: Jaimin Shah <>
Cc:
Dear Sir,
It gives me the following message:
Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269
2153.
583 2.103
openf5__224_> Open 11 OLD SEQUENTIAL align.ali
rdpir___376W> Not enough fields in the second line of the sequence entry:
struc
tureX:1piea:9 : :396 : :galactokinase:Lactococcus lactis: 2.10
Actual fields, should be: 9 10
(Fields are separated by a colon, :)
rdpir___376W> Not enough fields in the second line of the sequence entry:
seque
nce:galk:1 : :392 : :galk:Homo sapiens
Actual fields, should be: 8 10
(Fields are separated by a colon, :)
Dynamically allocated memory at amaxbnd [B,kB,MB]: 8050641
7861.
954 7.678
openf5__224_> Open 11 OLD SEQUENTIAL align.ali
rdpir___376W> Not enough fields in the second line of the sequence entry:
struc
tureX:1piea:9 : :396 : :galactokinase:Lactococcus lactis: 2.10
Actual fields, should be: 9 10
(Fields are separated by a colon, :)
rdpir___376W> Not enough fields in the second line of the sequence entry:
seque
nce:galk:1 : :392 : :galk:Homo sapiens
Actual fields, should be: 8 10
(Fields are separated by a colon, :)
Read the alignment from file : align.ali
Total number of alignment positions: 402
# Code #_Res #_Segm PDB_code Name
-------------------------------------------------------------------------------
1 1piea 388 1 1piea galactokinase
2 galk 392 1 galk galk
TOP_________> 121 107 CHECK_ALIGNMENT
check_a_343_> >> BEGINNING OF COMMAND
pdbnam__217W> Filename for PDB code not found: 1piea
Directories: ./
Extensions : :.atm:.pdb:.ent:.crd
rdabrk__288W> Protein not accepted: 1
check_a_337E> Structure not read in: 1
recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]: 8050641
7861.
954 7.678
Starting time : 2004/01/13
11:55:59.
546
Closing time : 2004/01/13
11:56:00.
718
Please guide me.
Thanking you,
> On Sun, Jan 11, 2004 at 10:20:34AM +0530, Jaimin Shah wrote:
>> I am a novice for this program. I would really appreciate it if you can
>> expedite matters for me by solving my hurdles.
>> I am getting the message:
>> check_a_343_> >> BEGINNING OF COMMAND
>> check_a_337E> Structure not read in: 1 1
>
> Perhaps you have a sequence mismatch between your structure and your
> alignment? It's hard to tell from the output you've posted here. What
> errors or warnings do you get prior to that? I suggest you also put
> SET OUTPUT_CONTROL = 1 1 1 1 1
> at the start of your TOP file, if you haven't already, to increase the
> amount of Modeller output.
>
> Ben Webb, Modeller Caretaker
> --
> http://www.salilab.org/modeller/
> Modeller mailing list: http://salilab.org/mailman/listinfo/modeller_usage
>
Jaimin Shah
M.Sc. (Biotechnology)
I.I.T. Powai