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Today's Topics:
1. hiii (Vijina C)
2. Re: hiii (Modeller Caretaker)
3. Error using local_alignment=True in salign (David Abia)
4. Re: Error using local_alignment=True in salign
(Modeller Caretaker)
----------------------------------------------------------------------
Message: 1
Date: Mon, 2 Nov 2015 10:36:15 +0530
From: Vijina C <">>
To: ">
Subject: [modeller_usage] hiii
Message-ID:
<CAAMS7Z==">>
Content-Type: text/plain; charset="utf-8"
hi sir
i did the programing part but it is not running.i just copied
modeller 9.10 coding...but i installed 9.15..is there any difference in the
coding part please reply
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Message: 2
Date: Mon, 2 Nov 2015 10:00:02 -0800
From: Modeller Caretaker <">>
To: Vijina C <">>, ">
Subject: Re: [modeller_usage] hiii
Message-ID: <">>
Content-Type: text/plain; charset=windows-1252; format=flowed
On 11/1/15 9:06 PM, Vijina C wrote:
> i did the programing part but it is not running.i just copied
> modeller 9.10 coding...but i installed 9.15..is there any difference in
> the coding part please reply
Generally speaking, a script that works with Modeller 9.10 will also
work with 9.15. If you can provide a few more details about the problem,
people may be able to help you resolve it.
Ben Webb, Modeller Caretaker
--
"> https://salilab.org/modeller/
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage
------------------------------
Message: 3
Date: Fri, 6 Nov 2015 10:38:50 +0100
From: David Abia <">>
To: ">
Subject: [modeller_usage] Error using local_alignment=True in salign
Message-ID: <">>
Content-Type: text/plain; charset=iso-8859-3; format=flowed
Dear Modeller users,
I'm trying to force a local alignment while using salign function in
mod9.15, and it fails with error:
"modeller.ModellerError: align_l_251E> MATRIX_OFFSET probably has an
invalid value: 0.0000"
My script ( mod-3nnt-prim.cons-aln.py ):
from modeller import *
env = environ()
aln = alignment(env)
m = model(env, file='./tmp-NmArZQ.pdb', model_segment=('FIRST:A', 'LAST:B'))
aln.append_model(m, atom_files='./tmp-NmArZQ.pdb', align_codes='3nnt_x')
aln.append( file='./tmp-q4VfPF.fasta', alignment_format='FASTA',
align_codes='prim.cons')
aln.salign(local_alignment=True)
aln.write(file='mod-3nnt-prim.cons.pir')
The output:
Traceback (most recent call last):
File "mod-3nnt-prim.cons-aln.py", line 8, in ?
aln.salign(local_alignment=True)
File "/usr/lib/modeller9.15/modlib/modeller/alignment.py", line 395,
in salign
nsegm, matrix_offset_3d, break_break_bonus)
_modeller.ModellerError: align_l_251E> MATRIX_OFFSET probably has an
invalid value: 0.0000
The error comes from a call to a function:
retval = func(self.modpt, ... , local_alignment, .... , nsegm,
matrix_offset_3d, break_break_bonus)
that is defined as:
func = _modeller.mod_salign
If I remove the option "local_alignment=True", it runs flawlessly.
Any idea about what can be happening?
Thanks in advance,
David.
------------------------------
Message: 4
Date: Fri, 6 Nov 2015 11:19:18 -0800
From: Modeller Caretaker <">>
To: David Abia <">>, ">
Subject: Re: [modeller_usage] Error using local_alignment=True in
salign
Message-ID: <">>
Content-Type: text/plain; charset=windows-1252; format=flowed
On 11/06/2015 01:38 AM, David Abia wrote:
> I'm trying to force a local alignment while using salign function in
> mod9.15, and it fails with error:
>
> "modeller.ModellerError: align_l_251E> MATRIX_OFFSET probably has an
> invalid value: 0.0000"
When doing local alignments, you need to set the matrix offset
appropriately (the salign function has a matrix_offset parameter). It
may take some experimentation to find a suitable value for your system.
Ben Webb, Modeller Caretaker
--
"> https://salilab.org/modeller/
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage
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