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Today's Topics:
1. Re: modeling a chimeric protein (Modeller Caretaker)
2. modeller_query (niki24@tezu.ernet.in)
3. Re: modeller_query (Modeller Caretaker)
4. Protein specified in ALIGN_CODES(i) was not found
(Ahmad Abdelzaher)
----------------------------------------------------------------------
Message: 1
Date: Mon, 23 Apr 2018 18:45:27 -0700
From: Modeller Caretaker <modeller-care@salilab.org>
To: Ayesha Fatima <ayeshafatima.69@gmail.com>,
modeller_usage@salilab.org
Subject: Re: [modeller_usage] modeling a chimeric protein
Message-ID: <8feda20f-aebe-9cf4-a345-a876d7f52df4@salilab.org>
Content-Type: text/plain; charset=utf-8; format=flowed
On 4/22/18 7:44 AM, Ayesha Fatima wrote:> is this the .ali file to give
for alignment.
Yes, an alignment file like that should work fine.
> Which script should I use.
Since it's a chimera most conventional alignment scripts are not going
to do the right thing for you, since they will try to make a global
alignment of the two proteins, which is precisely not what you want. I
would combine them manually, unless you have another structure of a
linker region to which both will align.
Ben Webb, Modeller Caretaker
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Message: 2
Date: Wed, 2 May 2018 12:54:47 +0530
From: niki24@tezu.ernet.in
To: modeller_usage@salilab.org
Subject: [modeller_usage] modeller_query
Message-ID:
<b5de950ef59eb2a611e9569ddbc5e967.squirrel@webmail.tezu.ernet.in>
Content-Type: text/plain;charset=utf-8
Dear Sir,
I have been trying to model some structures using the modeller.
I would like to know the meaning of the B factor for the modeller
generated structures.
For most of the structures i am getting a higher B value for some regions
of my model.
Yours faithfully
Nikita Bora
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Message: 3
Date: Wed, 2 May 2018 12:50:26 -0700
From: Modeller Caretaker <modeller-care@salilab.org>
To: niki24@tezu.ernet.in, modeller_usage@salilab.org
Subject: Re: [modeller_usage] modeller_query
Message-ID: <54b2acf6-07a4-4a2d-ca65-bc341c89ca69@salilab.org>
Content-Type: text/plain; charset=utf-8; format=flowed
On 5/2/18 12:24 AM, niki24@tezu.ernet.in wrote:
> I have been trying to model some structures using the modeller.
> I would like to know the meaning of the B factor for the modeller
> generated structures.
This is the violations profile, as per
https://salilab.org/modeller/9.19/manual/node256.html Ben Webb, Modeller Caretaker
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Message: 4
Date: Thu, 10 May 2018 16:24:02 -0400
From: Ahmad Abdelzaher <underoath006@gmail.com>
To: modeller_usage@salilab.org
Subject: [modeller_usage] Protein specified in ALIGN_CODES(i) was not
found
Message-ID:
<CAL1o8vOPGjn8TfwRWC3Ys9xy97pGFrN4+c_uQ4Zv3GGdPemX2w@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
I know this error usually happens when I get the names incorrectly.
However, in this case, everything is fine and it seems to run for a little
while, then it starts writing stuff to my .ali file and give the below
error.
readlinef__W> File: alpha_tubulin.pdb, Line: 4611
Modeller will only read the first 80 characters of this line.
readlinef__W> File: alpha_tubulin.pdb, Line: 4612
Modeller will only read the first 80 characters of this line.
readlinef__W> File: alpha_tubulin.pdb, Line: 4613
Modeller will only read the first 80 characters of this line.
readlinef__W> File: alpha_tubulin.pdb, Line: 4614
Modeller will only read the first 80 characters of this line.
readlinef__W> File: alpha_tubulin.pdb, Line: 4615
Modeller will only read the first 80 characters of this line.
readlinef__W> File: alpha_tubulin.pdb, Line: 4616
No more warnings will be printed for truncated lines in this
file.
mkapsa__637W> No residue topology library is in memory.
Better radii would be used if topology.read() is called first.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: N --> N
This message is written only for the first such atom.
Pairwise dynamic programming alignment (ALIGN2D):
Residue-residue metric : $(LIB)/as1.sim.mat
Diagonal : 100
Overhang : 0
Maximal gap length : 999999
Local alignment : F
MATRIX_OFFSET (local aln): 0.0000
FIX_OFFSETS : 0.0 -1.0 -2.0 -3.0 -4.0
N_SUBOPT : 0
SUBOPT_OFFSET : 0.0000
Alignment block : 1
Gap introduction penalty : -100.0000
Gap extension penalty : 0.0000
Gap diagonal penalty : 0.0000
Structure gap penalties : 3.500 3.500 3.500 0.200 4.000
6.500 2.000 0.000
Break-break bonus : 10000.0000
Length of alignment : 441
Score : 258659.2969
read_al_230W> Alignment code alpha_tubulin is present multiple times in the
alignment file! Only the first entry will be read.
Suggest you remove the duplicate(s) to avoid confusion.
read_al_373E> Protein specified in ALIGN_CODES(i) was not found
in the alignment file; ALIGN_CODES( 1) =
alpha_tubulin.pdb
Traceback (most recent call last):
File "<ipython-input-12-d935bbc074eb>", line 1, in <module>
runfile('/home/labusr/Desktop/chlamy_paper/denovo_prediction/alpha_tubulin/Modeller/modeller.py',
wdir='/home/labusr/Desktop/chlamy_paper/denovo_prediction/alpha_tubulin/Modeller')
File
"/home/labusr/anaconda3/lib/python3.5/site-packages/spyderlib/widgets/externalshell/sitecustomize.py",
line 714, in runfile
execfile(filename, namespace)
File
"/home/labusr/anaconda3/lib/python3.5/site-packages/spyderlib/widgets/externalshell/sitecustomize.py",
line 89, in execfile
exec(compile(f.read(), filename, 'exec'), namespace)
File
"/home/labusr/Desktop/chlamy_paper/denovo_prediction/alpha_tubulin/Modeller/modeller.py",
line 35, in <module>
a.make()
File
"/home/labusr/anaconda3/lib/python3.5/site-packages/modeller/automodel/automodel.py",
line 112, in make
self.homcsr(exit_stage)
File
"/home/labusr/anaconda3/lib/python3.5/site-packages/modeller/automodel/automodel.py",
line 535, in homcsr
aln = self.read_alignment()
File
"/home/labusr/anaconda3/lib/python3.5/site-packages/modeller/automodel/automodel.py",
line 502, in read_alignment
aln.append(file=self.alnfile, align_codes=codes)
File
"/home/labusr/anaconda3/lib/python3.5/site-packages/modeller/alignment.py",
line 80, in append
allow_alternates)
ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not
found in the alignment file; ALIGN_CODES( 1) = alpha_tubulin.pdb
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