Dear Modellers,
Whenever the SAlign is implemented with a set of templates, it generates a matrix showing some mutual similarity of templates (pairwise equivalences), something like this (against the target with 326 residues).
1SMQA 1H0OA
1SMQA 0 168
1H0OA 0 0
Now, answer me a set of queries.
1. Is 168 showing the count of similar residues, falling within the specified RMSD threshold?
2. Is this calculation considering LGA algorithm?
3. As there are certain folds existing in every such alignment, is there any lower limit of the existing residues in every such chunk to be considered similar. Like, if a fold is more than 3 residues long, i will take it similar in the matrix, and thus i would leave all the nuclear aligned residues.
Is it considered this way in the program?
Best,
Ashish
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
----- Original Message -----
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To: "modeller usage" <>
Sent: Tuesday, November 20, 2012 9:54:46 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: modeller_usage Digest, Vol 11, Issue 109
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Today's Topics:
1. Re: Modeller Help (Modeller Caretaker)
2. optimization protocol and HETATM flexibility (sdimicco)
3. Error while running compare.py (Anogna)
----------------------------------------------------------------------
Message: 1
Date: Mon, 19 Nov 2012 13:15:30 -0800
From: Modeller Caretaker <>
To: mario rossi <>
Cc: "" <>
Subject: Re: [modeller_usage] Modeller Help
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 11/19/2012 05:59 AM, mario rossi wrote:
> I'am Simone an italian student, ineed to learn to use modeller to do
> homology modelingbut i have some trouble.
> I downloaded and installed both modeller and python on my pc (windows
> 7). To learn what to do I tried to follow the basic tutorial but I find
> serious problems in giving the input. I can not even load the sequence
> as the file (.ali) is not recognized by python and if the command is
> entered manually, I get syntax error?? Can you help me to understand
> where is the mistake?
It's difficult to know what the problem is without a clearer description
of what you did, and what results you got.
Ben Webb, Modeller Caretaker
--
http://www.salilab.org/modeller/
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage
------------------------------
Message: 2
Date: Tue, 20 Nov 2012 15:32:18 +0100
From: sdimicco <>
To: <>
Subject: [modeller_usage] optimization protocol and HETATM flexibility
Message-ID: <>
Content-Type: text/plain; charset="utf-8"
Dear Modellers,
I am tring to set up my script to build a
multimeric model with loop refinement. The script looks like:
log.verbose()
class dope_loopmodel(dope_loopmodel):
def
special_patches(self, aln):
# Rename both chains and renumber the
residues in each
self.rename_segments(segment_ids=['A', 'B'],
renumber_residues=[1, 1])
env = environ()
env.io.hetatm = True
a =
dope_loopmodel(env, alnfile='TvLDH-1bdm.ali',
knowns='1bdm',
sequence='TvLDH',
assess_methods=(assess.DOPE,
assess.GA341))
a.starting_model = 1
a.ending_model = 2
# Very thorough
VTFM optimization:
a.library_schedule =
autosched.slow
a.max_var_iterations = 300
# Thorough MD
optimization:
a.md_level = refine.very_slow
# Repeat the whole cycle 2
times and do not stop unless obj.func. > 1E6
a.repeat_optimization =
2
a.max_molpdf = 1e6
a.loop.starting_model = 1 # First loop
model
a.loop.ending_model = 1 # Last loop model
a.loop.md_level =
refine.fast # Loop model refinement
level
a.make()
automodel.final_malign3d = True
It seems that the
script works but I would like to check if all optimization steps have
been done. How could I check it? Please, if you note errors in the
script, give me suggestions
Moreover, I built a model with an HETATM
residue. If I want to treat it as flexible residue: how could I do that?
Thank you in advance.
Bests
Simone
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Message: 3
Date: Tue, 20 Nov 2012 21:54:43 +0530
From: Anogna <>
To:
Subject: [modeller_usage] Error while running compare.py
Message-ID:
<CAG-gr8ES7FzTByanV39XS+>
Content-Type: text/plain; charset="iso-8859-1"
Dear Modeller Users,
I trying simple modelling methodology to model required protein structure.
Till build_profile.py everything went well.
But when gave compare.py.....i am get an error as follows
*Traceback (most recent call last):*
* File "compare.py", line 11, in ?*
* m = model(env, file=pdb, model_segment=('FIRST:'+chain, 'LAST:'+chain))
*
* File "C:\Program Files\Modeller9v7\modlib\modeller\model.py", line 72,
in __in*
*it__*
* self.read(**vars)*
* File "C:\Program Files\Modeller9v7\modlib\modeller\model.py", line 117,
in rea*
*d*
* model_format, model_segment)*
*IOError: pdbnam_____E> Filename for PDB code not found: 3d3l*
* Directories: .;atom_files*
* Extensions : ;.atm;.pdb;.ent;.crd*
* (Also tried prepending 'pdb', looking for .Z, .gz, .bz2, .7z,
*
* and trying PDB-style subdirectories - e.g. ab for
pdb1abc.ent)*
Do I need make any modifications in my compare.py file....I am attaching
compare.py file which i used.
Please help me with this problem.
Thanking You,
Anogna
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