Dear Sir,
No need to manual compilation of pooling of models in single PDB file.
You can use linux with a simple bash script.
cat *.pdb > Single.pdb
Then you may end MODEL and ENDMDL manually
or you can also write a for loop to automatically append these strings on ends of every single PDB file called.
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
----- Original Message -----
From: "modeller usage-request" <>
To: "modeller usage" <>
Sent: Wednesday, November 2, 2011 12:57:24 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: modeller_usage Digest, Vol 10, Issue 136
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Today's Topics:
1. automodel.max_molpdf recommended values and usage format
(Andrew Voronkov)
2. Re: Build a model with multiple models (Modeller Caretaker)
3. Re: automodel.max_molpdf recommended values and usage format
(Modeller Caretaker)
4. flexible ligand parametrization using nonstd_restraints(aln)
(Andrew Voronkov)
----------------------------------------------------------------------
Message: 1
Date: Tue, 01 Nov 2011 21:28:48 +0400
From: Andrew Voronkov <>
Subject: [modeller_usage] automodel.max_molpdf recommended values and
usage format
To:
Message-ID: <>
Content-Type: text/plain
Dear Modeller users, how on your opinion modeller objective function correlates with quality of the models. For example I have objective function value 1730 for one modelk and -750 which as I understand reflects free energy. Does it mean that I shouldn t consider the first one at all?
Let's say I want to make cutoff -100 for the objective function.
In which format it should be done?
automodel.max_molpdf -100
is that correct?
Sincerely yours,
Andrey
------------------------------
Message: 2
Date: Tue, 01 Nov 2011 11:47:21 -0700
From: Modeller Caretaker <>
Subject: Re: [modeller_usage] Build a model with multiple models
To: junior <>
Cc:
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 10/31/2011 07:16 AM, junior wrote:
> How do I build a PDB file containing more than 10 models?
If you really mean you want to make a single PDB file containing
multiple models (which the PDB format allows, with a MODEL record at the
start of each model and an ENDMDL record at the end) then you can't do
that with MODELLER, for any number of models (10 or otherwise). The
models produced by MODELLER are each in their own PDB file.
If you simply want to make more than 10 models, each in a *different*
PDB file, then go with Mensur's suggestions. If you really want a single
PDB file containing multiple models, you will have to first produce
multiple PDB files, then stick them together manually, inserting MODEL
and ENDMDL records, either with a text editor or with some simple scripting.
Ben Webb, Modeller Caretaker
--
http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
------------------------------
Message: 3
Date: Tue, 01 Nov 2011 11:55:27 -0700
From: Modeller Caretaker <>
Subject: Re: [modeller_usage] automodel.max_molpdf recommended values
and usage format
To: Andrew Voronkov <>
Cc:
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 11/01/2011 10:28 AM, Andrew Voronkov wrote:
> how on your opinion modeller objective function correlates with
> quality of the models. For example I have objective function value
> 1730 for one modelk and -750 which as I understand reflects free
> energy. Does it mean that I shouldn t consider the first one at
> all?
The Modeller objective function is simply a measure of how many
restraints were violated in building your model. While the score could
be thought of roughly as an "energy" (not free energy) this is certainly
not a rigorous measure of model quality. Use an assessment function such
as normalized DOPE for this purpose.
> Let's say I want to make cutoff -100 for the objective function. In
> which format it should be done?
>
> automodel.max_molpdf -100
Build your models, then assess them and pick the best ones. max_molpdf
is designed as a filter to throw away the very worst models - it doesn't
act on the final PDF, but the score of intermediate (partially
optimized) models - the reasoning being to not waste time on trying to
optimize a model that is very bad. Thus max_molpdf is not really what
you want here.
Ben Webb, Modeller Caretaker
--
http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
------------------------------
Message: 4
Date: Tue, 01 Nov 2011 23:21:23 +0400
From: Andrew Voronkov <>
Subject: [modeller_usage] flexible ligand parametrization using
nonstd_restraints(aln)
To:
Message-ID: <>
Content-Type: text/plain; charset=utf-8
I have a task to remodel the loop conformation which binds ligand in order to optimize the ligand-protein structure. Structure is X-ray, but ligand position is not known, so I take it from docking assuming that docking gives pose close to correct. So the goal is to model flexibility. I have asked this question couple of days a ago, but now it is more specific.
I have used loop modeling with lgiand transfer and it works relatively well, but as I understand as far as this is non conventional residue it is treated as rigid and its interactions with protein are also treated as rigid according to what is written in the manual (listed below).
So is it possible to define ligand as flexible using nonst restrains, I need to consult with someone who did.
Actually it s kind of usage of Modeller as docking software, I don t knwo whether it is possible to parametrize ligand and optimize its position using simulated annealing and loop rmodeling, so kind of imitating induced fit. Has anyone tried this and question to Modeller Caretaker - is it potentially possible?
Best regards,
Andrew
nonstd restraints(aln)
44 CHAPTER 4. COMPARATIVE MODELING CLASS REFERENCE
This routine adds restraints to keep non-standard residues (anything treated as a HETATM or BLK residue,
such as ligands or metal ions) in a reasonable conformation. You can override this method if you need to
change these restraints.
By default, four sets of restraints are built:
? For each residue that has no defined topology (generally BLK residues, used to transfer ligands directly
from templates, as described in Section 2.2.1), intra-residue distances are all constrained to their
template values. This causes each residue to behave as a rigid body.
? Inter-residue distances are constrained to template values if these are 7?A or less. This has the effect of
preserving multiple-HETATM structures such as DNA chains. If the distances are 2.3?A or less they are
assumed to be bonds and so are restrained more strongly and also excluded from the nonbonded list.
? Residue-protein atom distances are strongly constrained to template values (and excluded from the
nonbonded list) if these are 2.3?A or less. This preserves chemical bonds between ligands and the
protein.
? Residue-protein C distances are constrained to template values if these are 10?A or less and are not
already bonded by the previous restraints. This preserves the ligand position.
- so I get protein-ligand interactions very much restrained and all final models are quite close to the initial coordinates.
------------------------------
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