Sir,
*****The whole protein will be moved, of course, but only the RMSD
of the selection will be minimized.**********
This is not the case. When we use the rotation and translation matrices, on X,Y, and Z sequentially as i did in my program, even if you specify chunk length, entire matrix is translated, you don't choose a subset there. So entire matrix transformation takes place. But lastly for RMSD fit, you just check for selected atoms. Hence, RMSD displayed seems for chunk, but in background entire protein RMSD can be computed, which is not asked by the user.
Ashish
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
----- Original Message -----
From: "modeller usage-request" <>
To: "modeller usage" <>
Sent: Tuesday, April 5, 2011 5:36:59 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: modeller_usage Digest, Vol 10, Issue 61
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Today's Topics:
1. Re: salign: specify chains to superpose (Modeller Caretaker)
2. Modeller 9.9 release (Modeller Caretaker)
3. modelling a protein withtow chains (Houcemeddine Othman)
----------------------------------------------------------------------
Message: 1
Date: Fri, 01 Apr 2011 13:47:28 -0700
From: Modeller Caretaker <>
Subject: Re: [modeller_usage] salign: specify chains to superpose
To: Yingjie Lin <>
Cc: modeller <>
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 03/31/2011 09:08 AM, Yingjie Lin wrote:
> I wonder what is the best way to superpose two multi-chain proteins,
> and explicitly specify the chains to include in superposition. I know
> that I can read only the wanted chains into the alignment, but I also
> want to make sure that the other chains move according to the
> superposition.
Just to be clear here, we should distinguish structural *alignment*
(which is what SALIGN does) from superposition (which is what
selection.superpose() does). Superposition simply rotates and translates
one protein, without changing the alignment, to minimize the RMSD
between Calpha atoms in aligned residues. Structural alignment also adds
or removes gaps, changing the aligned residues.
If you really want to do superposition, simply use selection.superpose()
and just give it a selection of atoms in the chains you want to
superpose. The whole protein will be moved, of course, but only the RMSD
of the selection will be minimized.
If you want to do a structural alignment, your first suggestion is
probably better - read in just the chains you want, make the alignment,
then rotate and translate the full protein accordingly.
Ben Webb, Modeller Caretaker
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------------------------------
Message: 2
Date: Mon, 04 Apr 2011 12:03:57 -0700
From: Modeller Caretaker <>
Subject: [modeller_usage] Modeller 9.9 release
To: ,
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
The new version of Modeller, 9.9, is now available for download! Please
see the download page at http://salilab.org/modeller/ for more information.
If you have a license key for Modeller 8 or 9, there is no need to
reregister for Modeller 9.9 - the same license key will work. (It won't
do any harm to reregister if you want to, though!)
9.9 is primarily a bugfix release relative to the last public release
(9v8). Major user-visible changes include:
# The Windows version of Modeller is now only supported on XP Service
Pack 2 or later. If you want to run Modeller on Windows 98, ME, 2000,
or NT, use Modeller 9v8.
# Added support for Python 2.7 to Windows and Linux Modeller; Python
2.5 is now supported on all platforms.
# Initial models generated by automodel now always contain valid PDB
coordinates, i.e. each coordinate is in the range -999.999 to
9999.999.
# During loop modeling, if atoms are missing from the initial model,
loopmodel.loop.write_defined_only can be set True to write out PDBs
containing only non-loop atoms present in the initial model.
# When reading new-style PDB files (with element names in columns
77-78) Modeller will now use this information to determine whether an
atom is a hydrogen. (With old-style or non-conformant PDB files, it
will continue to guess based on the atom name, so will not read
mercury ions for example unless env.io.hydrogen=True, since it cannot
unambiguously determine whether HG is mercury or "hydrogen bonded to
CG".)
See the Modeller manual for a full change log:
http://salilab.org/modeller/9.9/manual/node38.html
If you encounter bugs in Modeller 9.9, please see
http://salilab.org/modeller/9.9/manual/node10.html for information on
how to report them.
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Ben Webb, Modeller Caretaker
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Message: 3
Date: Tue, 5 Apr 2011 01:06:57 +0100
From: Houcemeddine Othman <>
Subject: [modeller_usage] modelling a protein withtow chains
To:
Message-ID: <BANLkTikUh9qOU-NsGxRqOB4+Q7Dqy+>
Content-Type: text/plain; charset="iso-8859-1"
Hi
I try to model an heterodimer using this alignment
>P1;1DZB2
structureX:1DZB2:1:A:107:B::::
QVKLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQRPEQGLEWIGRIDPANGNTKYDPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCAR-----WDWYFDVWGQGTTVTVSSG/
------------DIELTQSPSSMYTSLGERVTITCKASQDINSYLRWFQQKPGKSPKTLIYYATSLADGVPSRFSGSGSGQDYSLTISSLESDDTTTYYCLQHGESPYTFGGGTKLEIK---------*
>P1;atc
sequence:::::::::
-VKLQQSGGGLVQPGGSLKLSCAASGFDFSRYWMSWVRQAPGKGLEWIGEINPDSSTINYTPSLKDTFIISRDNAKNTLYLQMSKVRSEDTALYYCARQGYDGYHWYFDVWGQGTTVTVSSE/
SLDLGGGGGGGGDIQLTQSPSSLSASVGETVTLTCGASENIYGGLNWYQRKQGKSPQLLIYGATKLADGMSSRFSGGGSGRQYFLKITSLHPDDVATYYCQNVLSNPLTFGAGTKLELKRADAAPTVS*
each time it gives me this error message
define__595E> Number of selected atoms in sets 2 & 3 is not the same:
121 128
Can you tell me please what's wrong in my alignment file
script used:
# Homology modeling by the automodel class
#
# Demonstrates how to build multi-chain models, and symmetry restraints
#
from modeller import *
from modeller.automodel import * # Load the automodel class
log.verbose()
# Override the 'special_restraints' and 'user_after_single_model' methods:
class MyModel(automodel):
def special_restraints(self, aln):
# Constrain the A and B chains to be identical (but only restrain
# the C-alpha atoms, to reduce the number of interatomic
distances
# that need to be calculated):
s1 = selection(self.chains['A']).only_atom_types('CA')
s2 = selection(self.chains['B']).only_atom_types('CA')
self.restraints.symmetry.append(symmetry(s1, s2, 1.0))
def user_after_single_model(self):
# Report on symmetry violations greater than 1A after building
# each model:
self.restraints.symmetry.report(1.0)
env = environ()
# directories for input atom files
env.io.atom_files_directory = './'
a = MyModel(env,
alnfile = 'ali.pir',
knowns = '1DZB2',
sequence = 'atc')
a.starting_model= 1
a.ending_model = 1
a.make()
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