My favorite tools for doing this are:
http://webapps.embl-hamburg.de/rapido/
and/or
http://www.theseus3d.org/
Reading some of the associated papers will not hurt inchoosing when to
apply which one!
A
On Nov 14, 2010, at 22:52, E rajakumar wrote:
Dear All
I have two structures of
http://cmp.sci.osaka-u.ac.jp/CMP/
-Original Message-
From: E rajakumar
Sent: Monday, November 15, 2010 6:52 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Question on calculation of RMSD
Dear All
I have two structures of homo-dimeric protein complex with different DNA.
I
///
G30 Chemistry/Biology Combined Major Program
http://cmp.sci.osaka-u.ac.jp/CMP/
-Original Message-
From: E rajakumar
Sent: Monday, November 15, 2010 6:52 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Question on calculation of RMSD
Dear All
I have
///
G30 Chemistry/Biology Combined Major Program
http://cmp.sci.osaka-u.ac.jp/CMP/
-Original Message- From: E rajakumar
Sent: Monday, November 15, 2010 6:52 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Question on calculation of RMSD
I would first calculate least square superposition of the first monomer between
2 structures (one to be fixed and one to be moved) using a program such as
lsqkap or any other programs suggested by others. You may need to define a
relevant region for the superimposition.
Then take the output
Raj,
There are many programs that will give you an RMSD per residue difference
between your bound and un-bound protein. Some will even write the RMSDs to
the B-factor column of your PDB. You can then visualize regions in your
protein that have structural changes/movement in the bound vs.
Dear All
I have two structures of homo-dimeric protein complex with different DNA.
I want to calculate RMS deviation between second monomer from these two
complexes by fixing superposed first monomer.
This I require to know what is the effect of DNA on relative orientation of two
monomers in
Coot
And I would use LSQKAB instead of the SSM method. First look at what stays
rigid in one subunit and define those residues for the superposition, then look
at the text window where it will report you the rmsd for each position and
chain.
Jürgen
-
Jürgen Bosch
Johns Hopkins Bloomberg
@JISCMAIL.AC.UK
Subject: [ccp4bb] Question on calculation of RMSD
Dear All
I have two structures of homo-dimeric protein complex with different DNA.
I want to calculate RMS deviation between second monomer from these two
complexes by fixing superposed first monomer.
This I require to know what
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Question on calculation of RMSD
Dear All
I have two structures of homo-dimeric protein complex with different DNA.
I want to calculate RMS deviation between second monomer from these two
complexes by fixing superposed first monomer.
This I require to know
: Monday, November 15, 2010 6:52 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Question on calculation of RMSD
Dear All
I have two structures of homo-dimeric protein complex with different DNA.
I want to calculate RMS deviation between second monomer from these
two complexes by fixing superposed first
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