Re: [ccp4bb] Question on calculation of RMSD

gt; /////////////////// >> 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 &g

Re: [ccp4bb] Question on calculation of RMSD

/// 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

Re: [ccp4bb] Question on calculation of RMSD

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 homo-d

Re: [ccp4bb] Question on calculation of RMSD

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. unbound

Re: [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 of

Re: [ccp4bb] Question on calculation of RMSD

81-6-6879-4580 > http://www.mls.eng.osaka-u.ac.jp/~bio_ext/mlsbe123/clement.html > /// > G30 Chemistry/Biology Combined Major Program > http://cmp.sci.osaka-u.ac.jp/CMP/ > > -Original Message- From: E rajakumar > Sent: Monday, Novemb

Re: [ccp4bb] Question on calculation of RMSD

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 want to calculate RMS deviation between second monomer from these two complexes by fixing superposed

Re: [ccp4bb] Question on calculation of RMSD

ber 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 monomer

Re: [ccp4bb] Question on calculation of RMSD

@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 is

Re: [ccp4bb] Question on calculation of RMSD

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 School

[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 is the effect of DNA on relative orientation of two monomers in the