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Take any protein where a helix moves as a rigid body and look at your results. Then fix the alpha helix and superimpose the rest of the structure on that moving helix and compare both results. If you want to give it a shot try 2pc4 and the unliganded structure. You see the difference in both methods ? From a structural/functional perspective one method will highlight the real differences in terms of movements. For an initial understanding I recommend SSM and a morphing movie, that helps dissecting what might be going on. Jürgen ...................... Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Nov 16, 2010, at 19:58, Clement Angkawidjaja <[log in to unmask]> wrote: > >>The lowest rmsd might not be the biological relevant one > True, however the least square fit using the right residues (thus producing the lowest rmsd possible) can really tell you the most significant differences (or not signifcant ones) that cause biological changes. Human eyes are often not good in doing this. Using automated lsq fit programs can give you precise (initial) information using the lowest human effort and low chance of human error. > > Clement > > >>As confucius would say, don't trust the output of a program if you have not programmed it yourself or know what it's doing. > >> > >>Last words of wisdom for tonight. > >> > >>Jürgen > - > Jürgen Bosch > Johns Hopkins Bloomberg School of Public Health > Department of Biochemistry & Molecular Biology > Johns Hopkins Malaria Research Institute > 615 North Wolfe Street, W8708 > Baltimore, MD 21205 > Phone: +1-410-614-4742 > Lab: +1-410-614-4894 > Fax: +1-410-955-3655 > http://web.mac.com/bosch_lab/ > > On Nov 14, 2010, at 8:32 PM, Clement Angkawidjaja wrote: > >> DALI server (http://ekhidna.biocenter.helsinki.fi/dali_server/). Choose the >> pairwise alignment function. It is all automatic and will give you the >> lowest rmsd. Note, however, that it will omit parts that are very different >> for calculation. >> >> Within CCP4, SUPERPOSE or COOT can also do that. You need to specify the >> residues you want to use for calculation for the lsq fit function. >> >> Regards, >> Clement Angkawidjaja, PhD >> Specially Appointed CMP Assistant Professor >> Graduate School of Engineering >> Osaka University >> 2-1 Yamadaoka GSE Commoon East 8F >> Suita-shi, Osaka 565-0871, Japan >> Tel/Fax +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, November 15, 2010 6:52 AM >> To: [log in to unmask] >> 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 the effect of DNA on relative orientation of >> two monomers in the dimer. >> >> Previously I was using MOLEMAN2 to do this calculation. >> >> Please can you suggest me any other program to do this calculation. >> >> Thanking you >> Raj >> >> >> E. Rajakumara >> Postdoctoral Fellow Strcutural Biology Program Memorial Sloan-Kettering >> Cancer Center New York-10021 NY 001 212 639 7986 (Lab) 001 917 674 6266 >> (Mobile) > >