Re: [ccp4bb] large domain motion and calculation of flip flop angle
Dear Rajan, You could also use the CCP4 program LSQKAB (Kabsch, 1976): First superimpose domains 1 of the two conformational states. Then take this first overlay as the starting position and superimpose domains 2. The log file of LSQKAB should give the angle in going from the first to the second superposition. Best regards, Navdeep --- On Sun, Mar 02, 2014 at 10:22:47PM +0530, rajan kumar wrote: Dear all, sorry for off topic question. My protein is composed to two domains connected by a flexible linker and shows large domain motion with large RMSD value of 9.0 A* difference with respect to the initial structure, when simulated for 20 ns. As the first domain doesn't shows any RMSD change when superimposed to initial structure but the other domain moves significantly. so my question is how i could be to calculate the angle of motion in degree of the flexible domain with respect to the initial structure after superimposition. thank you all in advance Regards *Rajan kumar choudhary* *Senior Research Fellow* *Department of Atomic Energy(Govt.Of India)* *ACTREC TATA Memorial Center * *Kharghar Navi-Mumbai* *Mumbai-410210* *India* --- Navdeep S. Sidhu Departments of Structural Chemistry Neuropediatrics University of Goettingen, Germany ---
[ccp4bb] large domain motion and calculation of flip flop angle
Dear all, sorry for off topic question. My protein is composed to two domains connected by a flexible linker and shows large domain motion with large RMSD value of 9.0 A* difference with respect to the initial structure, when simulated for 20 ns. As the first domain doesn't shows any RMSD change when superimposed to initial structure but the other domain moves significantly. so my question is how i could be to calculate the angle of motion in degree of the flexible domain with respect to the initial structure after superimposition. thank you all in advance Regards *Rajan kumar choudhary* *Senior Research Fellow* *Department of Atomic Energy(Govt.Of India)* *ACTREC TATA Memorial Center * *Kharghar Navi-Mumbai* *Mumbai-410210* *India*
Re: [ccp4bb] large domain motion and calculation of flip flop angle
Dear Rajan, you can superpose the two domains, e.g. with Coot. Coot will display the transformation matrix and maybe even the angle and axis of rotation. If the latter is not the case, you can extract the angle and axis from the transformation matrix (one of the eigenvalues and eigenaxes, I suppose). Best, Tim On 03/02/2014 05:52 PM, rajan kumar wrote: Dear all, sorry for off topic question. My protein is composed to two domains connected by a flexible linker and shows large domain motion with large RMSD value of 9.0 A* difference with respect to the initial structure, when simulated for 20 ns. As the first domain doesn't shows any RMSD change when superimposed to initial structure but the other domain moves significantly. so my question is how i could be to calculate the angle of motion in degree of the flexible domain with respect to the initial structure after superimposition. thank you all in advance Regards *Rajan kumar choudhary* *Senior Research Fellow* *Department of Atomic Energy(Govt.Of India)* *ACTREC TATA Memorial Center * *Kharghar Navi-Mumbai* *Mumbai-410210* *India* -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital signature
Re: [ccp4bb] large domain motion and calculation of flip flop angle
As usual, I'd recommend the program Dyndom which is available from CCP4i. This will identify domain borders + hinge regions as well. Best, Matthias - Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549; Fax (+44) 1865 287547 Email matth...@strubi.ox.ac.uk Website http://www.strubi.ox.ac.uk - On 3/2/2014 4:52 PM, rajan kumar wrote: Dear all, sorry for off topic question. My protein is composed to two domains connected by a flexible linker and shows large domain motion with large RMSD value of 9.0 A* difference with respect to the initial structure, when simulated for 20 ns. As the first domain doesn't shows any RMSD change when superimposed to initial structure but the other domain moves significantly. so my question is how i could be to calculate the angle of motion in degree of the flexible domain with respect to the initial structure after superimposition. thank you all in advance Regards *Rajan kumar choudhary* *Senior Research Fellow* *Department of Atomic Energy(Govt.Of India)* *ACTREC TATA Memorial Center * *Kharghar Navi-Mumbai* *Mumbai-410210* *India*
