Re: [ccp4bb] size of a flexible pdb structure
Dear Rajan kumar choudhary, could you explain why you expect the volume to depend on the conformation of the molecule? Do you have some effective volume in mind, e.g. the elution volume during size exclusion chromatography? Regards, Tim On Wed, Mar 05, 2014 at 08:42:21PM +0530, rajan kumar wrote: Dear all, sorry for asking an off topic question. My protein is composed of two domains connected by a flexible linker (15aa). after 50ns simulation i came across the fact that one domain is flexible. so my question is that how could i be able to calculate the size of molecule or radius of my molecule and which conformation i should prefer to calculate the size of molecule. your any suggestion will be very helpful. thank you all in advance with best 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: Digital signature
Re: [ccp4bb] size of a flexible pdb structure
Hi rajan I guess calculating radius of gyration for your whole protein with time will tell you about the size variation at difeerent time points or you canm say different frames. This is how you can cluster your whole trajectory PDBs into a few clusters and then get the representative PDBs from each cluster to finally select what you want. Best Monica On Wed, Mar 5, 2014 at 8:42 PM, rajan kumar rajugunju...@gmail.com wrote: Dear all, sorry for asking an off topic question. My protein is composed of two domains connected by a flexible linker (15aa). after 50ns simulation i came across the fact that one domain is flexible. so my question is that how could i be able to calculate the size of molecule or radius of my molecule and which conformation i should prefer to calculate the size of molecule. your any suggestion will be very helpful. thank you all in advance with best 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] size of a flexible pdb structure
Dear Rajan, Since you raised your question about calculating the radius of your molecule. here my suggestion, a bit long back I heard about the program HYDROPRO I am not sure its going to be work for you, but you may give a try. I think the program calculates the radius of gyration ! best wishes, Dr. S. M. Jaimohan On Wednesday, 5 March 2014 8:53 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Rajan kumar choudhary, could you explain why you expect the volume to depend on the conformation of the molecule? Do you have some effective volume in mind, e.g. the elution volume during size exclusion chromatography? Regards, Tim On Wed, Mar 05, 2014 at 08:42:21PM +0530, rajan kumar wrote: Dear all, sorry for asking an off topic question. My protein is composed of two domains connected by a flexible linker (15aa). after 50ns simulation i came across the fact that one domain is flexible. so my question is that how could i be able to calculate the size of molecule or radius of my molecule and which conformation i should prefer to calculate the size of molecule. your any suggestion will be very helpful. thank you all in advance with best 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
