Dear Pymol Users! Within the Pymol session I have 2 loaded superimposed objects: 1) one experimental pdb consisted of protein with cofactors (ligand and metals); 2) ensemble of 20 md snapshots of the same proteins superimposed on each others without any cofactors;
For my particular task I need 1) to copy the selection (which include metals and ligand atoms) from the reference structure to each model of the MD ensemble (via Pymol), 2) make quick geometrical optimization of side-chains (I guess it better to do it using Chimera) within the active side of each model from MD ensemble 3) perform post-processing - analysis of the distances between cofactors and optimized side-chains of each MD conformers to obtain statistical distribution of averaged distances (I guess it better to do it via some MD software like Gromacs). I will be very thankful for any suggestions for practical realization of those steps! James ------------------------------------------------------------------------------ Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net