[PyMOL] rmsd fit for concatenated PDBs

2015-07-30 Thread Ara Abramyan
Hi all, I have several concatinated PDB files and am trying to calculate RMSDs of each state(or frame) within the PDB files with respect to reference file. How can I loop over the states within the concatenated PDB files? I tried to do this: #load PDBs load reference.pdb, ref load 100samples-1.p

[PyMOL] Phosphorylation

2015-07-30 Thread Melanie Prakash
Hi! Recently, i have been trying to assemble a PyMol video of the phosphorylation of the MAP kinase ERK from deactivated to activated to deactivated stages. While I have had success showing the conformational change from inactivated to activated (using *morph mout, 1ERK, 2ERK*), not only am I not