Re: [gmx-users] Projection of crystal structure on PCA plot

Thanks a lot Tsjerk :) -Anirban On Thu, Jun 6, 2013 at 4:42 PM, Tsjerk Wassenaar wrote: > Hi Anirban, > > Indeed. > > :) > > Tsjerk > > > On Thu, Jun 6, 2013 at 1:11 PM, Anirban >wrote: > > > Dear Tsjerk, > > > > Thank you very much for the explanation. > > > > So, in other words, as I have ca

Re: [gmx-users] Projection of crystal structure on PCA plot

Hi Anirban, Indeed. :) Tsjerk On Thu, Jun 6, 2013 at 1:11 PM, Anirban wrote: > Dear Tsjerk, > > Thank you very much for the explanation. > > So, in other words, as I have carried out PCA on the basis of CA atoms from > the MD trajectory, so if I wish to project the crystal structure onto the

Re: [gmx-users] Projection of crystal structure on PCA plot

Dear Tsjerk, Thank you very much for the explanation. So, in other words, as I have carried out PCA on the basis of CA atoms from the MD trajectory, so if I wish to project the crystal structure onto the EV, then I need to consider only the CA atoms of the crystal structure (which in that case wo

Re: [gmx-users] Projection of crystal structure on PCA plot

Hi Anirban, The eigenvectors obtained from the simulation are a way of rewriting the coordinates of your structures, not in terms of atoms-XYZ, but as combinations of these. Because they are combinations of atom-positions, they are defined for the selection of atoms used for the calculation. If yo

[gmx-users] Projection of crystal structure on PCA plot

Hi ALL, I have carried out a simulation of a protein and have carried out PCA on the entire trajectory. I have obtained a 2D projection plot of EV1 on EV2. Now I want to locate the conformation of the crystal structure (with which I started the MD) on this map. How to do this? Can I use "g_anaeig