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 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 won't be the exact crystal structure) as well. Right? > > > > Thanks a lot again. > > > > Regards, > > > > Anirban > > > > On Thu, Jun 6, 2013 at 3:56 PM, Tsjerk Wassenaar > > wrote: > > > > > 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 > > > your crystal structure has the same atoms, which is true if you did not > > use > > > hydrogen atoms, or modeled parts for the covariance analysis, then you > > can > > > project that structure onto the eigenvectors determined, in exactly the > > way > > > you describe in your question. > > > > > > Hope it helps, > > > > > > Tsjerk > > > > > > > > > > > > On Thu, Jun 6, 2013 at 12:06 PM, Anirban < > reach.anirban.gh...@gmail.com > > > >wrote: > > > > > > > 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 -v > > > > Prt_MD_Eigenvec.trr -s Prt.tpr -f crystal.pdb -proj 12.xvg -n > > Prt_CA.ndx > > > > -first 1 -last 2 -2d 2dproj.xvg" to obtain the crystal structure > > > position? > > > > Or do I need to calculate covariance matrix for the crystal str.(I > > need a > > > > set of them in that case) and then use g_anaeig? > > > > Thanks a lot in advance. > > > > > > > > Regards, > > > > > > > > Anirban > > > > -- > > > > gmx-users mailing listgmx-users@gromacs.org > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > > * Please don't post (un)subscribe requests to the list. Use the > > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > > > > > -- > > > Tsjerk A. Wassenaar, Ph.D. > > > -- > > > gmx-users mailing listgmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > * Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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 > EV, then I need to consider only the CA atoms of the crystal structure > (which in that case won't be the exact crystal structure) as well. Right? > > Thanks a lot again. > > Regards, > > Anirban > > On Thu, Jun 6, 2013 at 3:56 PM, Tsjerk Wassenaar > wrote: > > > 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 > > your crystal structure has the same atoms, which is true if you did not > use > > hydrogen atoms, or modeled parts for the covariance analysis, then you > can > > project that structure onto the eigenvectors determined, in exactly the > way > > you describe in your question. > > > > Hope it helps, > > > > Tsjerk > > > > > > > > On Thu, Jun 6, 2013 at 12:06 PM, Anirban > >wrote: > > > > > 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 -v > > > Prt_MD_Eigenvec.trr -s Prt.tpr -f crystal.pdb -proj 12.xvg -n > Prt_CA.ndx > > > -first 1 -last 2 -2d 2dproj.xvg" to obtain the crystal structure > > position? > > > Or do I need to calculate covariance matrix for the crystal str.(I > need a > > > set of them in that case) and then use g_anaeig? > > > Thanks a lot in advance. > > > > > > Regards, > > > > > > Anirban > > > -- > > > gmx-users mailing listgmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > * Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > -- > > Tsjerk A. Wassenaar, Ph.D. > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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 won't be the exact crystal structure) as well. Right? Thanks a lot again. Regards, Anirban On Thu, Jun 6, 2013 at 3:56 PM, Tsjerk Wassenaar wrote: > 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 > your crystal structure has the same atoms, which is true if you did not use > hydrogen atoms, or modeled parts for the covariance analysis, then you can > project that structure onto the eigenvectors determined, in exactly the way > you describe in your question. > > Hope it helps, > > Tsjerk > > > > On Thu, Jun 6, 2013 at 12:06 PM, Anirban >wrote: > > > 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 -v > > Prt_MD_Eigenvec.trr -s Prt.tpr -f crystal.pdb -proj 12.xvg -n Prt_CA.ndx > > -first 1 -last 2 -2d 2dproj.xvg" to obtain the crystal structure > position? > > Or do I need to calculate covariance matrix for the crystal str.(I need a > > set of them in that case) and then use g_anaeig? > > Thanks a lot in advance. > > > > Regards, > > > > Anirban > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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 your crystal structure has the same atoms, which is true if you did not use hydrogen atoms, or modeled parts for the covariance analysis, then you can project that structure onto the eigenvectors determined, in exactly the way you describe in your question. Hope it helps, Tsjerk On Thu, Jun 6, 2013 at 12:06 PM, Anirban wrote: > 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 -v > Prt_MD_Eigenvec.trr -s Prt.tpr -f crystal.pdb -proj 12.xvg -n Prt_CA.ndx > -first 1 -last 2 -2d 2dproj.xvg" to obtain the crystal structure position? > Or do I need to calculate covariance matrix for the crystal str.(I need a > set of them in that case) and then use g_anaeig? > Thanks a lot in advance. > > Regards, > > Anirban > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
