Hi Ankitha, Taking the backbone for analysis doesn't give you more information than using only C-alphas. These are extremely correlated.
Cheers, Tsjerk On Sun, Jun 9, 2013 at 5:28 PM, Ankita naithani <ankitanaith...@gmail.com>wrote: > Hi Tsjerk, > > Thank you so much for the helpful insight. It will surely help in clearing > some basic concepts about eigenvectors and the projections. > Also, since in the end you mentioned about my matrix being derived only > from C-alpha atoms which proves a limitation, would you reckon a backbone > analysis would be better suited to gain some helpful insight into protein > motions (Allosteric transitions, effector signalling??). It would however > be intensively complicated to derive for the whole protein considering mine > is a tetramer and a huge system. > > > Kind regards, > > Ankita > > > On Sat, Jun 8, 2013 at 9:18 PM, Tsjerk Wassenaar <tsje...@gmail.com> > wrote: > > > Hi Ankita, > > > > It is important to use the correct names for things. The projection is > the > > (scalar) inner product of the configuration (coordinates) with the > > eigenvector. This is also named the score of the configuration on the > > selected eigenvector. With g_anaeig -proj you get the projection. Each > > configuration of a trajectory has a projection, and you can plot them > over > > time, or plot the projection on one eigenvector against another (-2d). > You > > can also make a 3D plot of three selected eigenvectors (-3d), which is > > written out as a PDB file. The projection is not a structure, and you > can't > > have a movie of structures. What you can do is extract the structures > > corresponding to the extreme projections (-extr). Those are always > written > > per eigenvector. Since the eigenvectors are uncorrelated, the extremes > are > > not defined for combinations of them. It is also possible to filter a > > trajectory on a set of eigenvectors. That will give a trajectory of > > (unphysical) structures, in which the projections on the non-selected > > eigenvectors are set to zero. This filtering is a matrix operation, using > > the matrix of selected eigenvectors and the corresponding atoms of the > > trajectory. Because the matrix of eigenvectors is derived from C-alpha > > atoms only in your case, it is not possible to get anything else out of > it. > > > > Hope it helps, > > > > Tsjerk > > > > > > > > On Sat, Jun 8, 2013 at 1:06 PM, Ankita naithani < > ankitanaith...@gmail.com > > >wrote: > > > > > Hi Tsjerk, > > > > > > [I am reposting it since my previous attachment was unable to proceed I > > > guess] > > > > > > Thank you for the reply. I am sorry but I don't have the snapshots with > > me > > > as my system was formatted and I lost that information. However, I > > > performed PCA again on Calpha atoms and this time my matrix is > 5976X5976 > > > wherein 1992 are my total number of calpha atoms. So, yes indeed I did > > > something foolish in the previous case to have got that result. > However, > > I > > > will try to look at it and find my mistake so as to not repeat it > again. > > > > > > I would be really grateful if you could help me with my another naive > > > query. I wanted to see the movie of first few eigenvectors as > individual > > > and also separately. I know I can extract that with the help of > g_anaeig > > > but as I did PCA on only calpha atoms, all I get in the projection of > > first > > > eigenvector is the calpha dots. Is there any way, I can visualise the > > > projection of whole protein on that particular eigenvector? > > > > > > Secondly, if I want to see the projection along first 10 eigenvectors > and > > > last 10 eigenvectors (slow modes and fast modes), how could I proceed > > > because when I choose -first 1 -last 10, it gives me individual pdb > files > > > corresponding to the eigenvectors. > > > > > > Third, as can be judged by my absolute naivety, I did a 2d projection > on > > PC > > > 1 and PC 2. I can visualise that plot in grace as a 2d plot. An example > > > file is appended herein. I know each dot might correspond to a > particular > > > conformation in the trajectory but I really have no idea as to how to > > > interpret the results and draw conclusions from these 2d plots and also > > 3d > > > pdb projections. Could you please guide me in the right direction to > > > understand these 2d plots and infer the significant results? > > > > > > > > > Kind regards, > > > > > > Ankita > > > > > > > > > On Thu, Jun 6, 2013 at 2:49 PM, Tsjerk Wassenaar <tsje...@gmail.com> > > > wrote: > > > > > > > >> Hi Ankita, > > > >> > > > >> Please provide the commands you've run and the screen output from > > > g_covar. > > > >> > > > >> Cheers, > > > >> > > > >> Tsjerk > > > >> > > > >> > > > >> > > > >> On Thu, Jun 6, 2013 at 3:44 PM, Ankita naithani < > > > ankitanaith...@gmail.com > > > >> >wrote: > > > >> > > > >> > Hi, > > > >> > > > > >> > I wanted to know about the eigenvectors and eigenvalues. I > recently > > > >> > performed the principal component analysis (only the backbone into > > > >> > consideration) on a trajectory of 2000 residues. I obtained 15641 > > > >> > eigenvectors and 17928 eigenvalues. There is a difference in the > > > number, > > > >> > which I am not quite sure off (perhaps that has to do with > > eigenvalue > > > >> for > > > >> > each eigenvector, and the eigenvector has 3 co-ordinates x,y,z. I > > > know I > > > >> > may be wrong completely but since there are 15641 eigenvectors, > then > > > >> > shouldn't there by only 15641 eigenvalues for those eigenvectors) > > > >> > > > > >> > My second problem lies that I am trying to extract information or > > say > > > >> RMSF > > > >> > values for the first 10 eigenvectors (10 slowest modes) and the > last > > > 10 > > > >> > eigenvectors (fastest modes) and there I face segmentation fault. > I > > > can > > > >> get > > > >> > information on the first 10 but when I try last 10 with the > command > > as > > > >> > follows: > > > >> > > > > >> > g_anaeig -v eigenvec.trr -eig eigenval.xvg -rmsf eig_rmsf.xvg > -first > > > >> 15631 > > > >> > > > > >> > [where -first should have the starting eigenvector ] > > > >> > > > > >> > (I choose, 15631 since I want the plot for last 10 but I get > > > >> segmentation > > > >> > fault, which is also to do with the fact that the eigenval.xvg has > > > 17928 > > > >> > values. This number doesn't match and so, maybe the plot is from > > > >> > 15631-17928). This has further confused me about the slowest and > > > fastest > > > >> > modes (and somehow I do need information on the first 10 slowest > > modes > > > >> and > > > >> > 10 fastest modes). In a broad way, the slowest modes would be the > > ones > > > >> with > > > >> > high eigenvalues say, first 10 eigenvectors in eigenval.xvg would > > give > > > >> the > > > >> > slowest 10 modes and the last 10 in eigenval.xvg should give the > > > >> fastest 10 > > > >> > modes. > > > >> > > > > >> > Here, again I feel quite confused because eigenval.xvg has 17928 > > > entries > > > >> > and in the legend, it says that x axis is the eigenvector index > and > > y > > > >> axis > > > >> > is eigenvalue index so it leaves me quite perplexed about the > > problem. > > > >> > > > > >> > I am sorry for this extremely long and confusing post, but any > help > > in > > > >> this > > > >> > regard would be really beneficial. > > > >> > > > > >> > > > > >> > Kind regards, > > > >> > > > > >> > Ankita > > > >> > > > > >> > -- > > > >> > Ankita Naithani > > > >> > -- > > > >> > gmx-users mailing list gmx-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 list gmx-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 > > > >> > > > > > > > > > > > > > > > > -- > > > > Ankita Naithani > > > > > > > > > > > > > > > > -- > > > Ankita Naithani > > > > > > > > > > > > -- > > > Ankita Naithani > > > -- > > > gmx-users mailing list gmx-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 list gmx-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 > > > > > > -- > Ankita Naithani > -- > gmx-users mailing list gmx-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 list gmx-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