Mark, By 'coverage' I mean the 1 value in the dot product of the comparing eigenvectors sets (between 1 and 1, 2 and 2 and so on eigenvectors) ( that indicate that both eigenvector set are identical as I suppose). In that case I had 2 identical pdp ensembles from which in 1 case I obtained normal filter trajectory and in the second case- with broken geometry. In the picture below you can see the conformations of the protein calculated in that 2 instances ( left conformation is fine and its preserved in all filter trajectory but in the second case as you can see all seven-helixes bulge of the protein was shrunken). I've tried to re-make the cov.analysis ( changing number of structures in the pdb ensemble as well as reference conformation but result was always the same ).
http://img138.imageshack.us/img138/2717/7tmpca.png James > > What do you mean by "coverage"? > > The eigenvectors are an orthonormal basis set for the observed variation. > If the observed variation is a mess (because the structural ensemble you're > treating as a black box is actually a mess, or your reference structure is > an outlier), then the eigensystem will not lead to a sensible filter. > > Since you chose not to follow my hints last time: > 1) Go and look at the X-ray ensemble. Is it one? Is your arbitrary choice > of reference structure appropriate? Is there even an appropriate choice? > 2) You can filter the trajectories based on the other's eigensystem. If the > eigensystems are equivalent, then the filtered trajectories should look the > same. If they don't, then your two ensembles differ. > > Mark > > James >> >> 2013/1/25 Mark Abraham <[email protected]>: >> > On Tue, Jan 22, 2013 at 8:22 PM, James Starlight <[email protected] >> >wrote: >> > >> >> Dear Gromacs users! >> >> >> >> >> >> There is some bug with g_anaeig the souce of which I could not fully >> >> understand. >> > >> > >> > Good Advice: until you can almost write a code patch to fix it, be very >> > hesitant in suggesting any software has a bug. The best people to help >> > solve the issue are often those who wrote the code, and you don't want >> them >> > annoyed with you :-) >> > >> > I have problems when I perform PCA of X-ray data set. >> >> Below you can my workflow. >> >> >> >> >> >> g_covar -f b2ar_xray_coors.pdb -s ref.pdb -o PCA_eigenval.xvg -v >> >> PCA_eigenvec.trr -av PCA_average.pdb -last 8 >> >> g_anaeig -v PCA_eigenvec.trr -s ref.pdb -f b2ar_xray_coors.pdb -rmsf >> >> eigrmsfPCA.xvg -filt >> >> >> >> >> >> here b2ar_xray_coors.pdb is the trajectory made from 10 X-ray >> >> structures of my protein (only main chain atoms are included) >> >> ref_pdb is the first frame of that trajectory >> >> >> >> >> >> As the result I've obtained reasonable eigenvalues and aigenvectors >> >> from g_covar BUT when I check filter trajectory ( produced by >> >> g_anaeig) fitted it to the ref.pdb or to the averaged structure in >> >> both cases I've obtained very distorted geometry of the protein in >> >> thefiltered trajectory. I have no such problems in case of PCA of MD >> >> trajectory ( when -f trajectory.trr is from the md snapshots not from >> >> x-ray structures) >> >> >> >> >> >> How it could be fixed ? >> >> >> > >> > How have you excluded the hypotheses that your reference structure is >> not a >> > valid representative of the middle of the range of variation? Or even >> that >> > the X-ray structural ensemble really is one? >> > >> > Mark >> > -- >> > gmx-users mailing list [email protected] >> > 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 [email protected]. >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
