I think superpose does not output CAs outwith a certain cut-off based on the quality of the superimposition. It does try to match as many as give reasonable RMSDs - but it is mainly focussed on the residues in matching secondary elements as this is where it starts the superimposition.
A simpler approach is to use LSQKAB which will report all CA RMSDs in a file if you specify that you want DELTAS. But notice that as Gert said this will probably give you a different kind of superimposition. A workaround would be to restrict LSQKAB to the residue ranges SUPERPOSE used - then it will produce the same superimposition but can report DELTAS for _all_ residues (! phew). A non-CCP4 approach is Chimera Multi-align Viewer which calculates RMSD without doing any superimposition. So you could run it on your SUPERPOSE output coordinate files. I recall RMSD is a 'header' in that tool and can be output to a file. https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html (You have to read your structures into Chimera before launching Multi-align viewer). hope that helps. Martyn Martyn Symmons Cambridge On Sun, Oct 30, 2016 at 10:54 AM, Anastassis Perrakis <a.perra...@nki.nl> wrote: > Dear Wenhe, > > Besides this advice, have a look at the > http://webapps.embl-hamburg.de/rapido/ server. > > Sometimes its goodo to re-think of what you want to do, and wonder why its > not easily doable in software (perhaps because its not the right thing to do > …) > > A. > > > On 30 Oct 2016, at 11:45, Gert Vriend <gerrit.vri...@radboudumc.nl> wrote: > > Dear Wenhe, > > No 3D superpose tool will always align/map all Calphas. If in the one > protein the loop turns left, and in the other it turns right, then mapping > those loops is meaningless and thus not done by good software. The other > problem is that often two proteins that get compared do not even have > equally many residues so that there will always be some unaligned/unmapped > Calphas left at the end. Look for some articles by Arthur M Lesk on this > topic, he has explained protein superposition (problems) very clearly. > > Gert > > Ps, if you want proteins superposed and get different output from what the > standard software gives you, just mail me those PDB files and I can see what > I can do. > > > On 29-10-2016 17:47, WENHE ZHONG wrote: > > Dear all, > > I always use the SUPERPOSE tool in CCP4 to superpose molecules. This time I > want to use the RMSD values of superposed C-alpha atoms to plot a RMSD graph > (instead of using the graph automatically made by the program). However, > there are many atoms missing in the RMSD list. > > In the settings I chose “Superpose specific atoms/residues”, checked “Output > all distances to a file”, fit “C-alpha atoms”. The superposed structures > have exactly the same sequence. > > My question is: is there any way to get the completed list of RMSD value for > each C-alpha atom? Or is there any other program for this purpose? > > Thank you! > > Kind regards, > Wenhe > >
