Dear Wenhe, Besides this advice, have a look at the http://webapps.embl-hamburg.de/rapido/ <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
