Dear all, Thanks a lot for your input. Later I found a R package called bio3d that is very suitable for my purpose.
Best, Chen On Wed, Oct 15, 2014 at 5:53 PM, Steven Chou <[email protected]> wrote: > Hi Chen, > I used SUPPOSE previously. It worked very well. The compositions of the > structures have to be the same! It works on Linux. > http://structbio.vanderbilt.edu/~jsmith/suppose/ > > If the compositions of your structures are different, you may first load > them to PyMOL, then align them use its commandline. > > http://pldserver1.biochem.queensu.ca/~rlc/work/teaching/BCHM823/pymol/alignment/ > > If the compositions/sequences of your structures are very very different, > but their overall structure are similar, you can do the alignment using a > PyMOL plugin called 'cealign'. It works on both Mac and Linux. > http://pymolwiki.org/index.php/Cealign > > > Here is my note on how to run SUPPOSE. > #### remove the outputs from the previous runs > rm -rf *.rot.pdb mean.pdb all.pdb > > # if the input file names are XXX.pdb, those of the output files are > XXX.rot.pdb and a mean.pdb > > > #### fit the structrue models based on the CA atoms, and then calculate > the RMSD of the backbone atoms > suppose -mat -rot -mean -fit ":11-52,85-97:CA" -calc ":11-52,85-97:C,CA,N" > restrt_*.pdb > # 0.639 > > #### fit the structrue models based on the CA atoms, and then calculte the > RMSD of the heavy atoms > suppose -mat -rot -mean -fit ":11-52,85-97:CA" -calc > ":11-52,85-97:C*,N*,O*,S*" restrt_*.pdb > # 1.23 > > # Do not visulize the rotated pdb files with molmol at this step, because > molmol will shift the individual files. > # That is, the output files have already been perfectly supperimposed, > # but molmol gives an illusion that they have not been rotated correctly. > > #### join the pdb with the AWK script > ./joinpdb -o all.pdb *.rot.pdb > # input files: *.rot.pdb > # output file: all.pdb > > #### display the rotated pdb with molmol now. > molmol all.pdb > # molmol can only display the combined pdb (i.e., 20 models in one file) > correctly!!! > > > HTH, > > Steven > > > > On Wed, Oct 15, 2014 at 4:05 PM, Chen Zhao <[email protected]> wrote: > >> Dear all, >> >> I am just wondering whether there is a simple command line tool for RMSD >> calculation between two aligned structures? I just cannot find a good >> answer online, and ccp4bb can always impress me. >> >> Thank you so much in advance, >> Chen >> > > > > -- > Steven Chou > > >
