WenHe, I'm not sure if you want to superimpose a number of structures (as rmsd would imply) or just compare two structures. If you want a complete list of the distances between corresponding atoms in two pdb files of identical sequence, you can use the fortran program http://www.cytbc1.net/berry/for/pdbdist2b.for (linux executable http://www.cytbc1.net/berry/for/pdbdist2b ). You need to superpose the structures (if necessary) with something else, and save the two files. Grep out C-alphas to two new files if you only care about them.
The program asks you for the names of the two files and the residue number at which to start (this latter is to synch the files in case they have different start residues. If sequences are identical, just give the first residue number) It also asks for last residue to compare in first file - just give a large number to do all. Then it asks for a threshold - only distances larger will be printed. Put -1 to print all. You can put all parameters on the command line if you run it with the shell script pdbd2b: echo 'Find distances greater than threshold between corresponding atoms in 2 PDB files' echo 'Usage: pdbd2b file1 file2 startres# [thresh]' pdbdist2b <<eof $1 $2 $3 100000 $3 $4 3.0 eof This makes it easy to redirect the output to a text file, then in MSWord replace white space with tabs and paste it into excel for plotting output looks like: CA SER A 10 CA SER A 10 0.0220 CA VAL A 11 CA VAL A 11 0.0245 CA PRO A 12 CA PRO A 12 0.0524 CA GLU A 13 CA GLU A 13 0.0604 CA THR A 14 CA THR A 14 0.0251 CA GLN A 15 CA GLN A 15 0.0220 CA VAL A 16 CA VAL A 16 0.0054 CA SER A 17 CA SER A 17 0.0082 CA GLN A 18 CA GLN A 18 0.0082 . . . >>> WENHE ZHONG <wenhezhong.xmu....@gmail.com> 10/29/16 11:49 AM >>> 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
