Look at CCP4 "compar" By default it averages RMSD over all atoms in mainchain and sidechain of the residue, but if you first awk out only CA (or use pdbset to pick CA) foreach structure, the mainchain value will presumably be the Euclidian CA distance (This may require identical sequences, at least no insertions):
#test with all-atom pdb files: cd $CEXAM/unix/runnable/ ./refmac5_tls.exam ./compar.exam output: RMS xyz and B AVERAGES RES , MAIN CH,SIDECHAIN RES MAIN CHAIN SIDE CHAIN MAIN CHAIN SIDE CHAIN MAIN CHAIN SIDE CHAIN MAIN CHAIN SIDE CHAIN 1 ASP A 0.21 10.1 0.44 24.9 2 VAL A 0.17 10.0 0.19 11.1 3 SER A 0.36 10.2 0.14 6.0 . . . #Awk the CA's into two new files: awk '$1~/ATOM/ && $3~/CA/' $CCP4_SCR/rnase_out.pdb > $CCP4_SCR/rnase_outCA.pdb awk '$1~/ATOM/ && $3~/CA/' $CEXAM/rnase/rnase.pdb > $CCP4_SCR/rn compar \ XYZIN1 $CCP4_SCR/rnaseCA.pdb \ XYZIN2 $CCP4_SCR/rnase_outCA.pdb \ RMSTAB $CCP4_SCR/rnaseCA.rms \ << END-compar comparing rnase coordinates before and after refinement 2 3.0 16 END-compar RMS xyz and B AVERAGES RES , MAIN CH,SIDECHAIN RES MAIN CHAIN SIDE CHAIN MAIN CHAIN SIDE CHAIN MAIN CHAIN SIDE CHAIN MAIN CHAIN SIDE CHAIN 1 ASP A 0.24 13.3 0.00 0.0 2 VAL A 0.12 6.6 0.00 0.0 3 SER A 0.05 8.1 0.00 0.0 4 GLY A 0.29 6.4 0.00 0.0 5 THR A 0.11 8.5 0.00 0.0 6 VAL A . . . #compare with independently calculated distances: pdbd2b $CCP4_SCR/rnaseCA.pdb $CCP4_SCR/rnase_outCA.pdb 1 0 | moreFind distances greater than threshold between corresponding atoms in 2 PDB files Usage: pdbd2b file1 file2 startres# [thresh] CA ASP A 1 CA ASP A 1 0.2376 CA VAL A 2 CA VAL A 2 0.1173 CA SER A 3 CA SER A 3 0.0462 CA GLY A 4 CA GLY A 4 0.2865 CA THR A 5 CA THR A 5 0.1128 CA VAL A 6 CA VAL A 6 0.2899 On 08/27/2017 07:09 AM, Johannes Sommerkamp wrote:
Hello everybody, I have superposed two structures based on the central beta-sheet CA atoms with the "super" command in Pymol. Now, I want to calculate the RMSD between ALL atoms or ALL CA atoms without moving the structures again. The rms_cur command in Pymol would do that, but only works if all atom identifiers match. Adding "transform=0" to the super, oder align command still does the alignment and moves the structure but does not show the movement. Is there an easy way to just calculate the all atom RMSD between two already superposed structures in pymol or any other programm? Thanks in advance! Johannes
