Hi Jenny, You can do this in LSQMAN (if I'm understanding your question correctly...) You'd first superimpose the residues in the "fixed region" to give a superimposed core using the 'EXplicit' command, eg: LSQMAN > ex m1 Range 1 ? (A1-10) "a4-10 a19-23 a28-36 a44-51 a53-66 a91-97 a106-111 a123:126" Mol 2 ? (M1) m2 Range 2 ? (A1) "a4 a19 a28 a44 a53 a91 a106 a123" Explicit fit of M1 "A4-10 A19-23 A28-36 A44-51 A53-66 A91-97 A106-111 A123:126" And M2 "A4 A19 A28 A44 A53 A91 A106 A123" Atom types | CA | N | C | O | CB | Nr of atoms to match : ( 295) The 295 atoms have an RMS distance of 0.892 A Rotation : -0.956932 0.127723 -0.260706 0.170532 -0.479456 -0.860837 -0.234946 -0.868222 0.437026 Translation : 13.787 26.800 38.541 Then use the "IMProve" command to iteratively improve the fit over all CAs...this only works for two molecules at a time though...I guess choose a fixed standard to align all the others against. Remember to write out the coordinates for the rotated (ie. "m2") molecules: * apply m1 m2 * wr m2 blah_rotated.pdb Then to calculate the RMSDs for just the loop regions compare the superimposed molecules to the fixed standard (ie. "m1" is the fixed standard, "m2" is your blah_rotated.pdb), explicitly using just the loop atoms this time in "m1" and "m2" ranges. I'm sure there is an easier way to do this, but works for me. HTH, Iain ________________________________ From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Jenny Sent: Thursday, May 10, 2007 5:46 PM To: [log in to unmask] Subject: [ccp4bb] rmsd calculation. . Hi, All, I have a question about rmsd calculation. I have some pdbs (100 residues ) and these pdbs differ pretty much only the loop region 40-60. Is there any easy way that I can superimpose the fixed region ( 1-40,60-100) and then calculate the rmsd for the loop?I need to calculate for each pair, so if there is any script or program available to do this quickly, that would be great. Thanks. Jenny