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:

 

Ø       apply m1 m2

Ø       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

 

 

 

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