-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Jenny and Iain,
But my understanding is that Iain's procedure gives the rmsds of the _aligned_ C-alphas, whereas Jenny actually seems to be more interested in those that she excludes from the alignment. I may be wrong, but in these cases, I use lsqman (from DVD) or lsqkab (from ccp4) to superpose the proteins (using one as reference) according to a particular scheme (Jenny's 1-40,60-100) and then write a script to calculate the rmsds for the "interesting" 41-59 residues. There may be an easier way, which I'll be interested to learn about. Cheers, M. Kerr, Iain escribió: > 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 > > > > > > ------------------------------------------------------------------------ > > *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of > *Jenny > *Sent:* Thursday, May 10, 2007 5:46 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *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 > - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: [EMAIL PROTECTED] www: http://www.pangea.org/mol/spip.php?rubrique2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Le travail est ce que l'homme a trouvé de mieux pour ne rien faire de sa vie. (Raoul Vaneigem) -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) iD8DBQFGRAwlF6oOrDvhbQIRAjmEAJ9UvAWXfIZU7bR1idcVqn8hE5zPwQCfc8Ko JkvZQL9IHdB+ENi92nVVUmI= =3HO2 -----END PGP SIGNATURE-----
