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Hello Valerie-- > Now the problem is that the secondary structure is perturbed. The > backbone RMSD between input and output structures is 1.1 Angstroms. I > called in the input structure in the create_PosDiffPot for the > comparison. Will adding pdbFile to create_PosDiffPot enforce the new > structure to adopt the same backbone atom positions? please try this: add this line before minimizeRefine: test.setScale(100) This will increase the weight on the reference structure backbone positions. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkrD0LEACgkQPK2zrJwS/lYe5wCdGQyIOG8rhOBrcWlqlQVUbptT +XoAn0lULuG3eCFlhZzYvoJ0CEn5TzI8 =34vS -----END PGP SIGNATURE-----
