Hello,

There is a bug in iris4d v6.2 when fitting models to the original structure using SET FINAL_MALIGN3D = 1. To be more precise, original models are reoriented properly, but loop-optimized models are not. It looks something like this:

HETATM 323 PCA 6.BL0 58.234 76.175 42.150 1.00110.73 1SG 324 HETATM 324 PCA 6.BL0 58.860 77.458 42.113 1.00110.73 1SG 325 HETATM 325 PCA 6.BL0 59.060 78.039 43.525 1.00110.73 1SG 326 HETATM 326 PCA 6.BL0 57.719 78.207 44.162 1.00110.73 1SG 327 HETATM 327 PCA 6.BL0 57.087 77.136 44.752 1.00110.73 1SG 328 HETATM 328 PCA 6.BL0 57.092 79.431 44.186 1.00110.73 1SG 329 HETATM 329 PCA 6.BL0 55.854 77.282 45.346 1.00110.73 1SG 330 HETATM 330 PCA 6.BL0 55.861 79.586 44.775 1.00110.73 1SG 331 HETATM 331 PCA 6.BL0 55.238 78.509 45.357 1.00110.73 1SG 332 HETATM 332 PCA 6.BL0 60.210 77.157 41.537 1.00110.73 1SG 333 HETATM 333 PCA 6.BL0 60.927 76.297 42.048 1.00110.73 1SG 334

while the original file before MALIGN looks like this:

ATOM 323 N PHE 42 58.234 76.175 42.150 1.00110.73 1SG 324 ATOM 324 CA PHE 42 58.860 77.458 42.113 1.00110.73 1SG 325 ATOM 325 CB PHE 42 59.060 78.039 43.525 1.00110.73 1SG 326 ATOM 326 CG PHE 42 57.719 78.207 44.162 1.00110.73 1SG 327 ATOM 327 CD1 PHE 42 57.087 77.136 44.752 1.00110.73 1SG 328 ATOM 328 CD2 PHE 42 57.092 79.431 44.186 1.00110.73 1SG 329 ATOM 329 CE1 PHE 42 55.854 77.282 45.346 1.00110.73 1SG 330 ATOM 330 CE2 PHE 42 55.861 79.586 44.775 1.00110.73 1SG 331 ATOM 331 CZ PHE 42 55.238 78.509 45.357 1.00110.73 1SG 332 ATOM 332 C PHE 42 60.210 77.157 41.537 1.00110.73 1SG 333 ATOM 333 O PHE 42 60.927 76.297 42.048 1.00110.73 1SG 334

If this is not informative enough, I can send whole files as attachments and also my .TOP scripts, though nothing seems to be wrong with them and everything else got executed fine.

Mensur

=========================================================================== | Mensur Dlakic, PhD | Tel: (734) 764-3554 | | Department of Biological Chemistry | Fax: (734) 615-3397 | | University of Michigan Medical School | http://www.umich.edu/~mensur/ | | 5416 Medical Science I | http://myprofile.cos.com/mensur | | Ann Arbor, MI 48109-0606 | E-mail: mensur@umich.edu | ===========================================================================