Hello Azat,
Thanks for your mail of 98/06/23 at 8:43 -0400.
>Initial alignment is probably bad which is indicated in diagnostics of >CHECK_ALIGNMENT and MALIGN3D. > Please bear with me for a moment: although I have used "Modeller" before, I never ran into problems so I never paid much attention to the diagnostics messages. However, CHECK_ALIGNMENT indicated no (zero) equivalent CA pairs with distance difference larger than 6.0 angstroms and no (zero) implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms. It did list 19 occurrences of the statements "drmsq1__W> n<2" and "drmsq3__W> n<2". We had seen these messages before (never 19 times, though), but still obtained good models. My deduction is that the alignment should be good enough to produce a model, so I cannot explain why it does not do so. Also, modelling the individual domains with the exact same sequence alignments did not lead to any problems.
>Please check your alignment manually > Done twice already.
>or use FIT = on in MALIGN3D to produce correct alignment. > We might give that a shot, just to see if that solves the problem (not because we think a better alignment would be produced <g>).
>If it won't help, then please send me .top, .pdb, alignment files and >other necessary input files > I am afraid I cannot do that as the files contain proprietary information. I have sent the lot off to MSI, though. I hope they can help. Thanks for the offer, anyway.
Cheers,
Pieter
Pieter Stouten || Nothing shocks me; Computer Aided Drug Design Group || The DuPont Merck Pharmaceutical Company || I am a scientist! P.O. Box 80500, Wilmington, DE 19880-0500 || Phone: +1 (302) 695 3515 || -- Fax: +1 (302) 695 9090 || Internet: pieter.stouten@dupontmerck.com || Indiana Jones Web: http://www.halcyon.com/stouten/ ||