Cc: modeller_usage <modeller_usage>, Tina Yeh <>, ,
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!
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