Hi Nicolas
It does happen sometimes although rarely, that "knots" show up. Like in your
case, when a very artificial setup is forced.
1., it would be better to have overlaps among the connected segments, that
will provide info about the relative orientation of each segment
2., (hit-and-miss approach) generate several models ("set FINAL_MODEL= 5"
(20)?) . And eliminate those ones that goes wrong. You can also introduce an
even more loosely defined starting conformation by increasing the deviation
(e.g "SET DEVIATION= 5.0", check the manual, RANDOMIZE_XYZ command )
Andras
> Dear users,
>
> I made a quite unusual model, with three structures as templates, linked
> by tethers which (presumably) do not present any secondary structures:
>
> >P1;tempA
> structureX:tempA:1::10:::::
> aaaaaaaaaa------------------------------
>
> >P1;tempB
> structureX:tempB:1::10:::::
> ---------------bbbbbbbbbb---------------
>
> >P1;tempC
> structureX:tempC:1::10:::::
> ------------------------------cccccccccc
>
> >P1;model
> sequence:model::::::::
> aaaaaaaaaaTTTTTbbbbbbbbbbTTTTTcccccccccc
>
> Everything's fine, except that in the final model one tether cross
> directly through the domain C! It is already the case in the file .ini
> and that seems related to the initial relative positions of the three
> templates. Is it supposed to occur? Any idea how to fix that?
>
> Regards,
>
> --
> Dr Nicolas Le Novère http://www-alt.pasteur.fr/~lenov
> Dpt of Zoology, Univ of Cambridge, Downing street, Cambridge CB2 3EJ, UK
> tel: +44 1223 336623 fax: +44 1223 336676 e-mail:
--
,
Andras Fiser, PhD # phone: (212) 327 7216
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras