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Re: [ccp4bb]: AMORE question (trying again)
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(1) what is the point group and the cell ?
> four molecules in the au, based on the Matthews'coefficient and
> self-rotation calculation.
(2) what is the matthew's coeff for 2, 3, 4 mol/ASU ?
(3) what information does your self-rot function give ?
(4) are there any off-origin peaks in the native patterson ?
> The rotation and translation results are quiet puzzling. Here is the four
> solutions for each molecules, after fixing them one by one
>
> SOLUTIONTF1 1 77.01 90.00 271.21 0.1013 0.4771 0.3473 46.1 52.5 41.1 2 58.5
> SOLUTIONTF2 1 15.47 48.52 87.74 0.4730 0.1005 0.1464 51.3 51.4 49.9 2 58.5
> SOLUTIONTF3 1 72.38 32.04 96.38 0.8958 0.5205 0.3605 54.2 50.6 52.7 1 59.0
> SOLUTIONTF4 1 81.25 38.07 83.60 0.0458 0.4842 0.3609 56.0 49.5 56.6 1 49.0
>
> These solutions are the best,even though there is no clear gap.
..... which is worrying and may well mean that the top 'solutions' are not
necessarily correct
(5) solutions 3 and 4 have a very small rotation between them - is
this consistent with your self-rot fun and with your native patterson ?
(6) solutions 1, 3 and 4 have very similar y and z translations; i would
be suspicious and would expect packing problems. unless you have
gigantic axes, solutions 1 and 4 obviously overlap since they also
have fairly similar x translations
> But, problem appears when I check their packing. Molecules overlap to each
> other, either directly or to their symmetry mates.
i.e., the solutions aren't
> 1.Could someone know why such CC and R-f doesn't produce right
> solution?
ask them ! on the other hand, it is well known that wrong and correct
solutions can produce similar CC and R-f scores and are often hard to
distinguish, esp. in cases in which the model and/or the data leave something
to be desired
> 2. Does Amore check the molecular packing during translation search? How
> to implement it?
not the ccp4 version of amore i don't think, but jorge navaza's own
version does if i'm not mistaken
--dvd
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Gerard J. Kleywegt
[Research Fellow of the Royal Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:gerard@xray.bmc.uu.se
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