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Dear Janxon;
First let me point out that guiSIDE is somehow deprecated, and that
unless you have a very complicated complex in your AsU you can ask
ARP/wARP to directly build side chains (which will be better, since
it gives more restraints to refmac earlier). If however the content
of your AsU contains different number of copies for different protein
(eg. 2xA, 1xB), then send me a mail and we'll sort out a way for you
to get a working interface.
Second, concerning the deletion of poorly ordered loops : there is
nothing to do about that, it is a designed feature of ARP/wARP : as
it build automatically a model, we want to get a result that the user
can rely on on (rather than you have to go through it again and
rebuild-it yourself). In other words, the current version of ARP/wARP
will build only model that it is very confident in, you have to build
the rest... it will optionally change in future, but that is how it
works now.
Finally to answer the question about the 'DUM' atoms : this is the
way ARP/wARP is modelling the electron density which is not explained
by the molecular model. You can think of it as a set of coordinates
where you put atoms just to model the density, still ARP/wARP will
put them in such a way that an important portion of the coordinates
are close to the real structure.
Also, note that there is a mailing list for help on how to use ARP/
wARP : [EMAIL PROTECTED]
Hope this helped, cheers;
Serge.
Le 14 janv. 07 à 14:18, JXQI a écrit :
Dear all,
I run the program ARP/wARP for automated model building starting
from existing model, then fit side chains into an existing model
using the guiSIDE program. and then build solvent atoms and refine
the model with REFMAC5.
However, the ARP/wARP program will delete the poorly ordered loops
and terminal residues, how can I construct these fragment?Another
thing I should point is that the output PDB file contain the "DUM"
atoms, what do these "DUM" atoms mean and how to solve this problem?
ATOM 1 DUM DUM Z 1 7.817 31.022 16.968 1.00 6.11 8
ATOM 1 DUM DUM Z 2 27.858 51.264 23.112 1.00 7.95 8
ATOM 1 DUM DUM Z 3 28.753 32.799 4.072 1.00 12.62 8
ATOM 1 DUM DUM Z 4 24.556 53.204 16.967 1.00 10.89 8
ATOM 1 DUM DUM Z 5 26.084 50.702 5.264 1.00 13.27 8
ATOM 1 DUM DUM Z 6 22.806 41.055 10.335 1.00 12.34 8
ATOM 1 DUM DUM Z 7 10.146 28.321 2.780 1.00 13.30 8
ATOM 1 DUM DUM Z 8 8.311 28.644 14.631 1.00 14.69 8
ATOM 1 DUM DUM Z 9 27.909 42.309 21.850 1.00 12.99 8
ATOM 1 DUM DUM Z 10 28.409 44.926 -0.102 1.00 14.25 8
ATOM 1 DUM DUM Z 11 28.175 38.202 9.397 1.00 17.63 8
.
.
.
.
.
.
ATOM 1 DUM DUM Z 131 22.074 46.534 23.732 1.00 34.00 8
ATOM 1 DUM DUM Z 132 15.511 42.358 19.101 1.00 34.00 8
ATOM 1 DUM DUM Z 133 19.091 25.057 6.946 1.00 34.00 8
ATOM 1 DUM DUM Z 134 18.494 24.460 -1.158 1.00 34.00 8
ATOM 1 DUM DUM Z 135 13.722 22.670 13.313 1.00 35.00 8
ATOM 1 DUM DUM Z 136 19.688 48.920 23.732 1.00 35.00 8
ATOM 1 DUM DUM Z 137 21.477 42.358 -6.946 1.00 35.00 8
ATOM 1 DUM DUM Z 138 -1.790 35.795 7.525 1.00 35.00 8
ATOM 1 DUM DUM Z 139 19.688 59.062 15.628 1.00 35.00 8
ATOM 1 DUM DUM Z 140 27.443 45.937 -5.209 1.00 35.00 8
ATOM 1 DUM DUM Z 141 27.443 37.585 -4.052 1.00 35.00 8
ATOM 1 DUM DUM Z 142 19.091 58.466 22.574 1.00 35.00 8
Any suggestions and references would be appreciated.
Thanks.
Janxon
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