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<DIV><FONT face=Arial size=2>Ethayathulla,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>from your description, it seems likely that the
last 10 residues of the C-termus may just be disordered, esp if you observe this
for each monomer. if that is true, no autobuilding program will
help you out (as far as I know), since they aren't as
efficient building into density that is very weak or not present at
all. I think manually building may be your best option which doesn't
sound too bad since it is only 10 residues/monomer. If you aren't using
Coot for building, i HIGHLY recommend it, since it makes these types of tasks
very trivial. With that, there are a few other options you might try,
but I recommend trying to manually build as well, since these may not
work. </FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>1- Have you tried Resolve's Prime and Switch?
While I have only used it once, there are many examples of PnS
significantly helping bring out some otherwise weak/missing density. You
may run this from a SOLVE/RESOLVE installation via command line or, [I think]
from within the PHENIX GUI (if i recall correctly). here is a link
for more info...</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2><A
href="http://www.solve.lanl.gov/Resolve/html_resolve_manual/resolve_table_of_contents.htm">http://www.solve.lanl.gov/Resolve/html_resolve_manual/resolve_table_of_contents.htm</A></FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2><A
href="http://www.solve.lanl.gov/Resolve/html_resolve_manual/resolve_introduction.htm#ps">http://www.solve.lanl.gov/Resolve/html_resolve_manual/resolve_introduction.htm#ps</A></FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2><A
href="http://www.solve.lanl.gov/Resolve/html_resolve_manual/resolve_examples.htm">http://www.solve.lanl.gov/Resolve/html_resolve_manual/resolve_examples.htm</A></FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>2- Another option might be to either do a
round of density modification and/or calculate a full-omit map.
People have reported either of these can sometimes improve weak
density. Again, i think these are options that you can explore within
PHENIX. It might be worth your while to try them before and after you
manually build the 10 extra residues/monomer....even if you only build the
Calpha trace or polyA. Check out the manuals for info on how to
set some of these things up if you aren't familiar, or just post
your questions here again, someone will surely help. </FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>3- and if you must venture away from PHENIX
(kidding), then the folks at GlobalPhasing might recommend you give Buster-TNT a
try. While i have never used it, I have heard Bricogne speak wonders about
the density maps that B-TNT produces, giving examples of much improved density
maps, esp where weak/no density was previously observed. Their
people are awesome (but not as awesome as the PHENIX support, hehe) about
helping people out with questions and with getting the software up and running
so it can be used. </FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Again, if it was me, I would
first manually build in the 10 residues from the density present, even if
just the Calpha or polyA. Then do density modification and make maps to
see if any additional density is present for the side-chains. Even a sigma
A-weighted 2fo-fc map should help you decide if the build was useful or
not. If there is no improvement, then it is very likely that this region
is simply disordered and the programs probably won't help (in my little
experience). It is quite common for the C- and/or N-termini of proteins to
be disordered, esp if they are recombinantly expressed and have an
engineered 'linker' for tag removal. If things do look better after DM,
then you can probably build as best as you can, and allow the
b-factors to inflate some (or however you deal with this). </FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I hope some of this helps you out and you are able
to build in your last 10 residues/monomer. If any of the programs
mentioned above works out for you, let us know, it would be good information for
a rainy day. Sorry I couldn't have been more help. Best of Luck on
your project!</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
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<DIV><FONT face=Arial size=2>Cheers,<BR>Nick</FONT></DIV>
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style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=ethayathulla@gmail.com
href="mailto:ethayathulla@gmail.com">Ethayathulla A.S</A> </DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=phenixbb@phenix-online.org
href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</A> </DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Thursday, April 19, 2007 2:18
AM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> [phenixbb] Remodelling using
Phenix</DIV>
<DIV><BR></DIV>
<DIV>hi</DIV>
<DIV> </DIV>
<DIV>I am doing structure at 2.3A resolution. It is a dimer not NCS. I
have probelm in tracing last 10 amino acids in the C-terminus in both chains.
Both chains come close each other and winds up. So Iam finding difficulty
in tracing the chain. I used phenix for rebuilding with all the amino
acid included. But autorebuilding is not rebuilding properly, whatever input
is given it rebuilds on that. Actually it should be a helix and only at lower
cuff off we can observe density for main chain so I tried phenix rebuild to
improve it but it's not working. Is there any option to use phenix. </DIV>
<DIV> </DIV>
<DIV>I used rebuilding with option automatic and input coordinates and
sequence.</DIV>
<DIV> </DIV>
<DIV>plz suggest do improve the phases.</DIV>
<DIV> </DIV>
<DIV><BR clear=all><BR>-- <BR>A.S.Ethayathulla<BR>Department of
BIophysics<BR>All India Institute of Medical Sciences<BR>Ansai Nagar<BR>New
Delhi-110029<BR>India </DIV>
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