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Hi Mike,
Several automated model building routines have the capability of
building missing parts and rebuilding bad parts (might be a good idea ... )
These are your some of options (in alphabetical(?) order)
1. ARP/wARP. If your density is clear enough, I would not be surprised
if ARP/wARP will build it for you, and possibly correct 'bad' parts
elsewhere. Check out the website (http://www.arp-warp.org) as well as
this paper in ARP/wARP and molecular replacement:
http://scripts.iucr.org/cgi-bin/paper?S0907444901014007
2. (The) AutoBuild wizard in Phenix (which uses resolve) allows to
'rebuild in place' or build from scratch and fill in gaps. You might
be able to only build missing loops if desired, but not sure how. I
suggest taking this issue up on the phenixbb.
(http://www.phenix-online.org)
3. Lafire. Never used it, heard good things about it though (especially
now non japanese versions are available;
http://altair.sci.hokudai.ac.jp/g6/Research/Lafire_English.html)
HTH
Peter
Kendall Nettles wrote:
Mike,
After adding a residue or a few residues to your loop with “add terminal
residue”, you can use the “Zone” tools to refine, regularize geometry,
and rotate/translate the residues to better fit the density. The Coot
manual explains these features. However, experience with model building
can make a big difference. Try to find an experienced crystallographer
who can show you how to build in the missing residues.
Kendall
------------------------------------------------------------------------
*From: *michael nelson <[EMAIL PROTECTED]>
*Date: *Wed, 25 Oct 2006 07:22:52 -0700 (PDT)
*To: *<[EMAIL PROTECTED]>
*Subject: *[ccp4bb]: loop generating
Hi,all.I have a structure solved by molecular replacement.However, there
is a 10 residue loop missing in the model and need to be regenerated.
The density is quite clear. I tried to use O and coot to generate the
loop but the result is not satisfactory.Is there a better way to do this?
Please advise.
Many thanks!
Mike
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