On 1 Aug 2007, at 22:55, Eric Liu wrote:
Hi All,
Here are the summary from all the answers to my questions:
1. Try use arp/warp to build the missing part of structure.
I have to clarify to avoid misunderstandings, that :
1. ARP/wARP autotracing is a bad way for building difficult parts
2. The maps from ARP/wARP however can sometimes be better than normal
maps for difficult parts
3. The new ARP/wARP 'Loop building' module can be useful for building
missing loops but not N- and C-termini for now,
and should be a considered a beta version for experimenting.
Tassos
2. Build as much as possible for the missing part and the current c-
terminal domain, using as low as 0.5 contour of the 2Fo-Fc density.
Generate mask and then do averaging and density modification using
DM/Resolev/pirate/buccaneer.
3. Align the c-terminal part of other closest kinases to the
current model, then try to find which N-terminal domain matches the
difference density the best by eyeballing.
4. Look into the possiblity of twinning
Thanks,
Eric
On 7/31/07, Eric Liu <[EMAIL PROTECTED]> wrote:
Hi All,
I would like to get some help from here for a data set I recently
worked on. I have been working on a new kinase data set which does
not have a close homolog. The data was collected to 2.1A
resolution in space group P212121 however the difference between a
and b is only 0.5A. If I index the data as P4, Rmerge is increased
from 13% to 39%. I used the most close homologs which have about
37% sequence identity as search model for molecular replacement and
it seemed I have got the solution by using Phaser with only the c-
terminal part of the search model and also a long loop removed.
After changed the different residues back to the target protein,
the structure was refined to Rfree/R 46% and 43% to 2.1 A
resolution. The existing c-terminal structure has well defined
density except 25ish residue at the very c-terminal end doesn't
have well connected density. Current model contains about 50% of
overall target residues. I can see some extented difference density
for several residues going to the N-terminal part and also extented
density for the C-terminal loop for several residues. I also see
tones of not well-conncted difference density in the N-terminal
region. There was no sever clashes between molecules after mount
all symmetry related molecules. My question is the following:
1. Have I got the correct solution for the molecular replacement?
2. How can I bring back the missing density for the N-terminal
residues and the loop region?
I would really appreciate any inputs or suggestions.
Eric
