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 <[log in to unmask]> 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