Dear Eric, For your question 2, the following paper provides some examples:
Acta Cryst. D63, 793-799 (2007). In one of the examples, there is shown a partial model from Phaser containing ~20% residues in the ASU can be extended to more than 90% of the ASU by the iteration of ARP/wARP-OASIS-DM. Detailed examples and scripts on using OASIS can be found on the download page of http://cryst.iphy.ac.cn Regards, Hai-fu On 8/1/07, 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 >
