Dear Jacob Wong, have you tried arp warp for model building? It should do a reasonably good job at 2.3A resolution. Alternatively buccaneer or resolve might also help.
For the overlapping: Does it help to give the subsequent fragment a different chain ID? Tim On Wed, May 04, 2011 at 02:48:11AM -0400, Jacob Wong wrote: > Dear all, I know I could use your help to work more effectively so here > comes my questions. > > I am building a fairly long polypeptide chain (quite a few hundreds of aa) > in Coot. I got the phases from Phenix, which traced much of the main chains > for me already, with each fragments assigned with numbers that are > apparently mismatched with the linear protein sequence. So, I begin to > mutate/fit these Ala fragments (one piece at a time) into correct residues > using Coot and also try to correct their numbers by doing "renumber > residues". The outcome is that now I have overlapped numbers as I move > along, prohibiting me to do real-space refinement effectively. How to get > around with this? Thank you! > > Also, are there any easily accessible programs that could help me build > these side-chains based on the very good experimental density map currently > at 2.3A? > > Thanks, Jacob Wong -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A
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