Thanks Tim for the timely tips. I haven't tried Arp/wARP but will follow your recommendation right away. I haven't installed Resolve yet but will look into it and Buccaneer as well - I was having fun modeling some of the apparent fragments into the density but with a protein so big, I ran exhausted before long ;p)... Due to the same fatigue, I wasn't patient enough to rename the Chain ID of the updated fragments. Practically, it seems that* I have to rename the chain ID before "Renumber Residues" as they are two different entities on the menu.* Actually, would Coot authors consider adding "Change Chain ID" into the "Renumber Residues" window so that I I could do both changes on the fly? Thanks, Jacob Wong
On Wed, May 4, 2011 at 3:59 AM, Tim Gruene <t...@shelx.uni-ac.gwdg.de> wrote: > 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 > > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.10 (GNU/Linux) > > iD8DBQFNwQd5UxlJ7aRr7hoRAqBAAJwNQOkDSZjzHe5Fsrj0hxuzf75nRQCfQEZq > s1BO9IHCwb66OhbVa6Gb/Hg= > =dbO3 > -----END PGP SIGNATURE----- > >
