I am a new user of Coot and I ran into problems with the regularize
option that I cannot figure out. My model consists of 4 fragments that
came out of Resolve. I noticed that the 5 C-terminal residues should
actually be connected between 2 fragments in the middle of the molecule.
So, I renumbered the C-terminal residues so that they would fit into the
sequence at the correct position. The geometry does not look too bad for
connecting these residues in their new environment. But if I try to
regularize the border region between the renumbered residues and the
surrounding molecule it doesn't work. I think the program still thinks
the renumbered residues are at the C-terminus.
Error message
click on 2 atoms (in the same molecule)
(0) N /1/chainid=""/77/LYS, occ: 1 with B-factor: 9.99 element: N at
(8.724,45.734,24.316) : 0.118271
(0) N /1/chainid=""/81/ALA, occ: 1 with B-factor: 12.25 element: N
at (9.137,40.656,20.993) : 0.14991
regularize: molecule 0 atom index 412 to 2106
DEBUG:: check_dictionary_for_residues returns OK!
INFO:: 218 residues selected for refined and flanking residues
WARNING:: Hit heuristic fencepost! Too many residues to refine
FYI: 218 > 20 (which is your current maximum).
Use (set-refine-max-residues 40) to increase limit
No restraints: regularize()
What do I need to change the place the C-terminal residues in the middle
of the molecule somewhere?
Thanks
Ursula
--
Ursula Schulze-Gahmen, PhD.
QB3, Tjian Lab
MCB, 16 Barker Hall #3204
University of California Berkeley
Berkeley, CA 94720-3204
Phone: (510) 642 8258
uschulze-gah...@lbl.gov
