Hi Tim,
For your second question, I think the function
map_peaks_near_point_from_list() would do something similar to what you
want. If you call it as
closePoints = map_peaks_near_point_from_list(mapNum, pointList, x, y, z,
radius)
then all the points in pointList will have symmetry
:
ERROR:: nucleotide_to_nucleotide() unassigned type mol_base_is_pyrimidine: -1
mol_base_is_purine: -1 std_base_is_pyrimidine: 0 std_base_is_purine: 1
mol_res_name: C std_base_name: A .
Thanks!
F
On Aug 16, 2011, at 2:21 PM, Kevin Keating wrote:
I think I've fixed the problem for adding
Francis, do you have CCP4 installed on this machine as well? What
version is it? Also, what's the naming on the newly created ideal RNA.
Is it using * or ' for prime?
If your installation of CCP4 isn't the newest version (6.2), that may
be causing your problem. Starting with rev
Using G instead of Gr is part of the new PDB3 standard. If I
remember correctly, a DNA G is now called DG, and I think CNS still uses
GUA. Regardless, it sounds like your distribution of Coot may still be
using the old-style monomer libraries. The status message you pasted
below
set_refinement_immediate_replacement(1) should stop Coot from prompting
you. I think you'll still need to call accept_regularizement() after
you run the refinement to actually accept the results.
In case your interested, set_refinement_immediate_replacement(0) will
set it back, and
I've just released a new Coot plugin to help with building RNA
structure, so I wanted to make a quick announcement to the mailing list
for any interested RNA crystallographers. The plugin, named RCrane, is
free for use and can be downloaded from
Lowering the matrix term further might help. I've set it to 10
when working with ~3 A RNA maps, so you might want to try values around
5-10. If you're using the most recent build of Coot (revision 3440),
you could also try using harmonic restraints. These allow an atom to
move slightly
