I tried today the new version (-0.6) and see some problems.
In general it helps if you can give revision numbers as things move
quickly (especially in the pre-releases).
1. Simple mutate for nucleotides. The program makes Gr, Cr etc. in
DNA
(should be Gd, Cd etc). And it does not mutate
Leonid Cherney wrote:
I tried today the new version (-0.6) and see some problems.
1. Simple mutate for nucleotides. The program makes Gr, Cr etc. in DNA
(should be Gd, Cd etc). And it does not mutate to thymine at all,
because there is no Tr. Where can I say that it's a DNA?
This has been
Hi all,
I am not sure but If I remember correctly Bernhard mentioned on the last CCP4
study weekend in Nottingham that Coot is able to merge the different water
chains, generated through repeated refinement runs, in one. If this function
exist, how can I use it?
Thanks in advance for your
Hi all,
I am refining a structure that contains RNA. I've added hydrogens in
the riding positions to help with maintaining proper geometry during
refinement. However, when I go to adjust the model between
refinements in coot using Real Space Refine (or even Regularize for
that matter)
Chris,
The hydrogens are at 0 occupancy so their positions are not
refined...the other atoms at non-zero occupancy do move leaving the Hs
behind..set the hydrogens to non-zero occupancy (eg. 0.01).
HTH,
Iain
CK wrote:
Hi all,
I am refining a structure that contains RNA. I've added
Also, does the resolution of your data warrant including the hydrogens
in the model ? Can you actually see them ?
You can add them in their riding positions, which may help stablise
your refinement, but not write them out to the coordinate file (uncheck
and output to coordinate file in the
On May 5, 2009, at 3:16 PM, CK wrote:
Hi all,
I am refining a structure that contains RNA. I've added hydrogens
in the riding positions to help with maintaining proper geometry
during refinement. However, when I go to adjust the model between
refinements in coot using Real Space Refine
I think perhaps I should clarify what I've been doing. I've been
refining my structure using phenix.refine and had reached a fairly
satisfactory point with suitably low R-factors (21/25) and very
reasonable RMSDs for bonds and angles. At this point I ran my
structure through the
