On 13/10/2020 14:59, Sorbhi Rathore wrote:
Hi Paul and Rob,
Many thanks for your prompt reply.
One more question. Would you use the same settings for fitting RNA?
my thinking would be the same.
(I have tried the exact settings shown in your YouTube video tutorial.
However, in the low resolution regions of the map it is extremely
tricky to move the RNA chain, especially when there is a
conformational change)
Can you explain this in more detail? Why is it tricky? How many bp? If
you refined your fragment without GM restraints and without dragging on
an atom, what would happen? What happens when you reduce the map weight?
Fitting RNA with a conformational change is one of the things that Coot
now does well (if I may be so bold).
Paul
On Oct 12, 2020, at 8:11 PM, Paul Emsley <[email protected]
<mailto:[email protected]>> wrote:
On 12/10/2020 13:44, Sorbhi Rathore wrote:
Dear all,
Could anyone please suggest the best way to decide which German-
McClure Alpha value to use during refinement (both at a higher
resolution and lower resolution areas for a cryo-EM map)?
I am using coot 0.9.1 pre EL(ccpem).
A carefully-worded question.
For cases, where the model doesn't initially fit the map:
In 0.9, there was the danger or tearing the protein apart with too
much yank and too much alpha (low weight). That's why I used to be
conservative - using an alpha of 0.03 or so (occasionally 0.1 or 0.001).
With proportional editing in 0.9.1, I find I yank less (instead,
using several micro yanks) and because the shift is distributed over
a far larger range and is ameliorated by distance from the yanked
atom, I find that protein either doesn't tear or usually re-anneals
very pleasingly even with a high alpha.
Proportional editing radius is changed by Ctrl-middle-mouse scroll.
For cases where the model more or less fits the map, I use 1 or (.3
or 10 (if I want to practically turn them off without deleting them))
Paul.
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