On 03/09/2019 14:47, Daniel Larsson wrote:
Now I got 0.9-pre working (thanks Colin Palmer for the suggestion!). In the new
version, I have problem generating ProSMART restraints for RNA.
The Pro in ProSMART refers to proteins. If you actually used ProSMART (rather than following the video) then
it will not work for RNA.
It works fine for proteins. Anyone else experiencing the same problem and know
how to solve it? I have also installed the latest version of CCP4.
And now I've made a rod for my own back. ProSMART-*like* simple/self local distance restraints can be
generated in Coot (as in the video). Real ProSMART restraints are created using the "ProSMART..." menu item
when in Coot - and who know how many other means when using ccp4 or other guis (I use the command line
needless to say). Recent Coots (as of 16th July) have auto RNA pairing and stacking restraints. One used to
be able to generated pairing and stacking restraints using LIBG (I haven't checked it recently).
One more thing that I didn't mention in the video: the graphics are nicer if
you use
Edit -> Settings -> Refinement Speed -> Molasses
Coot will, from time to time, reset itself to Crocodile mode - which is not as good. I haven't sorted out
why yet.
Aside: The video was made using my desktop and the speed is OK/meh (I think more speed should be available
after optimising the linear algebra and tweaking the thread scheduling). It should be pretty slick on a
Threadripper2 - I wonder if anyone's tried it?
Paul.
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