>> 4 sep. 2019 kl. 01:12 skrev Paul Emsley <[email protected]>: >> >> 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.
Mea culpa. That makes a lot of sense. I admit I did not read the paper and used the function like a black box. > >> 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). Yes, in 0.8.9.2 I was using the ProSMART menu to generate self restraints. I guess they are not strictly speaking ProSMART restraints. > 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). Ok, I will try that. > > 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. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
