Hi Paul, I just gave it a try and it worked perfectly. Thanks so much. I should’ve asked sooner.
For anyone wanting to perform this, I downloaded the latest nightly build of the ccp-em suite for Mac which includes Coot 0.9-pre. Then I added the curlew-chain-refine.scm extension to Coot (add it to ~/.coot-preferences/) so that I could do the all atom refine after adding ProSmart distance restraints. With a little pulling on the atoms, the DNA moved from an area of the map of no density into the appropriate blob on density. Best, Brady > On Oct 10, 2019, at 9:00 AM, Paul Emsley <[email protected]> wrote: > > > On 09/10/2019 15:35, Brady Travis wrote: >> I have a low-resolution EM map and have been having difficulty modeling a >> 50mer piece of curved double-stranded DNA into. The global resolution is 6.5 >> A and the local resolution for the DNA is lower. I started by making an >> ideal B-form DNA from ‘other modeling tools.’ The map for the DNA curves >> slightly throughout the length. If I try to real space refine the DNA into >> the map it doesn’t work well. The base pairs don’t stay together and the DNA >> backbone ends up getting distorted. I’ve tried adding base pairing >> restraints with ‘Extensions > User-defined Restraints > DNA B form bond >> restraints’ but when I try to real space refine after this I run into the >> same issues. I’m using Coot 0.8.9.2. Is there a better way to model this? > > > For Cryo-EM, you should be using Coot 0.9-pre - Coot 0.8.x is a pain at > low resolution/cryo-EM. > > > Modern Coot (0.9-pre 2725429e483f002268cc8b9b6264ef7c7ee5428e or later > (mid-July)) will add base pair and stacking restraints automatically. > > > This video (for RNA) plays upon some of the themes of your message: > > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.youtube.com_watch-3Fv-3DZzim3SXnDSk&d=DwIDaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=9jz7FfHxYEDR9cQEgduiuFDrjuwiPCas9wF7v0uExa0&m=f2pWYfD9FVs9YH-rHyHfCFRXfmzEjusG6eb4Zk2P2J0&s=aWpp-HDQ-29mBSY4DpIFtCxR16W3xWI36KSy8vvksuI&e= > > > > I'd add a bit of Local Distance Restraints (say 4.4A) for the fragment - > and that should be enough to stabilize the refinement (do an "All Atom" > refine of course. > > > Paul. > > > p.s. rather embarrassingly, the super-coiling of the DNA model is > incorrect (I haven't got around to fixing it :-(). Maybe the real-space > refinement will "just fix it"... > > > ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
