This is very useful. I tried Nautilus to build DNA into the density but I ended up with fragments all over the map. As a second option I was able to build a ds DNA in Coot using Calculate > Other Modeling Tools > DNA & RNA Models. However I couldn't control the exact position of the DNA. I ended up using Pymol to put the DNA in roughly the right place and than I was able to do the refinement. If anyone could suggest an easier way to build the DNA in the right place in Coot I would greatly appreciated that.
@@PaulEmsley Thanks Paul, great algorithm. However, my problem is that when I build the DNA initially it maybe in the wrong orientation. Let's say I put my cursor in the middle of the DNA density type in the DNA sequence and the DNA produced maybe 90 degrees off. Is Jiggle-fit able to handle that?
@@EMSV66 Yes. Jiggle-fit is a local Rotation/Translation search algorithm. It seems in your case that the map to which you'd want to fit *is* the residual map (post-masking), unlike the above video.
@@PaulEmsley Thanks Paul for the prompt response! However, I used the command curlew() and no extension shows up in the Wrangler. I am using the Coot 0.9-pre EL installed with the CCP-EM for mac. Is the curlew() currently only working for linux system?
This is very useful. I tried Nautilus to build DNA into the density but I ended up with fragments all over the map. As a second option I was able to build a ds DNA in Coot using Calculate > Other Modeling Tools > DNA & RNA Models. However I couldn't control the exact position of the DNA. I ended up using Pymol to put the DNA in roughly the right place and than I was able to do the refinement. If anyone could suggest an easier way to build the DNA in the right place in Coot I would greatly appreciated that.
Jiggle-fit is the Coot algorithm for optimizing a rough fit. See this video for an example: th-cam.com/video/93-Us_ywMJo/w-d-xo.html
@@PaulEmsley Thanks Paul, great algorithm. However, my problem is that when I build the DNA initially it maybe in the wrong orientation. Let's say I put my cursor in the middle of the DNA density type in the DNA sequence and the DNA produced maybe 90 degrees off. Is Jiggle-fit able to handle that?
@@EMSV66 Yes. Jiggle-fit is a local Rotation/Translation search algorithm. It seems in your case that the map to which you'd want to fit *is* the residual map (post-masking), unlike the above video.
@@PaulEmsley That worked beautifully. I had to run it a few times to coax the DNA but it moved to the right place eventually. Thanks so much!
I spoke too early. The two DNA strands moved with respect to each other. I will just use ProSMART with the restraints.
I can see only four selections under "ProSMART" menu. How to install all choices as shown in this video?
These days you need to use the "Restraints" and the "Refine" Module - Not ProSMART.
@@PaulEmsley thanks!
why I did not find the refine tab in coot?
It's installed using the "Chain Refine" extension in CURLEW. See the intro to the SBGrid Coot Cryo-EM Video th-cam.com/video/hhB8qUBBnJQ/w-d-xo.html
@@PaulEmsley Thanks Paul for the prompt response! However, I used the command curlew() and no extension shows up in the Wrangler. I am using the Coot 0.9-pre EL installed with the CCP-EM for mac. Is the curlew() currently only working for linux system?
@@AmazingIsScience We fixed this recently. Last time I checked, you need to use latest nightly build (not the release).
@@PaulEmsley Now the problem is fixed. Thanks a lot!!!