On 10/12/2020 05:05, manikandank wrote:
On 2020-12-09 18:26, Paul Emsley wrote:
On 09/12/2020 12:44, manikandank wrote:
I would like to build a model of both single and double strand RNA
into a 3A cryoEM map.
In this regard, i would like to know the options in coot to do the
following,
How to do real space refinement of ds RNA (different kind of RNA
secondary structures) , both strand together to the fit the map
(bases come from different regions of RNA primary sequence) ?
Have you watched the "Coot with RNA" video?
https://www.youtube.com/watch?v=Zzim3SXnDSk
<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.youtube.com%2Fwatch%3Fv%3DZzim3SXnDSk&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7Ca2d4aa1fe7af4ffec8cc08d89cc0eebd%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637431700167552678%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=A6EA9mPWfMucH2HCfblwotn0ekQ15SHdOr2l3GuJBMY%3D&reserved=0>
See the comments.
Paul.
Hi Paul,
Thank you very much for the quick response.
I have now seen the video and the comments.
As i have very long RNA (~2000 bases from ribosomal rna) that makes
different secondary structures, i donot have often the ideal situation
show in the video.
First, i do not have the ProSMART menu for 'Generate Restraint' and i
use wincoot 0.9.2 EL (please see the attachment).
How to generate the restraint for a selected set of bases as they come
from different chain?
for ex. strand1: 10 to 25 from chain A and strand2: 40-55 chain B .
I would like to restraint part of a ds strand or stem loop and fit only
the selection using real space refine option.
thank you very much for your suggestions
There seems to be some bug (and some features missing) in the WinCoot
version. Sorry about this. I will fix this for 0.9.3. In the meantime
you can download the updated the extension file and replace the existing
directory (yourwincoot/lib/python2.7/site-packages/coot/):
https://raw.githubusercontent.com/bernhardcl/coot/refinement64/python/extensions.py
Then you need to launch the module "Restraints".
I will update this for 0.9.3.
HTH,
B
with kind regards
Mani.
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***************************************************
Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent
Div. Molecular Structural Biology/Biomedicum D9
Dept. of Medical Biochemistry and Biophysics (MBB) |
Karolinska Institutet
SE-171 77 Stockholm
Sweden
+46 8 52487055
[email protected] | ki.se
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