From 920cea2a2ba0357d04a5b11fdbfb10db9445fec0 Mon Sep 17 00:00:00 2001 From: Paul Emsley Date: Mon, 20 May 2024 20:05:26 +0100 Subject: [PATCH] Add minor tweaks to the Cryo-EM tutorial --- blog/_posts/2024-05-20-Moorhen-Cryo-EM-Tutorial.md | 13 +++---------- 1 file changed, 3 insertions(+), 10 deletions(-) diff --git a/blog/_posts/2024-05-20-Moorhen-Cryo-EM-Tutorial.md b/blog/_posts/2024-05-20-Moorhen-Cryo-EM-Tutorial.md index a0ab595..90e6b21 100644 --- a/blog/_posts/2024-05-20-Moorhen-Cryo-EM-Tutorial.md +++ b/blog/_posts/2024-05-20-Moorhen-Cryo-EM-Tutorial.md @@ -42,17 +42,11 @@ You should now see a map with three unfitted parts ![Moorhen 3 Domains]({{"../../../images/moorhen-3-domains.png"}}) -Let's fit the nanobody! ### Fitting the Nanobody -Now we want to model the nanobody domain. - We have done a BLAST search for the sequence of our nanobody and know that the structure was published already in a different complex - it's the "E" chain in the entry ``6GDG``. So let's fetch that structure, extract the "E" chain and then fit it to our reconstruction. - - First centre the view on the centre of the nanobody/immunoglobulin domain. - - Fetch the Reference Structure: - **File** → **Fetch from Online Services** → `6gdg` @@ -66,7 +60,8 @@ Now make the fragment we need from that: So now we have the "E" chain floating around in space... - - Delete the `6gdg` model +Delete the `6gdg` model: + - **Models** Click on the gear icon of the `6gdg` molecule and **Delete molecule** Change the representation of the '//E' chain @@ -113,10 +108,8 @@ To refine this domain/chain: - Atom Selection is `//` (i.e. "all atoms") - **OK** - - You will see that the nanobody is now highlighted with green bonds and atoms. -A dialog will appear middle top +A dialog will appear at the middle top ![Moorhen Selection Panel]({{"../../../images/moorhen-selection-panel.png"}})