Template create using crystal structure

[Ravi.Thakkar369]

Hi,
I am working on CTLA4 protein fused with Fc chimera. My main interest is to solve CTLA4 sturcture using cryoEM. The particles are crowded and difficult to pick it up.
So, I have imported volume from crystal strucure of CTLA4 (grid size 43,39,69, pixel 1.67,1.67,1.67, shown at level 0.617, step 1, values float32).
I am getting an erorr while creating template :
“ValueError: could not broadcast input array from shape (69,39,43) into shape (42,42,42)”

I have tried using output size 300, 69 and zeropading factors: 0,1,2 but none of the options worked.

[cryofun]

Hi Ravi, it wants a cube volume

Once you have the molmap volume from the pdb, you can make it a cube by vop resample onto a cube volume in chimera or use relion image handler as in the below:

relion_image_handler --i input.mrc --new_box 40 --o output.mrc

Creating templates from imported 3D volume using Chimera

I encountered a bug when trying to pick particles by generating templates from a .mrc map file. The map was produced in Chimera from a pdb file with the command molmap #0 15 and saved as a map file (.mrc). Then imported into cryoSPARC (2.15.0+200513) with the “Import 3D Volumes” job. This volume was then used to “Create Templates” job which produces the following error: Traceback (most recent call last): File "cryosparc2_worker/cryosparc2_compute/run.py", line 85, in cryosparc2_compute.ru…