Parameter change

Tips
1

I test TRPV1 data and got the structure with 7 angstrom, how many iterations should I run to achieve
4 angstrom ? Is there any parameters which are needed to be changed for high resolution change ?

2

Hi @cwang,
The TRPV1 EMPIAR test data should go to <4A with no parameter tweaks and just a single ab-initio reconstruction followed by a single refinement. The only parameter you need to be sure to set is the C4 symmetry in the refinement experiment.

3

Hi,
The resolution I got from refined map with C4 symmetry for TRPV1 test data was about 10 angstrom and 6.36 angstrom with tight mask. I tried 2D classification and selected classes. But the 2D classification did not really help much. I would really appreciate it if you could advise how I could do better. Thanks!

4

If you

  1. Download the data
  • Import the .star file
  • Run ab-initio with defaults
  • Start refinement from ab-initio with defaults + C4

then you will get the structure. What else did you do?

5

That was exactly what I did. Interestingly, I started it over this morning and it passed 4 angstrom.

6

Hi @GuobinHu, good to know it worked this morning - let us know if any further issues

7

Thanks a lot! It is amazing! I look forward to trying it with our own data.

8

Just wondering - which EMPIAR dataset was this? The 2013 amphipol TRPV1 or the 2015 nanodisc one?

Also is it possible that previously you had looked at an earlier iteration the the final one? Did you repeat the ab initio as well as the refinement? If so, are the ab initio structures different in any particular way?

9

Sorry for missed your questions. I do not know which dataset it is except it is the example data set on CryoSPARC website. I believe I did new ab initio and new refinment. I did not compare the new ab initio mode to the old one.

10