2023-06-09 (Fri)

Replying to 1, 2, 3: I wouldn't feel sad if RELION was taken over by another open-source program, but domination of black-box software is very very sad. What is worse, people are switching not only for the speed or the Web GUI but for features (e.g. small membrane proteins). For example, I haven't been able to solve a small membrane protein, PfCRT, EMPIAR-10330 (https://ebi.ac.uk/empiar/EMPIAR-10330/) with RELION from scratch, while CryoSPARC apparently solves it with ease (not tested myself, as I don't want to use it). Many people tell me similar stories. This means many structures in EMDB can be solved only by a black box at the moment. I don't know what is the fundamental difference. This is very uncomfortable for me (but apparently many biologists don't care).

Also to 1: I know. This is one of the reasons why I shifted my focus from SPA back to crystallography (time-resolved SFX for proteins and MicroED for small molecules). I don't share biologists' values. My interest is in technology and chemistry.

Speaking of crystallography, my preference is: CCP4 traditional interface > command line > PHENIX >>> CCP4i2

Do you review papers for MDPI journals?

I had reviewed some in the past but haven't done so recently because they kept sending me review request for papers that were not my expertise and some people say MDPI journals are predatory.

Then I received another one. This time the paper was my expertise and the abstract looked interesting. But I eventually decided to decline the request. I reviewed another paper only last week for another journal. The past papers from the group didn't make their code open-source. If this had been from another journal, I would have written to the editor and accepted to review it on the condition that the code becomes open-source. But I didn't feel like taking the trouble for this journal...

MicroED beam time

The sample that looked least promising is diffracting very well while back-up samples are not doing well. They diffracted well last time and I wanted to increase the multiplicity but today they didn't stick well to the grid and/or diffract only poorly. Chemists said they are stable in air at room temperature but probably nano-crystals are less stable due to the increased surface-to-volume ratio.


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