mdoc to tlt converter and python run scripts

[sagarbiophysics]

Hi Alex,

I am trying to setup standalone protomo and would like to know how you generate .tlt file from .mdoc file. Could you share any script you might have to do so.

I would also like to know if you could share python run scripts such protomo2aligner.py used to run protomo alignment.

Best wishes,
Sagar

[alexjnoble]

Hi Sagar,

Everything you ask and more is explained in the Installation instructions and the tilt-series upload and alignment walkthrough here:

https://github.com/nysbc/appion-protomo#appion-protomo

Best,
-Alex

[sagarbiophysics]

Hi Alex,

I am not working within the Appion enviroinment!

It is a standalone installation of protomo (not appion-protomo) which requires .tlt file.

I understand that this is out of your scope as appion developer; but I realised that you might have these routines already written and would be willing to share!

Best,
Sagar

[alexjnoble]

Hi Sagar,

I don't have any Protomo scripts that work outside of Appion.

You can find protomo2aligner.py in myami-trunk/appion/bin/ here:

https://drive.google.com/open?id=1AJ2sLSgUAk4n-b2S22Ip896P6OL-3J_r

But it has hundreds of parameters and options. It is 100% intended to be used from inside Appion and not supported otherwise.

Appion-Protomo takes almost no effort to install... may I ask why you would want to use native Protomo? Also, how did you learn to use Protomo?

Best,
-Alex

[sagarbiophysics]

Hi Alex,

Well, we cannot install appion on our cluster! Doesn't support docker installation. We also wanted to see if it could be incorporated with inhouse pipeline at Baumeister dept. I am still learning.. mostly from the user guide written by Hanspeter.

Do you have any template .param file for K2 tomograms?
I also seem to have trouble with .mrc frames! invalid image dimension ERROR.
Did you encounter anything similar during the development of appion protomo.

Best,
Sagar

[alexjnoble]

Hi Sagar,

Oh I see, this makes sense. I've been surprised how many IT departments completely lock down every computer in an institution/university, not even allowing workstation-owners to have access to their own root. This is a lot more common than I ever imagined.

We are currently working on an Amazon EC2 instance of Docker Appion-Protomo. Please contact me directly if you want to try it: anoble [at] nysbc.org

You are free to try learning Protomo on your own, of course. You should know, however, that it took me about 2 years as a graduate student to get comfortable with using Protomo (and that was with Hanspeter available to talk to in person) and 4-5 years to have a complete and practical understanding of Protomo. I'm still learning little things about Protomo and the algorithm. I've been using Protomo and developing Appion-Protomo a few times per week since 2013. Appion-Protomo critically simplifies the entire process, and the Readme here on github encapsulates a lot of this knowledge.

To answer your questions:
-My .param files are all generated automatically through the Appion website.
-I have never seen an invalid dimension error. Check that all of your tilt images have the same dimensions. You should also try running all your images through proc3d without any options to normalize and standardize the headers: proc3d [input.mrc] [output.mrc]

Best,
-Alex

[alexjnoble]

Correction: proc2d [input.mrc] [output.mrc]