McHelixTrace Questions

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Colin Deniston

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Sep 18, 2017, 4:46:43 PM9/18/17
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Hello,

I'm a graduate student new to the Spring software suite and I'm trying to use the MicHelixTrace function to select microtubules (MT) from cryo-EM images. I have a couple questions about some of the required inputs. My first question is in regards to the helix reference file. Should this just be a good looking MT portion from my own data or would you recommend downloading a high resolution 3D model and generating a projection as a reference? How sensitive is the reference to protofilament (PF) number, for example will a 13 PF reference pick a 14 PF MT? What length should my reference be? (Just longer than one full turn of the helix?)

My second question is about the diagnostic plot pattern input. I'm unfamiliar with what this is suppose to be and could not find an explanation online. Any info on how to generate it for a stack of images and what it should contain would be very appreciated!

Thanks for all the help,
Colin Deniston

Carsten Sachse

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Sep 19, 2017, 7:42:12 AM9/19/17
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Dear Colin,

Be sure to use the latest version of Spring, ie. version 0.85.1617 as of now. 
On Monday, 18 September 2017 22:46:43 UTC+2, Colin Deniston wrote:
Hello,

I'm a graduate student new to the Spring software suite and I'm trying to use the MicHelixTrace function to select microtubules (MT) from cryo-EM images. I have a couple questions about some of the required inputs. My first question is in regards to the helix reference file. Should this just be a good looking MT portion from my own data or would you recommend downloading a high resolution 3D model and generating a projection as a reference?
This is something you need to test. The clearer your reference is the better. However, be sure that the reference has the same pixel size as your data set.
 
How sensitive is the reference to protofilament (PF) number, for example will a 13 PF reference pick a 14 PF MT? What length should my reference be? (Just longer than one full turn of the helix?)
We found it quite sensitive to different states of other helical assemblies, e.g. TMV the helical vs the stacked disc form. If you have very good data, I expect it to discriminate between 13 and 14 PF as they have different diameters. However, you will have to test it on your data. 

My second question is about the diagnostic plot pattern input. I'm unfamiliar with what this is suppose to be and could not find an explanation online.
The input 'mypattern.pdf'
will create a series of PDF files mypatter001.pdf, mypattern002.pdf, mypattern003.pdf ... , where the number corresponds to the corresponding micrograph.

Best wishes,


Carsten 
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