About creat_gridpoint.m issue2

[zhao-xigua]

Hi, Euan I have runned this script successfully, but I found its result is uncorrected. This picture shows the x,y,z value is very low or very high, and I opened .em in chimera, I found the arrow have a long distance away from my surface. I changed the 'thr' many times, but it performs similar as well. My input data is whole tomogram(not sub-tomogram) , and my segment is done by tomosegmemTV, and then used chimera segger to saved as a surface. Although the segment process has a little different from yours, I have found that the 'max' and 'mean' etc are normal. So, Is my data's problem? or Any points I have to pay attention to use the script? Thank you Euan!

[EuanPyle]

Hmm it's hard for me to judge without actual access to the data. Can you send a picture of the segmented membrane on its own, and overlaid on the tomogram, and another picture of the particles which have been picked on the tomogram?

[zhao-xigua]

The first picture is that I opened in chimera, and the last two pictures are that I opened in 3dmod. And I don't pick particles in the tomogram. Is it a necessary step to pick particles before using creat_gridpoint.m?

[zhao-xigua]

[zhao-xigua]

And the result with arrows opened in chimera is

[EuanPyle]

Oh ok, so in Segger you are going to want to only select one membrane, not all of them, and do one at a time. If you select all membranes at the same time in Segger the script will not work properly.

[zhao-xigua]

Thank you Euan. But I found it doesn't works well either. I tried a closed sphere and a single membrane sheet. The results which are opened in chimera are shown in .doc file. pictures.docx

[zhao-xigua]

Hi Euan, could you please help me run my data on your device? I want to know if it's my data's problem. Many thanks!
data.tar.gz

[EuanPyle]

Hi I will give it a go, but will need some time as I'm very busy at the moment