Leginon

Hi, Venkata,

I will look into this later today. You might want to try not to adjust Focus node target position now to get past this until we locate the source and update 2.1 release which I presume you are using.

To turn off adjustment for Focus node, open the settings window for Focus node. It is probably set to "Adjust target using one ancestor". Change that to "No ancestor".

Anchi

Dear Anchi,

I will change it and give my feedback.

Thanks,

Venkata

Hi, Venkata,

I was not able to reproduce your error. You will need to give me details. According to the source code, when drift is declared or detected, Target_Adjustment does not reject targets by type. Its logger output looks like this:

Exposure node is meant to reject focus target and have it processed first which is why it is the Focus node that triggered Target_Adjustment. You should see in Exposure node logger somthing like this:

In the Focus node logger, you should see a sequence similar to this:

You should also know that target adjustment is not done if there is no reason to suspect drift. For example, if you are using "Depth-Traveral", i.e., non-queuing mode, and the move type for Focus and Exposure nodes are of image-shift, the stage would have already at the right position. Therefore, it will not initiate target adjustment at the start of target processing in this node. Instead, if one of your focus sequence contains a drift check and drift is detected when it did so, a target adjustment will be done before Leginon repeats the focus sequence after the drift detection.

What you described might be associated with a completely different problem. Please check your Focus node setting. Go into Advanced settings and check if the target process type (on the right most panel) says that it is set to process "focus" targets. Here is what
the default should look like:

If your settings look very different from this, the defaults might not be set properly. Try this:
Revert_Settings

Dear Anchi,

Thank you, for your reply. It is my mistake to mention exposure targetting node instead of exposure node. The message in exposure node is same as you mentioned, but the focus node in not the same.

After the targets are submitted, the exposure node process it as you said and in the focus node logger I cannot see anything. I attached images of the logger details.

for your reference,our microscope is 100kv, 1k x 1k camera, working at 54000x for 3.2 angstroms resolution and zfocus node details are also attached. once again I am working with continous carbon negatively stained grids.

thanks,

regards,
venkata

forget to mention...the settings are same as default settings.

regard,
venkata.

Venkata,

That is odd. The only possible reason for no logger message would be that it does not have the proper binding between Exposure and Focus node. Follow the instruction in this wiki page to export MSI-Raster to the screen in "easy-to-read" format, and check to see if you have this one:

If not, the application you imported is corrupted. Just import it again manually according to the instruction on the same wiki page. It will create a new version and use it in Leginon instead.

Dear Anchi,

As per your instructions, I have solved the problem. But I still not sure, whether it has taken latest version. After import it is creating like MSI-Raster(1.6)-1 and again when I go back to leginon to use this version it shows MSI-RASTER and without extension of ¨1¨. So, I was bit confused and tried to import for four times and now, can you tell me how to delete the other three versions names in the list? in application version directory.sorry, may be I missed some part of documentation.

Thanks for your immediate support.

with regards,
venkata

Sorry, no delete gui for you, once the application is imported into database. Leginon automatically takes the latest version of the application of the same name. Unless you are familiar with mysql or tools to administrate that, it is better leave it alone. We do plan to create a tool to remove application since we have way too many in our development database, but it is not a high priority item.

Anchi